| 1. |
Fitzgerald C,
Sherwood R,
Gheesling LL,
Brenner FW,
Fields PI,
( 2003 ) Molecular analysis of the rfb O antigen gene cluster of Salmonella enterica serogroup O:6,14 and development of a serogroup-specific PCR assay. PMID : 14532067 : DOI : 10.1128/aem.69.10.6099-6105.2003 PMC : PMC201254 Abstract >>
The Kauffmann-White scheme for serotyping Salmonella recognizes 46 somatic (O) antigen groups, which together with detection of the flagellar (H) antigens form the basis for serotype identification. Although serotyping has become an invaluable typing method for epidemiological investigations of Salmonella, it does have some practical limitations. We have been characterizing the genes required for O and H antigen biosynthesis with the goal of developing a DNA-based system for the determination of serotype in Salmonella. The majority of the enzymes involved in O antigen biosynthesis are encoded by the rfb gene cluster. We report the sequencing of the rfb region from S. enterica serotype Sundsvall (serogroup O:6,14). The S. enterica serotype Sundsvall rfb region is 8.4 kb in length and comprises six open reading frames. When compared with other previously characterized rfb regions, the serogroup O:6,14 sequence is most related to serogroup C(1). On the basis of DNA sequence similarity, we identified two genes from the mannose biosynthetic pathway, two mannosyl transferase genes, the O unit flippase gene and, possibly, the O antigen polymerase. The whole cluster is derived from a low-G+C-content organism. Comparative sequencing of an additional serogroup O:6,14 isolate (S. enterica serotype Carrau) revealed a highly homologous sequence, suggesting that O antigen factors O:24 and O:25 (additional O factors associated with serogroup O:6,14) are encoded outside the rfb gene cluster. We developed a serogroup O:6,14-specific PCR assay based on a region of the putative wzx (O antigen flippase) gene. This provides the basis for a sensitive and specific test for the rapid identification of Salmonella serogroup O:6,14.
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2. |
Leung KY,
Ruschkowski SR,
Finlay BB,
( 1992 ) Isolation and characterization of the aadA aminoglycoside-resistance gene from Salmonella choleraesuis. PMID : 1406282 : DOI : 10.1111/j.1365-2958.1992.tb01421.x Abstract >>
The streptomycin- and spectinomycin-resistance gene of Salmonella choleraesuis was cloned and its nucleotide sequence determined. The gene is 789 bases long, encoding a protein of a predicted size of 29,353 Da. The gene product inactivated streptomycin and spectinomycin by an adenylation modification. It is homologous (c. 40% total identity) to streptomycin adenylyltransferase, a 3'(9)-O-nucleotidyltransferase (AAD(3')(9)), which is encoded by the aadA gene in Escherichia coli, Agrobacterium tumefaciens, Klebsiella pneumonia, and Serratia marcescens. The AadA protein of S. choleraesuis differs significantly from the other AadA proteins, indicating that it may have diverged from the other members of this family earlier in evolution. Southern hybridization analysis revealed that homologous aadA sequences were also present in other streptomycin-resistant Salmonella species.
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3. |
Wang L,
Romana LK,
Reeves PR,
( 1992 ) Molecular analysis of a Salmonella enterica group E1 rfb gene cluster: O antigen and the genetic basis of the major polymorphism. PMID : 1372579 : PMC : PMC1204862 Abstract >>
Salmonella enterica is highly polymorphic for the O antigen, a surface polysaccharide that is subject to intense selection by the host immune system. This polymorphism is used for serotyping Salmonella isolates. The genes encoding O antigen biosynthesis are located in the rfb gene cluster. We report here the cloning and sequence of the 19-kb rfb region from strain M32 (serovar anatum, group E1) and compare it with that of strain LT2 (serovar typhimurium, group B). Genes for biosynthetic pathways common to both strains are conserved and have very similar sequences. In contrast, the five genes for CDP-abequose synthesis, present in strain LT2, are absent in strain M32; three open reading frames (ORFs) of strain LT2, thought to include genes for transferases, are not present in strain M32 but are replaced by three different ORFs with little or low level of similarity. Both rfb gene clusters are low in G + C content, indicating that they were transferred from a common ancestral species with low G + C content to S. enterica relatively recently (in the evolutionary sense). We discuss the recombination and lateral transfer events which may have been involved in the evolution of the polymorphism.
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4. |
Brown PK,
Romana LK,
Reeves PR,
( 1992 ) Molecular analysis of the rfb gene cluster of Salmonella serovar muenchen (strain M67): the genetic basis of the polymorphism between groups C2 and B. PMID : 1379320 : DOI : 10.1111/j.1365-2958.1992.tb00859.x Abstract >>
The rfb (O antigen) gene cluster of group C2 Salmonella differs from that of group B in a central region of 12.4 kb: we report the sequencing of this region of strain M67 (group C2) and a subsequent comparison with the central region of strain LT2 (group B). We find a block of seven open reading frames unique to group C2 which encode the O antigen polymerase (rfc) and the transferases responsible for assembly of the group C2 O antigen. The remaining rfb genes are common to strains M67 and LT2, but rfbJ (CDP-abequose synthase) and rfbM and rfbK (GDP-mannose synthesis), which are immediately adjacent to the central region, are highly divergent. All these genes have a low G+C content and appear to have been recent additions to Salmonella enterica. We discuss the evolutionary significance of the arrangement and divergence of the genes in the polymorphism of the rfb cluster.
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5. |
Lee SJ,
Romana LK,
Reeves PR,
( 1992 ) Sequence and structural analysis of the rfb (O antigen) gene cluster from a group C1 Salmonella enterica strain. PMID : 1383393 : DOI : 10.1099/00221287-138-9-1843 Abstract >>
The rfb (O antigen) gene cluster of a group C1 Salmonella enterica strain was sequenced; it comprised seven open reading frames which precisely replaced the 16 open reading frames of a group B strain. Two genes of the mannose biosynthetic pathway were present: rfbK (phosphomannomutase) had a G+C content of 0.61 and had only 40% identity to rfbK of group B but was very similar to cpsG of the capsular polysaccharide pathway with 96% identity, whereas rfbM [guanosine diphosphomannose (GDP-Man) pyrophosphorylase] had a G+C content of 0.39. Other genes had G+C contents ranging from 0.24 to 0.28. rfbM(C1) and rfbM(B) had 60% identity, which is much less than expected within a species, but nonetheless indicates a much more recent common ancestor than for rfbK. The other genes showed much lower or no similarity to rfb genes of other S. enterica strains. It appears that the gene cluster evolved outside of Salmonella in a species with low G+C content: the rfbM gene presumably derives from that period whereas the rfbK gene appears to have arisen after transfer of the cluster to S. enterica by duplication of the S. enterica cpsG gene, presumably replacing an rfbK gene of low G+C content.
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6. |
Wu WS,
Hsieh PC,
Huang TM,
Chang YF,
Chang CF,
( 2002 ) Cloning and characterization of an iron regulated locus, iroA, in Salmonella enterica serovar Choleraesuis. PMID : 12652904 : Abstract >>
To identify genes belonging to the Ferric update regulator (Fur) regulon of Salmonella enterica serovar Choleraesuis, the Fur titration assay (FURTA) was used to screen a genomic library for Fur promoters and iron-regulated genes. Fifteen FURTA positive clones were identified from this assay. DNA sequence analysis of these clones showed that 11 out of 15 clones had a Fur binding site (Fur box), and 6 of these clones showed homology to the iron-regulated genes of S. enterica serovar Typhi and/or E. coli. One of these clones (pSC4) was homologous to the iroB gene of the iroA locus of S. enterica serovar Typhi. The iroA locus of S. enterica serovar Choleraesuis was cloned from a lambda-dash library and subjected to DNA sequencing. The complete nucleotide sequence of 9848 bp of the iroA locus of S. enterica serovar Choleraesuis consists of iroB, C, D, E and N genes, which are transcriptionally regulated by Fur. The amino acid sequence of IroB, C, D, E and N was 95%, 86, 89, 96 and 96% identity to that of S. enterica serovar Typhi. The IroN gene was homologous to the family of TonB-dependent outer membrane receptors and the putative virulence factor, IroNE. coli, of the extraintestinal pathogenic E. coli. The convalescent porcine sera contained antibodies against the three major iron-regulated outer membrane proteins of S. enterica serovar Choleraesuis. An insertional inactivation of the iroN gene of S. enterica serovar Choleraesuis by allelic exchange resulted in the loss of expression of the 78 kDa protein. However, this mutant had a similar LD50 to mice compared to the parent strain when given intraperitoneally.
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7. |
Barton WA,
Biggins JB,
Jiang J,
Thorson JS,
Nikolov DB,
( 2002 ) Expanding pyrimidine diphosphosugar libraries via structure-based nucleotidylyltransferase engineering. PMID : 12374866 : DOI : 10.1073/pnas.192468299 PMC : PMC129684 Abstract >>
In vitro "glycorandomization" is a chemoenzymatic approach for generating diverse libraries of glycosylated biomolecules based on natural product scaffolds. This technology makes use of engineered variants of specific enzymes affecting metabolite glycosylation, particularly nucleotidylyltransferases and glycosyltransferases. To expand the repertoire of UDP/dTDP sugars readily available for glycorandomization, we now report a structure-based engineering approach to increase the diversity of alpha-d-hexopyranosyl phosphates accepted by Salmonella enterica LT2 alpha-d-glucopyranosyl phosphate thymidylyltransferase (E(p)). This article highlights the design rationale, determined substrate specificity, and structural elucidation of three "designed" mutations, illustrating both the success and unexpected outcomes from this type of approach. In addition, a single amino acid substitution in the substrate-binding pocket (L89T) was found to significantly increase the set of alpha-d-hexopyranosyl phosphates accepted by E(p) to include alpha-d-allo-, alpha-d-altro-, and alpha-d-talopyranosyl phosphate. In aggregate, our results provide valuable blueprints for altering nucleotidylyltransferase specificity by design, which is the first step toward in vitro glycorandomization.
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8. |
Liu M,
Ren Z,
Lei C,
Wen Y,
Yan W,
Zheng Z,
( 2002 ) Sequence analysis and characterization of plasmid pSFD10 from Salmonella choleraesuis. PMID : 12206756 : Abstract >>
The nucleotide sequence of a small plasmid, designated pSFD10, is isolated from the vaccine strain Salmonella choleraesuis C500 in China, has been determined. This plasmid is 4091 bp long with a total G+C content of 51.4%, which is in the range of Salmonella genomic DNA. Analysis of the complete nucleotide sequence reveals that pSFD10 has a high degree of similarity to ColE1-type plasmid, having the possible cer and rom genes, and a putative mobilization origin of ColE1-type. Plasmid pSFD10 possesses six main open reading frames (ORFs), five of which have a very high degree of amino acid identity to ColE1-type plasmid gene products involved in mobilization and copy number control. The other ORF (ORF6) encodes a putative protein, which has 49% homology to the invasion plasmid antigen J protein (IpaJ) secreted by the type III secretion apparatus of Shigella flexneri. In addition, pSFD10 belongs to a different incompatibility group than ColE1-type and pMB1-type to which it is related. Plasmid pSFD10 can be mobilized by the plasmid RP4 in E. coli.
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9. |
Brown EW,
Kotewicz ML,
Cebula TA,
( 2002 ) Detection of recombination among Salmonella enterica strains using the incongruence length difference test. PMID : 12128032 : Abstract >>
Particular serovars of Salmonella enterica have emerged as significant foodborne pathogens in humans. At the chromosomal level, discrete regions in the Salmonella genome have been identified that are known to play important roles in the maintenance, survival, and virulence of S. enterica within the host. Interestingly, several of these loci appear to have been acquired by horizontal transfer of DNA among and between bacterial species. The profound importance of recombination in pathogen emergence is just now being realized, perhaps explaining the sudden interest in developing novel and facile ways for detecting putative horizontal transfer events in bacteria. The incongruence length difference (ILD) test offers one such means. ILD uses phylogeny to trace sequences that may have been acquired promiscuously by exchange of DNA during chromosome evolution. We show here that the ILD test readily detects recombinations that have taken place in several housekeeping genes in Salmonella as well as genes composing the type 1 pilin complex (14 min) and the inv-spa invasion gene complex (63 min). Moreover, the ILD test indicated that the mutS gene (64 min), whose product helps protect the bacterial genome from invasion by foreign DNA, appears to have undergone intragenic recombination within S. enterica subspecies I. ILD findings were supported using additional tests known to be independent of the ILD approach (e.g., split decomposition analysis and compatibility of sites). Taken together, these data affirm the application of the ILD test as one approach for identifying recombined sequences in the Salmonella chromosome. Furthermore, horizontally acquired sequences within mutS support a model whereby evolutionarily important recombinants of S. enterica are rescued from strains carrying defective mutS alleles via horizontal transfer.
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10. |
Boyd D,
Cloeckaert A,
Chaslus-Dancla E,
Mulvey MR,
( 2002 ) Characterization of variant Salmonella genomic island 1 multidrug resistance regions from serovars Typhimurium DT104 and Agona. PMID : 12019080 : DOI : 10.1128/aac.46.6.1714-1722.2002 PMC : PMC127246 Abstract >>
Strains of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (DT104) and S. enterica serovar Agona (Agona) have been found to harbor Salmonella genomic island 1 (SGI1), a 43-kb genomic region that contains many of the drug resistance genes. Such strains are resistant to ampicillin (pse-1), chloramphenicol/florfenicol (floR), streptomycin/spectinomycin (aadA2), sulfonamides (sul1), and tetracycline [tet(G)] (commonly called the ACSSuT phenotype). All five resistance genes are found in a 13-kb multidrug resistance (MDR) region consisting of an unusual class I integron structure related to In4. We examined DT104 and Agona strains that exhibited other resistance phenotypes to determine if the resistance genes were associated with variant SGI1 MDR regions. All strains were found to harbor variant SGI1-like elements by using a combination of Southern hybridization, PCR mapping, and sequencing. Variant SGI1-like elements were found with MDR regions consisting of (i) an integron consisting of the SGI1 MDR region with the addition of a region containing a putative transposase gene (orf513) and dfrA10 located between duplicated qacEDelta1/sulI genes (SGI1-A; ACSSuTTm); (ii) an integron with either an aadA2 (SSu) or a pse-1 (ASu) cassette (SGI1-C and SGI1-B, respectively); (iii) an integron consisting of the SGI1-C MDR region plus an orf513/dfrA10 region as in SGI1-A (SGI1-D; ASSuTm; ampicillin resistance due to a TEM beta-lactamase); and (iv) an integron related to that in SGI1 but which contains a 10-kb inversion between two copies of IS6100, one which is inserted in floR (SGI1-E; ASSuT). We hypothesize that the MDR of SGI1 is subject to recombinational events that lead to the various resistance phenotypes in the Salmonella strains in which it is found.
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11. |
Naderer M,
Brust JR,
Knowle D,
Blumenthal RM,
( 2002 ) Mobility of a restriction-modification system revealed by its genetic contexts in three hosts. PMID : 11948154 : DOI : 10.1128/jb.184.9.2411-2419.2002 PMC : PMC135005 Abstract >>
The flow of genes among prokaryotes plays a fundamental role in shaping bacterial evolution, and restriction-modification systems can modulate this flow. However, relatively little is known about the distribution and movement of restriction-modification systems themselves. We have isolated and characterized the genes for restriction-modification systems from two species of Salmonella, S. enterica serovar Paratyphi A and S. enterica serovar Bareilly. Both systems are closely related to the PvuII restriction-modification system and share its target specificity. In the case of S. enterica serovar Paratyphi A, the restriction endonuclease is inactive, apparently due to a mutation in the subunit interface region. Unlike the chromosomally located Salmonella systems, the PvuII system is plasmid borne. We have completed the sequence characterization of the PvuII plasmid pPvu1, originally from Proteus vulgaris, making this the first completely sequenced plasmid from the genus Proteus. Despite the pronounced similarity of the three restriction-modification systems, the flanking sequences in Proteus and Salmonella are completely different. The SptAI and SbaI genes lie between an equivalent pair of bacteriophage P4-related open reading frames, one of which is a putative integrase gene, while the PvuII genes are adjacent to a mob operon and a XerCD recombination (cer) site.
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12. |
Dauga C,
( 2002 ) Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. PMID : 11931166 : DOI : 10.1099/00207713-52-2-531 Abstract >>
Phylogenetic trees showing the evolutionary relatedness of Enterobacteriaceae based upon gyrB and 16S rRNA genes were compared. Congruence among trees of these molecules indicates that the genomes of these species are not completely mosaic and that molecular systematic studies can be carried out. Phylogenetic trees based on gyrB sequences appeared to be more reliable at determining relationships among Serratia species than trees based on 16S rRNA gene sequences. gyrB sequences from Serratia species formed a monophyletic group validated by significant bootstrap values. Serratia fonticola had the most deeply branching gyrB sequence in the Serratia monophyletic group, which was consistent with its atypical phenotypic characteristics. Klebsiella and Enterobacter genera seemed to be polyphyletic, but the branching patterns of gyrB and 16S rRNA gene trees were not congruent. Enterobacter aerogenes was grouped with Klebsiella pneumoniae on the gyrB phylogenetic tree, which supports that this species could be transferred to the Klebsiella genus. Unfortunately, 16S rRNA and gyrB phylogenetic trees gave conflicting evolutionary relationships for Citrobacter freundii because of its unusual gyrB evolutionary process. gyrB lateral gene transfer was suspected for Hafnia alvei. Saturation of gyrB genes was observed by the pairwise comparison of Proteus spp., Providencia alcalifaciens and Morganella morganii sequences. Depending on their level of variability, 16S rRNA gene sequences were useful for describing phylogenetic relationships between distantly related Enterobacteriaceae, whereas gyrB sequence comparison was useful for inferring intra- and some intergeneric relationships.
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13. |
Innes D,
Beacham IR,
Beven CA,
Douglas M,
Laird MW,
Joly JC,
Burns DM,
( 2001 ) The cryptic ushA gene (ushA(c)) in natural isolates of Salmonella enterica (serotype Typhimurium) has been inactivated by a single missense mutation. PMID : 11429465 : DOI : 10.1099/00221287-147-7-1887 Abstract >>
Two mutational mechanisms, both supported by experimental studies, have been proposed for the evolution of new or improved enzyme specificities in bacteria. One mechanism involves point mutation(s) in a gene conferring novel substrate specificity with partial or complete loss of the original (wild-type) activity of the encoded product. The second mechanism involves gene duplication followed by silencing (inactivation) of one of these duplicates. Some of these 'silent genes' may still be transcribed and translated but produce greatly reduced levels of functional protein; gene silencing, in this context, is distinct from the more common associations with bacterial partitioning sequences, and with genes which are no longer transcribed or translated. Whereas most Salmonella enterica strains are ushA(+), encoding an active 5'-nucleotidase (UDP-sugar hydrolase), some natural isolates, including most genetically related strains of serotype Typhimurium, have an ushA allele (designated ushA(c)) which produces a protein with, comparatively, very low 5'-nucleotidase activity. Previous sequence analysis of cloned ushA(c) and ushA(+) genes from serotype Typhimurium strain LT2 and Escherichia coli, respectively, did not reveal any changes which might account for the significantly different 5'-nucleotidase activities. The mechanism responsible for this reduced activity of UshA(c) has hitherto not been known. Sequence analysis of Salmonella ushA(+) and ushA(c) alleles indicated that the relative inactivity of UshA(c) may be due to one, or more, of four amino acid substitutions. One of these changes (S139Y) is in a sequence motif that is conserved in 5'-nucleotidases across a range of diverse prokaryotic and eukaryotic species. Site-directed mutagenesis confirmed that a Tyr substitution of Ser-139 in Salmonella UshA(+) was solely responsible for loss of 5'-nucleotidase activity. It is concluded that the corresponding single missense mutation is the cause of the UshA(c) phenotype. This is the first reported instance of gene inactivation in natural isolates of bacteria via a missense mutation. These results support a model of evolution of new enzymes involving a 'silent gene' which produces an inactive, or relatively inactive, product, and are also consistent with the evolution of a novel, but unknown, enzyme specificity by a single amino acid change.
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14. |
Allard ST,
Giraud MF,
Whitfield C,
Graninger M,
Messner P,
Naismith JH,
( 2001 ) The crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-l-rhamnose pathway. PMID : 11243820 : DOI : 10.1006/jmbi.2000.4470 Abstract >>
l-Rhamnose is a 6-deoxyhexose that is found in a variety of different glycoconjugates in the cell walls of pathogenic bacteria. The precursor of l-rhamnose is dTDP-l-rhamnose, which is synthesised from glucose- 1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway requiring four enzymes. Significantly this pathway does not exist in humans and all four enzymes therefore represent potential therapeutic targets. dTDP-D-glucose 4,6-dehydratase (RmlB; EC 4.2.1.46) is the second enzyme in the dTDP-L-rhamnose biosynthetic pathway. The structure of Salmonella enterica serovar Typhimurium RmlB had been determined to 2.47 A resolution with its cofactor NAD(+) bound. The structure has been refined to a crystallographic R-factor of 20.4 % and an R-free value of 24.9 % with good stereochemistry.RmlB functions as a homodimer with monomer association occurring principally through hydrophobic interactions via a four-helix bundle. Each monomer exhibits an alpha/beta structure that can be divided into two domains. The larger N-terminal domain binds the nucleotide cofactor NAD(+) and consists of a seven-stranded beta-sheet surrounded by alpha-helices. The smaller C-terminal domain is responsible for binding the sugar substrate dTDP-d-glucose and contains four beta-strands and six alpha-helices. The two domains meet to form a cavity in the enzyme. The highly conserved active site Tyr(167)XXXLys(171) catalytic couple and the GlyXGlyXXGly motif at the N terminus characterise RmlB as a member of the short-chain dehydrogenase/reductase extended family. The quaternary structure of RmlB and its similarity to a number of other closely related short-chain dehydrogenase/reductase enzymes have enabled us to propose a mechanism of catalysis for this important enzyme.
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15. |
Valdivia RH,
Cirillo DM,
Lee AK,
Bouley DM,
Falkow S,
( 2000 ) mig-14 is a horizontally acquired, host-induced gene required for salmonella enterica lethal infection in the murine model of typhoid fever. PMID : 11083839 : DOI : 10.1128/iai.68.12.7126-7131.2000 PMC : PMC97824 Abstract >>
We have characterized a host-induced virulence gene, mig-14, that is required for fatal infection in the mouse model of enteric fever. mig-14 is present in all Salmonella enterica subspecies I serovars and maps to a region of the chromosome that appears to have been acquired by horizontal transmission. A mig-14 mutant replicated in host tissues early after infection but was later cleared from the spleens and livers of infected animals. Bacterial clearance by the host occurred concomitantly with an increase in gamma interferon levels and recruitment of macrophages, but few neutrophils, to the infection foci. We hypothesize that the mig-14 gene product may repress immune system functions by interfering with normal cytokine expression in response to bacterial infections.
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16. |
Li Q,
Reeves PR,
( 2000 ) Genetic variation of dTDP-L-rhamnose pathway genes in Salmonella enterica. PMID : 10974117 : DOI : 10.1099/00221287-146-9-2291 Abstract >>
The genetic variation in the dTDP-L-rhamnose pathway gene set (rmlB, rmlD, rmlA, rmlC) in Salmonella enterica was examined after sequencing the four genes from 11 rml-containing gene clusters encoding seven O antigens, and a 903 bp rmlB segment from another 23 strains representing the seven subspecies. There was considerable sequence variation and strong polarity in the nature and level of variation among rml genes. The 5' end of the rml gene set, including rmlB, rmlD and most of rmlA, is in general subspecies specific. In contrast, the 3' end, including part of rmlA and all of rmlC, is O antigen specific. The G+C content of the 3' end is lower than that of the 5' end. The variation in the 3' end of the gene set is much greater than that of the 5' end. It is apparent that the rml gene set of S. enterica includes genes with two different evolutionary histories. In addition, there has been extensive recombination in the gene set, probably related to O antigen transfer between subspecies. These findings provide evidence for the lateral transfer of O antigen genes between species and among subspecies of S. enterica. The results have also shown that conserved genes at the end of an O antigen gene cluster play a major role in mediating exchange of the central serogroup-specific regions.
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17. |
Schippa S,
Bonci A,
Berlutti F,
Thaller MC,
( 1999 ) Genetic rearrangements in the tyrB-uvrA region of the enterobacterial chromosome: a potential cause for different class B acid phosphatase regulation in Salmonella enterica and Escherichia coli. PMID : 10564784 : DOI : 10.1111/j.1574-6968.1999.tb08821.x Abstract >>
Unlike in Escherichia coli, in Salmonella enterica production of class B acid phosphatase (AphA) was detectable also in cells growing in the presence of glucose. Characterization of the aphA locus from a S. enterica ser. typhi strain showed that the aphA determinant is very similar to the E. coli homolog, and that its chromosomal location between the highly conserved tyrB and uvrA genes is retained. However, the aphA flanking regions were found to be markedly different in the two species, either between tyrB and aphA or between aphA and uvrA. The differences in the aphA 5'-flanking region, which in S. enterica is considerably shorter than in E. coli (183 vs. 1121 bp) and includes potential promoter sequences not present in E. coli, could be responsible for the different regulation of class B acid phosphatase observed in the two species.
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18. |
Löfdahl S,
Advani A,
Sukupolvi S,
Pfeifer JD,
Normark S,
( 1999 ) Multiple insertions of fimbrial operons correlate with the evolution of Salmonella serovars responsible for human disease. PMID : 10417651 : DOI : 10.1046/j.1365-2958.1999.01508.x Abstract >>
On centisome 7, Salmonella spp. contain a large region not present in the corresponding region of Escherichia coli. This region is flanked by sequences with significant homology to the E. coli tRNA gene aspV and the hypothetical E. coli open reading frame yafV. The locus consists of a mosaic of differentially acquired inserts forming a dynamic cs7 region of horizontally transferred inserts. Salmonella enterica subspecies I, responsible for most Salmonella infections in warm-blooded animals, carries a fimbrial gene cluster (saf) in this region as well as a regulatory gene (sinR). These genes are flanked by inverted repeats and are inserted in another laterally transferred region present in most members of Salmonella spp. encoding a putative invasin (pagN). S. enterica subspecies I serovar Typhi, the Salmonella serovar that causes the most severe form of human salmonellosis, contains an additional insert of at least 8 kb in the sinR-pagN intergenic region harbouring a novel fimbrial operon (tcf) similar to the coo operon encoding the CS1 fimbrial adhesin expressed by human-specific enterotoxigenic E. coli. It is suggested that the multiple insertions of fimbrial genes that have occurred in the cs7 region have contributed to phylogenetic diversity and host adaptation of Salmonella spp.
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19. |
Kosti? T,
Weilharter A,
Rubino S,
Delogu G,
Uzzau S,
Rudi K,
Sessitsch A,
Bodrossy L,
( 2007 ) A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of nonpathogens. PMID : 17123456 : DOI : 10.1016/j.ab.2006.09.026 Abstract >>
A major challenge in microbial diagnostics is the parallel detection and identification of low-bundance pathogens within a complex microbial community. In addition, a high specificity providing robust, reliable identification at least at the species level is required. A microbial diagnostic microarray approach, using single nucleotide extension labeling with gyrB as the marker gene, was developed. We present a novel concept applying competitive oligonucleotide probes to improve the specificity of the assay. Our approach enabled the sensitive and specific detection of a broad range of pathogenic bacteria. The approach was tested with a set of 35 oligonucleotide probes targeting Escherichia coli, Shigella spp., Salmonella spp., Aeromonas hydrophila, Vibrio cholerae, Mycobacterium avium, Mycobacterium tuberculosis, Helicobacter pylori, Proteus mirabilis, Yersinia enterocolitica, and Campylobacter jejuni. The introduction of competitive oligonucleotides in the labeling reaction successfully suppressed cross-reaction by closely related sequences, significantly improving the performance of the assay. Environmental applicability was tested with environmental and veterinary samples harboring complex microbial communities. Detection sensitivity in the range of 0.1% has been demonstrated, far below the 5% detection limit of traditional microbial diagnostic microarrays.
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20. |
Fitzgerald C,
Gheesling L,
Collins M,
Fields PI,
( 2006 ) Sequence analysis of the rfb loci, encoding proteins involved in the biosynthesis of the Salmonella enterica O17 and O18 antigens: serogroup-specific identification by PCR. PMID : 17056694 : DOI : 10.1128/AEM.01046-06 PMC : PMC1694211 Abstract >>
We report sequencing of the O antigen encoded by the rfb gene cluster of Salmonella enterica serotype Jangwani (O17) and Salmonella serotype Cerro (O18). We developed serogroup O17- and O18-specific PCR assays based on rfb gene targets and found them to be sensitive and specific for rapid identification of Salmonella serogroups O17 and O18.
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21. |
Chouchani C,
Berlemont R,
Masmoudi A,
Galleni M,
Frere JM,
Belhadj O,
Ben-Mahrez K,
( 2006 ) A novel extended-spectrum TEM-type beta-lactamase, TEM-138, from Salmonella enterica serovar Infantis. PMID : 16940125 : DOI : 10.1128/AAC.00388-06 PMC : PMC1563563 Abstract >>
A novel natural TEM beta-lactamase with extended-spectrum activity, TEM-138, was identified in a ceftazidime-resistant clinical isolate of Salmonella enterica serovar Infantis. Compared to TEM-1, TEM-138 contains the following mutations: E104K, N175I, and G238S. The bla(TEM-138) gene was located on a 50-kb transferable plasmid. Expression studies with Escherichia coli revealed efficient ceftazidimase and cefotaximase activities for TEM-138.
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22. |
Delmas J,
Breysse F,
Devulder G,
Flandrois JP,
Chomarat M,
( 2006 ) Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene. PMID : 16626902 : DOI : 10.1016/j.diagmicrobio.2006.02.003 Abstract >>
Real-time polymerase chain reaction and sequencing were used to characterize a 506-bp-long DNA fragment internal to the gyrB gene (gyrBint). The sequences obtained from 32 Enterobacteriaceae-type strains and those available in the Genbank nucleotide sequence database (n = 24) were used as a database to identify 240 clinical enterobacteria isolates. Sequence analysis of the gyrBint fragment of 240 strains showed that gyrBint constitutes a discriminative target sequence to differentiate between Enterobacteriaceae species. Comparison of these identifications with those obtained by phenotypic methods (Vitek 1 system and/or Rapid ID 32E; bioM?rieux, Marcy l'Etoile, France) revealed discrepancies essentially with genera Citrobacter and Enterobacter. Most of the strains identified as Enterobacter cloacae by phenotypic methods were identified as Enterobacter hormaechei strains by gyrBint sequencing. The direct sequencing of gyrBint would be useful as a complementary tool in the identification of clinical Enterobacteriaceae isolates.
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23. |
Rodríguez I,
Rodicio MR,
Mendoza MC,
Cruz Martín M,
( 2006 ) Large conjugative plasmids from clinical strains of Salmonella enterica serovar virchow contain a class 2 integron in addition to class 1 integrons and several non-integron-associated drug resistance determinants. PMID : 16569896 : DOI : 10.1128/AAC.50.4.1603-1607.2006 PMC : PMC1426967 Abstract >>
Two large conjugative resistance (R) plasmids from clinical strains of Salmonella enterica serovar Virchow carried a class 2 integron with the 5' conserved sequence (5'CS)-dfrA1-sat1-aadA1-3'CS gene array, which is associated with defective Tn7 transposons. In addition, each contained a different class 1 integron (with 5'CS-aadA1-3'CS or 5'CS-sat-smr-aadA1-3'CS gene arrays) linked to Tn21-Tn9 sequences, and several non-integron-associated R determinants. An intact copy of Tn7 (including the class 2 integron) was present in the chromosome of each strain.
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24. |
Brandl MT,
Miller WG,
Bates AH,
Mandrell RE,
( 2005 ) Production of autoinducer 2 in Salmonella enterica serovar Thompson contributes to its fitness in chickens but not on cilantro leaf surfaces. PMID : 15870357 : DOI : 10.1128/AEM.71.5.2653-2662.2005 PMC : PMC1087538 Abstract >>
Food-borne illness caused by Salmonella enterica has been linked traditionally to poultry products but is associated increasingly with fresh fruits and vegetables. We have investigated the role of the production of autoinducer 2 (AI-2) in the ability of S. enterica serovar Thompson to colonize the chicken intestine and the cilantro phyllosphere. A mutant of S. enterica serovar Thompson that is defective in AI-2 production was constructed by insertional mutagenesis of luxS. The population size of the S. enterica serovar Thompson parental strain was significantly higher than that of its LuxS(-) mutant in the intestine, spleen, and droppings of chicks 12 days after their oral inoculation with the strains in a ratio of 1:1. In contrast, no significant difference in the population dynamics of the parental and LuxS(-) strain was observed after their inoculation singly or in mixtures onto cilantro plants. Digital image analysis revealed that 54% of S. enterica serovar Thompson cells were present in large aggregates on cilantro leaves but that the frequency distributions of the size of aggregates formed by the parental strain and the LuxS(-) mutant were not significantly different. Carbon utilization profiles indicated that the AI-2-producing strain utilized a variety of amino and organic acids more efficiently than its LuxS(-) mutant but that most sugars were utilized similarly in both strains. Thus, inherent differences in the nutrients available to S. enterica in the phyllosphere and in the chicken intestine may underlie the differential contribution of AI-2 synthesis to the fitness of S. enterica in these environments.
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25. |
Hakanen AJ,
Lindgren M,
Huovinen P,
Jalava J,
Siitonen A,
Kotilainen P,
( 2005 ) New quinolone resistance phenomenon in Salmonella enterica: nalidixic acid-susceptible isolates with reduced fluoroquinolone susceptibility. PMID : 16272517 : DOI : 10.1128/JCM.43.11.5775-5778.2005 PMC : PMC1287832 Abstract >>
We describe the emergence of a new quinolone resistance pattern in Salmonella enterica isolates from Southeast Asia. These isolates are susceptible to nalidixic acid but exhibit reduced susceptibility to ciprofloxacin. The increase of such strains may threaten the value of the nalidixic acid disk test to screen for reduced fluoroquinolone susceptibility in salmonellas.
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26. |
Daly M,
Villa L,
Pezzella C,
Fanning S,
Carattoli A,
( 2005 ) Comparison of multidrug resistance gene regions between two geographically unrelated Salmonella serotypes. PMID : 15722395 : DOI : 10.1093/jac/dki015 Abstract >>
The aim of this study was to identify chromosomally integrated genes conferring multidrug resistance to a Salmonella enterica (S.) serotype Typhimurium isolate, phage type DT193, isolated in Ireland and to compare them with resistance genes conferring plasmid-mediated multidrug resistance to a S. Enteritidis isolate from Italy. A complete DNA sequence of the regions containing the resistance genes was obtained from the chromosome of the S. Typhimurium DT193 isolate and from the IncI plasmid of the S. Enteritidis isolate. The plasmid was also characterized by conjugation and incompatibility grouping. Two 10 kb multidrug resistance non-Salmonella Genomic Island 1 type clusters were independently identified in the S. Enteritidis plasmid and in the chromosome of the S. Typhimurium isolate. Detailed characterization identified an IP-type 2 integron containing a dfrA1-aadA1 gene cassette and other common resistance determinants derived from the RSF1010 plasmid. These multidrug resistance regions originate following chromosomal integration of key resistance markers encountered on plasmids circulating in other Salmonella serotypes. This mechanism of marker acquisition may have future implications for the evolution of similar structures in previously susceptible serotypes, leading to an increased public health risk.
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27. |
Panutdaporn N,
Kawamoto K,
Asakura H,
Makino SI,
( 2006 ) Resuscitation of the viable but non-culturable state of Salmonella enterica serovar Oranienburg by recombinant resuscitation-promoting factor derived from Salmonella Typhimurium strain LT2. PMID : 16213054 : DOI : 10.1016/j.ijfoodmicro.2005.06.022 Abstract >>
A gene encoding the resuscitation-promoting factor (Rpf) from Salmonella Typhimurium LT2 was cloned and characterized. The amino acid sequence encoded by S. Typhimurium LT2 rpf gene shares 24.2% homology with Micrococcus luteus Rpf, which is secreted by growing cells, and required to resuscitate from viable but non-culturable (VNC) state. The S. Typhimurium LT2 rpf gene is 696 bp long, and shared a conserved segment with Salmonella enterica serovar Oranienburg (99.4%). Recombinant Rpf (rRpf) proteins of S. Typhimurium LT2 after expression in E. coli BL21 harboring the pET15-b plasmid was approximately 25 kDa. Since S. Oranienburg cells are relatively quick to enter the VNC state just after incubating in the presence of 7% NaCl at 37 degrees C for 3 days, we evaluated the biological effect of rRpf by using S. Oranienburg VNC cells. The rRpf not only promoted proliferation but also induced resuscitation of VNC cells to the culturable state in a dose-dependent manner. Therefore, rRpf may be useful for detection of bacterial contaminants present in the VNC form in food samples and the environment.
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28. |
Winfield MD,
Groisman EA,
( 2004 ) Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes. PMID : 15569938 : DOI : 10.1073/pnas.0406038101 PMC : PMC534605 Abstract >>
Phenotypic differences among closely related bacteria have been largely ascribed to species-specific genes, such as those residing in pathogenicity islands. However, we now report that the differential regulation of homologous genes is the mechanism responsible for the divergence of the enteric bacteria Salmonella enterica and Escherichia coli in their ability to make LPS modifications mediating resistance to the antibiotic polymyxin B. In S. enterica serovar Typhimurium, the PmrA/PmrB two-component system governing polymyxin B resistance is induced in low Mg(2+) in a process that requires the PmrD protein and by Fe(3+) in a PmrD-independent fashion. We establish that E. coli K-12 induces PmrA-activated gene transcription and polymyxin B resistance in response to Fe(3+), but that it is blind to the low Mg(2+) signal. The highly divergent PmrD protein is responsible for this phenotype as replacement of the E. coli pmrD gene by its Salmonella counterpart resulted in an E. coli strain that transcribed PmrA-activated genes and displayed polymyxin B resistance under the same conditions as Salmonella. Molecular analysis of natural isolates of E. coli and Salmonella revealed that the PmrD proteins are conserved within each genus and that selection might have driven the divergence between the Salmonella and E. coli PmrD proteins. Investigation of PmrD function demonstrated statistically different distributions for the Salmonella and E. coli isolates in PmrD-dependent transcription occurring in low Mg(2+). Our results suggest that the differential regulation of conserved genes may have ecological consequences, determining the range of niches a microorganism can occupy.
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29. |
Perelle S,
Dilasser F,
Malorny B,
Grout J,
Hoorfar J,
Fach P,
( 2004 ) Comparison of PCR-ELISA and LightCycler real-time PCR assays for detecting Salmonella spp. in milk and meat samples. PMID : 15488381 : DOI : 10.1016/j.mcp.2004.07.001 Abstract >>
In a previous study, we reported the performance of a PCR assay amplifying 285-bp of the invA gene of Salmonella spp. through an international ring-trial involving four participating laboratories [Int. J. Food Microbiol. 89 (2003) 241]. Based on the validated set of primers and recent advancements in PCR technology, we have designed two specific PCR assays for detecting Salmonella spp. We have compared PCR-enzyme-linked immunosorbent assay (PCR-ELISA) and LightCycler real-time PCR assay (LC-PCR) with the standard ISO 6579 bacteriological reference method. The two PCR tests incorporated an internal amplification control (IAC) co-amplified with the invA gene of Salmonella to monitor potential PCR inhibitors and ensure successful amplification. The selectivity study involved 84 Salmonella and 44 non-Salmonella strains and the samples tested were represented by 60 artificially-contaminated samples of fish, minced beef and raw milk, and 92 naturally-contaminated milk and meat samples. When using either PCR-ELISA or LC-PCR assays, only Salmonella strains were detected. PCR-ELISA and LC-PCR assays gave with pure Salmonella cultures the same detection limit level of 10(3)CFU/ml, which corresponds respectively to 50 and 10 cells per PCR tube. Data on artificially contaminated samples indicated that both PCR methods were able to detect after enrichment less than five Salmonella cells in 25 g of food, giving 100% concordance with the ISO 6579 reference method. The results on naturally contaminated samples demonstrated that despite certain inhibition problems, LC-PCR and PCR-ELISA assays were highly specific and sensitive, and provide a powerful tool for detection of Salmonella in food samples.
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30. |
Giles WP,
Benson AK,
Olson ME,
Hutkins RW,
Whichard JM,
Winokur PL,
Fey PD,
( 2004 ) DNA sequence analysis of regions surrounding blaCMY-2 from multiple Salmonella plasmid backbones. PMID : 15273090 : DOI : 10.1128/AAC.48.8.2845-2852.2004 PMC : PMC478531 Abstract >>
The emergence in the United States of resistance to expanded-spectrum cephalosporin (e.g., ceftriaxone) within the salmonellae has been associated primarily with three large (>100-kb) plasmids (designated types A, B, and C) and one 10.1-kb plasmid (type D) that carry the blaCMY-2 gene. In the present study, the distribution of these four known blaCMY-2-carrying plasmids among 35 ceftriaxone-resistant Salmonella isolates obtained from 1998 to 2001 was examined. Twenty-three of these isolates were Salmonella enterica serotype Newport, 10 were Salmonella enterica serotype Typhimurium, 1 was Salmonella enterica serotype Agona, and 1 was Salmonella enterica serotype Reading. All 23 serotype Newport isolates carried a type C plasmid, and 5, 4, and 1 serovar Typhimurium isolate carried type B, A, and C plasmids, respectively. Both the serotype Agona and serotype Reading isolates carried type A plasmids. None of the isolates carried a type D plasmid. Hybridization data suggested that plasmid types A and C were highly related replicons. DNA sequencing revealed that the region surrounding blaCMY-2 was highly conserved in all three plasmid types analyzed (types B, C, and D) and was related to a region surrounding blaCMY-5 from the Klebsiella oxytoca plasmid pTKH11. These findings are consistent with a model in which blaCMY-2 has been disseminated primarily through plasmid transfer, and not by mobilization of the gene itself, to multiple Salmonella chromosomal backbones.
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31. |
McQuiston JR,
Parrenas R,
Ortiz-Rivera M,
Gheesling L,
Brenner F,
Fields PI,
( 2004 ) Sequencing and comparative analysis of flagellin genes fliC, fljB, and flpA from Salmonella. PMID : 15131150 : DOI : 10.1128/jcm.42.5.1923-1932.2004 PMC : PMC404605 Abstract >>
Salmonella isolates have traditionally been classified by serotyping, the serologic identification of two surface antigens, O-polysaccharide and flagellin protein. Serotyping has been of great value in understanding the epidemiology of Salmonella and investigating disease outbreaks; however, production and quality control of the hundreds of antisera required for serotyping is difficult and time-consuming. To circumvent the problems associated with antiserum production, we began the development of a system for determination of serotype in Salmonella based on DNA markers. To identify flagellar antigen-specific sequences, we sequenced 280 alleles of the three genes that are known to encode flagellin in Salmonella, fliC, fljB, and flpA, representing 67 flagellar antigen types. Analysis of the data indicated that the sequences from fliC, fljB, and flpA clustered by the antigen(s) they encode not by locus. The sequences grouped into four clusters based on their conserved regions. Three of the four clusters included multiple flagellar antigen types and were designated the G complex, the Z4 complex, and the alpha cluster. The fourth cluster contained a single antigen type, H:z(29). The amino acid sequences of the conserved regions within each cluster have greater than 95% amino acid identity, whereas the conserved regions differ substantially between clusters (75 to 85% identity). Substantial sequence heterogeneity existed between alleles encoding different flagellar antigens while alleles encoding the same flagellar antigen were homologous, suggesting that flagellin genes may be useful targets for the molecular determination of flagellar antigen type.
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32. |
Bacciu D,
Falchi G,
Spazziani A,
Bossi L,
Marogna G,
Leori GS,
Rubino S,
Uzzau S,
( 2004 ) Transposition of the heat-stable toxin astA gene into a gifsy-2-related prophage of Salmonella enterica serovar Abortusovis. PMID : 15231789 : DOI : 10.1128/JB.186.14.4568-4574.2004 PMC : PMC438552 Abstract >>
The horizontal transfer and acquisition of virulence genes via mobile genetic elements have been a major driving force in the evolution of Salmonella pathogenicity. Serovars of Salmonella enterica carry variable assortments of phage-encoded virulence genes, suggesting that temperate phages play a pivotal role in this process. Epidemic isolates of S. enterica serovar Typhimurium are consistently lysogenic for two lambdoid phages, Gifsy-1 and Gifsy-2, carrying known virulence genes. Other serovars of S. enterica, including serovars Dublin, Gallinarum, Enteritidis, and Hadar, carry distinct prophages with similarity to the Gifsy phages. In this study, we analyzed Gifsy-related loci from S. enterica serovar Abortusovis, a pathogen associated exclusively with ovine infection. A cryptic prophage, closely related to serovar Typhimurium phage Gifsy-2, was identified. This element, named Gifsy-2AO, was shown to contribute to serovar Abortusovis systemic infection in lambs. Sequence analysis of the prophage b region showed a large deletion which covers genes encoding phage tail fiber proteins and putative virulence factors, including type III secreted effector protein SseI (GtgB, SrfH). This deletion was identified in most of the serovar Abortusovis isolates tested and might be dependent on the replicative transposition of an adjacent insertion sequence, IS1414, previously identified in pathogenic Escherichia coli strains. IS1414 encodes heat-stable toxin EAST1 (astA) and showed multiple genomic copies in isolates of serovar Abortusovis. To our knowledge, this is the first evidence of intergeneric transfer of virulence genes via insertion sequence elements in Salmonella. The acquisition of IS1414 (EAST1) and its frequent transposition within the chromosome might improve the fitness of serovar Abortusovis within its narrow ecological niche.
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33. |
Doublet B,
Butaye P,
Imberechts H,
Boyd D,
Mulvey MR,
Chaslus-Dancla E,
Cloeckaert A,
( 2004 ) Salmonella genomic island 1 multidrug resistance gene clusters in Salmonella enterica serovar Agona isolated in Belgium in 1992 to 2002. PMID : 15215102 : DOI : 10.1128/AAC.48.7.2510-2517.2004 PMC : PMC434189 Abstract >>
Salmonella genomic island 1 (SGI1) harbors a multidrug resistance (MDR) gene cluster which is a complex class 1 integron. Variant SGI1 MDR gene clusters conferring different MDR profiles have also been identified in several Salmonella enterica serovars and classified as SGI1-A to -F. A retrospective study was undertaken to characterize MDR regions from serovar Agona strains harboring SGI1 isolated from poultry in Belgium between 1992 and 2002. A total of 171 serovar Agona strains, displaying resistance to at least one antibiotic, were studied for the presence of SGI1. SGI1 was detected in 94 serovar Agona strains. The most prevalent variant was SGI1-A (85%), which harbors within the SGI1 complex class 1 integron a common region (CR1) containing orf513, a putative transposase gene, adjacent to the dfrA10 trimethoprim resistance gene. A new variant SGI1 named SGI1-G was identified in two strains. It consisted of the pse-1 gene cassette, as in SGI1-B, but with additional insertion of the orf513/dfrA10 region structure. Seven strains displaying the typical SGI1 MDR profile (Ap Cm Ff Sm Sp Su Tc) showed genetic variation at the 3' end of SGI1. These strains harbored the insertion of the CR1 containing orf513 as in SGI1-A, -D, and -G. However, downstream the right end of CR1, they presented different 7.4- to 8.5-kb deletions of the SGI1 3' end that extended to the chromosomal genes yieE and yieF. These results suggest a possible role of CR1 in deletion formation, as has been reported for some insertion sequences. Pulsed-field gel electrophoresis analysis showed that all the serovar Agona SGI1-carrying strains belonged to a single clone. Thus, SGI1 is largely encountered in serovar Agona strains isolated from poultry in Belgium, the most prevalent variant being SGI1-A. SGI1 MDR region undergoes recombinational events resulting in a diversity of MDR gene clusters.
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34. |
Brown EW,
Mammel MK,
LeClerc JE,
Cebula TA,
( 2003 ) Limited boundaries for extensive horizontal gene transfer among Salmonella pathogens. PMID : 14671318 : DOI : 10.1073/pnas.2634406100 PMC : PMC307627 Abstract >>
Recombination is thought to be rare within Salmonella, as evidenced by absence of gene transfer among SARC strains that represent the broad genetic diversity of the eight primary subspecies of this common facultative intracellular pathogen. We adopted a phylogenetic approach to assess recombination within the mutS gene of 70 SARB strains, a genetically homogeneous population of Salmonella enterica subspecies I strains, which have in common the ability to infect warm-blooded animals. We report here that SARB strains show evidence for widespread recombinational exchange in contrast to results obtained with strains exhibiting species-level genetic variation. Besides extensive allele shuffling, SARB strains showed notably larger recombinagenic patch sizes for mutS (at least approximately 1.1 kb) than previously reported for S. enterica SARC strains. Explaining these experimental dichotomies provides important insight for understanding microbial evolution, because they suggest likely ecologic and genetic barriers that limit extensive gene transfer in the feral setting.
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35. |
Gueneau de Novoa P,
Williams KP,
( 2004 ) The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. PMID : 14681369 : DOI : 10.1093/nar/gkh102 PMC : PMC308836 Abstract >>
tmRNA combines tRNA- and mRNA-like properties and ameliorates problems arising from stalled ribosomes. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA website (http://www.indiana.edu/~ tmrna), a collection of sequences, alignments, secondary structures and other information. Because many of these sequences are not in GenBank, a BLAST server has been added; another new feature is an abbreviated alignment for the tRNA-like domain only. Many tmRNA sequences from plastids have been added, five found in public sequence data and another 10 generated by direct sequencing; detection in early-branching members of the green plastid lineage brings coverage to all three primary plastid lineages. The new sequences include the shortest known tmRNA sequence. While bacterial tmRNAs usually have a lone pseudoknot upstream of the mRNA segment and a string of three or four pseudoknots downstream, plastid tmRNAs collectively show loss of pseudoknots at both postions. The pseudoknot-string region is also too short to contain the usual pseudoknot number in another new entry, the tmRNA sequence from a bacterial endosymbiont of insect cells, Tremblaya princeps. Pseudoknots may optimize tmRNA function in free-living bacteria, yet become dispensible when the endosymbiotic lifestyle relaxes selective pressure for fast growth.
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36. |
Granier SA,
Hidalgo L,
San Millan A,
Escudero JA,
Gutierrez B,
Brisabois A,
Gonzalez-Zorn B,
( 2011 ) ArmA methyltransferase in a monophasic Salmonella enterica isolate from food. PMID : 21859937 : DOI : 10.1128/AAC.00308-11 PMC : PMC3195062 Abstract >>
The 16S rRNA methyltransferase ArmA is a worldwide emerging determinant that confers high-level resistance to most clinically relevant aminoglycosides. We report here the identification and characterization of a multidrug-resistant Salmonella enterica subspecies I.4,12:i:- isolate recovered from chicken meat sampled in a supermarket on February 2009 in La Reunion, a French island in the Indian Ocean. Susceptibility testing showed an unusually high-level resistance to gentamicin, as well as to ampicillin, expanded-spectrum cephalosporins and amoxicillin-clavulanate. Molecular analysis of the 16S rRNA methyltransferases revealed presence of the armA gene, together with bla(TEM-1), bla(CMY-2), and bla(CTX-M-3). All of these genes could be transferred en bloc through conjugation into Escherichia coli at a frequency of 10(-5) CFU/donor. Replicon typing and S1 pulsed-field gel electrophoresis revealed that the armA gene was borne on an ~150-kb broad-host-range IncP plasmid, pB1010. To elucidate how armA had integrated in pB1010, a PCR mapping strategy was developed for Tn1548, the genetic platform for armA. The gene was embedded in a Tn1548-like structure, albeit with a deletion of the macrolide resistance genes, and an IS26 was inserted within the mel gene. To our knowledge, this is the first report of ArmA methyltransferase in food, showing a novel route of transmission for this resistance determinant. Further surveillance in food-borne bacteria will be crucial to determine the role of food in the spread of 16S rRNA methyltransferase genes worldwide.
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37. |
Wang M,
Luo Z,
Du H,
Xu S,
Ni B,
Zhang H,
Sheng X,
Xu H,
Huang X,
( 2011 ) Molecular characterization of a functional type VI secretion system in Salmonella enterica serovar Typhi. PMID : 21487806 : DOI : 10.1007/s00284-011-9935-z Abstract >>
The type VI secretion system (T6SS) of Salmonella enterica serovar Typhi (S. typhi) is associated with Salmonella pathogenicity island 6 (SPI-6). Though the T6SS gene cluster is intact in S. typhi, the protein complex is believed to be non-functional due to the presence of a pseudogene form of SciI (VipB homolog), a key component. We detected the SciK-his6 in the supernatant of the wild type strain of S. typhi containing the plasmid over-expressing SciK (hcp homolog) with a his6 epitope at the C-terminus, which suggested that the T6SS in S. typhi is functional. We also identified four genes that were essential to T6SS function: sciC (vasA homolog), sciS (vasK homolog), sciG (clpV homolog), and vrgS (vgrG homolog). Further analysis revealed that S. typhi T6SS is cytotoxic to human epithelial cells, but does not influence bacterial growth and mobility. RcsB, PmrA, and Hfq were identified as regulators of S. typhi T6SS gene expression; however, PhoP appears to not be involved. Taken together, the data demonstrate the functionality of S. typhi T6SS and confirm the important role of T6SS for S. typhi's ability to invade and infect epithelial cells.
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38. |
Chen HD,
Jewett MW,
Groisman EA,
( 2011 ) Ancestral genes can control the ability of horizontally acquired loci to confer new traits. PMID : 21811415 : DOI : 10.1371/journal.pgen.1002184 PMC : PMC3140997 Abstract >>
Horizontally acquired genes typically function as autonomous units conferring new abilities when introduced into different species. However, we reasoned that proteins preexisting in an organism might constrain the functionality of a horizontally acquired gene product if it operates on an ancestral pathway. Here, we determine how the horizontally acquired pmrD gene product activates the ancestral PmrA/PmrB two-component system in Salmonella enterica but not in the closely related bacterium Escherichia coli. The Salmonella PmrD protein binds to the phosphorylated PmrA protein (PmrA-P), protecting it from dephosphorylation by the PmrB protein. This results in transcription of PmrA-dependent genes, including those conferring polymyxin B resistance. We now report that the E. coli PmrD protein can activate the PmrA/PmrB system in Salmonella even though it cannot do it in E. coli, suggesting that these two species differ in an additional component controlling PmrA-P levels. We establish that the E. coli PmrB displays higher phosphatase activity towards PmrA-P than the Salmonella PmrB, and we identified a PmrB subdomain responsible for this property. Replacement of the E. coli pmrB gene with the Salmonella homolog was sufficient to render E. coli resistant to polymyxin B under PmrD-inducing conditions. Our findings provide a singular example whereby quantitative differences in the biochemical activities of orthologous ancestral proteins dictate the ability of a horizontally acquired gene product to confer species-specific traits. And they suggest that horizontally acquired genes can potentiate selection at ancestral loci.
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39. |
Li Y,
Perepelov AV,
Guo D,
Shevelev SD,
Senchenkova SN,
Shahskov AS,
Liu B,
Wang L,
Knirel YA,
( 2011 ) Structural and genetic relationships of two pairs of closely related O-antigens of Escherichia coli and Salmonella enterica: E. coli O11/S. enterica O16 and E. coli O21/S. enterica O38. PMID : 21205000 : DOI : 10.1111/j.1574-695X.2010.00771.x Abstract >>
The O-antigen is a part of the lipopolysaccharide molecule present in the outer membrane of Gram-negative bacteria, and is essential for the full function of the microorganisms. Salmonella enterica and Escherichia coli are taxonomically closely related species. In this study, the O-antigen structures of S. enterica O16 and O38 and E. coli O11 were determined. Salmonella enterica O38 and E. coli O21 were found to have identical O-antigen structures, whereas S. enterica O16 and E. coli O11 had closely related structures, differing only in the presence of a lateral glucose residue and O-acetylation of a mannose residue in the former. The O-antigen gene clusters of S. enterica O16 and O38 and E. coli O11 were sequenced and analyzed together with that of E. coli O21 retrieved from the GenBank. Each S. enterica/E. coli pair was found to contain the same set of genes organized in the same manner and to share 56-78% overall DNA identity. These data suggest that the O-antigen gene clusters of each pair studied originated from a common ancestor. Thus, it has become evident that in the past, the degree of relatedness between the O-antigens of S. enterica and E. coli was underestimated.
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40. |
Povilonis J,
?eputien? V,
Ružauskas M,
?iugždinien? R,
Virgailis M,
Pavilonis A,
Sužied?lien? E,
( 2010 ) Transferable class 1 and 2 integrons in Escherichia coli and Salmonella enterica isolates of human and animal origin in Lithuania. PMID : 20578916 : DOI : 10.1089/fpd.2010.0536 Abstract >>
Antibiotic-resistant Escherichia coli (n = 191) and Salmonella enterica (n = 87) isolates of human and animal origin obtained in Lithuania during 2005-2008 were characterized for the presence and diversity of class 1 and 2 integrons. E. coli isolates were obtained from patients with urinary tract infections (UTIs) (n = 59) and both healthy and diseased farm animals, including poultry (n = 54), swine (n = 35), and cattle (n = 43). Isolates of non-typhoidal S. enterica were recovered from salmonellosis patients (n = 37) and healthy animals, including poultry (n = 31) and swine (n = 19). The presence of integrons, their gene cassette structure, and genome location were investigated by polymerase chain reaction, restriction fragment-length polymorphism, DNA sequencing, Southern blot hybridization, and conjugation experiments. Forty percent of the E. coli and 11% of the S. enterica isolates carried class 1 integrons, whereas class 2 integrons were found in E. coli isolates (9%) only. The incidence of integrons in human UTIs and cattle isolates was most frequent (p < 0.01). A total of 23 different gene cassettes within 15 different variable regions were observed. Seven different integron types, all of them transferable by conjugation, were common for isolates from human infections and for one or more groups of animal isolates. The most prevalent integron types contained arrays dfrA1-aadA1 (36%), dfrA17-aadA5 (23%), and dfrA1-sat1-aadA1 (78%). Two E. coli isolates from humans with UTIs harbored class 1 integron on conjugative plasmid with the novel array type of 4800 bp/dfrA17-aadA5�G-IS26-�GintI1-aadB-aadA1-cmlA residing on the Tn21-like transposon. Three S. enterica isolates from swine contained class 1 integron with the newly observed array type of 1800 bp/aadA7-aadA7. Integrons of 10 different types of both classes were located on transferable plasmids in E. coli and S. enterica. Our study demonstrated the existence of a considerable and common pool of transferable integrons in E. coli and S. enterica present in clinical and livestock environment in Lithuania.
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41. |
Hu B,
Perepelov AV,
Liu B,
Shevelev SD,
Guo D,
Senchenkova SN,
Shashkov AS,
Feng L,
Knirel YA,
Wang L,
( 2010 ) Structural and genetic evidence for the close relationship between Escherichia coli O71 and Salmonella enterica O28 O-antigens. PMID : 20482625 : DOI : 10.1111/j.1574-695X.2010.00676.x Abstract >>
O-antigen is the most variable cell wall constituent of Gram-negative bacteria. Escherichia coli and Salmonella enterica are closely related species. In this work, we present structural and genetic evidence for the close relationship between O-antigens of E. coli O71 and S. enterica O28. The E. coli O71 O-antigen was found to consist of tetrasaccharide-repeating units containing d-GalpNAc, d-Galp, l-Rhap, and d-Quip3NAc, with multiple O-acetyl lateral groups. It is very similar to the known structure of the S. enterica O28 O-antigen, which has the same backbone units, but with a lateral Glc residue instead of O-acetyl groups. The O-antigen gene clusters of E. coli O71 and S. enterica O28 were sequenced and found to contain the same genes with high-level similarity. All of the genes expected for the synthesis of the common backbone structure of the two O-antigens were identified based on homology. It is proposed that the two gene clusters had originated from the same ancestor, and diverged by acquiring prophage genes to carry out side-chain modifications. This is a new pair of the closely related E. coli and S. enterica O-serogroups. The serogroup-specific genes of E. coli O71 and S. enterica O28 were also identified.
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42. |
Liu B,
Perepelov AV,
Li D,
Senchenkova SN,
Han Y,
Shashkov AS,
Feng L,
Knirel YA,
Wang L,
( 2010 ) Structure of the O-antigen of Salmonella O66 and the genetic basis for similarity and differences between the closely related O-antigens of Escherichia coli O166 and Salmonella O66. PMID : 20185508 : DOI : 10.1099/mic.0.037325-0 Abstract >>
O-antigen is a component of the outer membrane of Gram-negative bacteria and is one of the most variable cell surface constituents, leading to major antigenic variability. The O-antigen forms the basis for bacterial serotyping. In this study, the O-antigen structure of Salmonella O66 was established, which differs from the known O-antigen structure of Escherichia coli O166 only in one linkage (most likely the linkage between the O-units) and O-acetylation. The O-antigen gene clusters of Salmonella O66 and E. coli O166 were found to have similar organizations, the only exception being that in Salmonella O66, the wzy gene is replaced by a non-coding region. The function of the wzy gene in E. coli O166 was confirmed by the construction and analysis of deletion and trans-complementation mutants. It is proposed that a functional wzy gene located outside the O-antigen gene cluster is involved in Salmonella O66 O-antigen biosynthesis, as has been reported previously in Salmonella serogroups A, B and D1. The sequence identity for the corresponding genes between the O-antigen gene clusters of Salmonella O66 and E. coli O166 ranges from 64 to 70 %, indicating that they may originate from a common ancestor. It is likely that after the species divergence, Salmonella O66 got its specific O-antigen form by inactivation of the wzy gene located in the O-antigen gene cluster and acquisition of two new genes (a wzy gene and a prophage gene for O-acetyl modification) both residing outside the O-antigen gene cluster.
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43. |
Liu B,
Perepelov AV,
Svensson MV,
Shevelev SD,
Guo D,
Senchenkova SN,
Shashkov AS,
Weintraub A,
Feng L,
Widmalm G,
Knirel YA,
Wang L,
( 2010 ) Genetic and structural relationships of Salmonella O55 and Escherichia coli O103 O-antigens and identification of a 3-hydroxybutanoyltransferase gene involved in the synthesis of a Fuc3N derivative. PMID : 20147450 : DOI : 10.1093/glycob/cwq015 Abstract >>
O-antigen (O-polysaccharide), a part of the outer membrane of Gram-negative bacteria, is one of the most variable cell constituents and is related to bacterial virulence. O-antigen diversity is almost entirely due to genetic variations in O-antigen gene clusters. In this study, the O-polysaccharide structures of Salmonella O55 and Escherichia coli O103 were elucidated by chemical analysis and nuclear magnetic resonance spectroscopy. It was found that the O-polysaccharides have similar pentasaccharide O-units, which differ only in one sugar (glucose versus N-acetylglucosamine) and in the N-acyl group (acetyl versus 3-hydroxybutanoyl) on 3-amino-3,6-dideoxy-d-galactose (d-Fuc3N). The Salmonella O55 antigen gene cluster was sequenced and compared with the E. coli O103 antigen gene cluster reported previously. The two gene clusters were found to share high-level similarity (DNA identity ranges from 53% to 76%), except for two putative acyl transferase genes (fdtC in Salmonella O55 and fdhC in E. coli O103) which show no similarity. Replacement of the fdtC gene in Salmonella O55 with the fdhC gene from E. coli O103 resulted in production of a modified O-antigen, which contains a 3-hydroxybutanoyl derivative of Fuc3N in place of 3-acetamido-3,6-dideoxygalactose. This finding strongly suggests that fdhC is a 3-hydroxybutanoyltransferase gene. The sequence similarity level suggested that the O-antigen gene clusters of Salmonella O55 and E. coli O103 originate from a common ancestor, and this evolutionary relationship is discussed.
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44. |
Call DR,
Singer RS,
Meng D,
Broschat SL,
Orfe LH,
Anderson JM,
Herndon DR,
Kappmeyer LS,
Daniels JB,
Besser TE,
( 2010 ) blaCMY-2-positive IncA/C plasmids from Escherichia coli and Salmonella enterica are a distinct component of a larger lineage of plasmids. PMID : 19949054 : DOI : 10.1128/AAC.00055-09 PMC : PMC2812137 Abstract >>
Large multidrug resistance plasmids of the A/C incompatibility complex (IncA/C) have been found in a diverse group of Gram-negative commensal and pathogenic bacteria. We present three completed sequences from IncA/C plasmids that originated from Escherichia coli (cattle) and Salmonella enterica serovar Newport (human) and that carry the cephamycinase gene blaCMY-2. These large plasmids (148 to 166 kbp) share extensive sequence identity and synteny. The most divergent plasmid, peH4H, has lost several conjugation-related genes and has gained a kanamycin resistance region. Two of the plasmids (pAM04528 and peH4H) harbor two copies of blaCMY-2, while the third plasmid (pAR060302) harbors a single copy of the gene. The majority of single-nucleotide polymorphisms comprise nonsynonymous mutations in floR. A comparative analysis of these plasmids with five other published IncA/C plasmids showed that the blaCMY-2 plasmids from E. coli and S. enterica are genetically distinct from those originating from Yersinia pestis and Photobacterium damselae and distal to one originating from Yersinia ruckeri. While the overall similarity of these plasmids supports the likelihood of recent movements among E. coli and S. enterica hosts, their greater divergence from Y. pestis or Y. ruckeri suggests less recent plasmid transfer among these pathogen groups.
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45. |
Krauland M,
Harrison L,
Paterson D,
Marsh J,
( 2010 ) Novel integron gene cassette arrays identified in a global collection of multi-drug resistant non-typhoidal Salmonella enterica. PMID : 19921331 : DOI : 10.1007/s00284-009-9527-3 PMC : PMC2824789 Abstract >>
Investigation of integron carriage in a global collection of multi-drug resistant Salmonella enterica identified 3 unique class 1 integron gene cassette arrays not previously reported in this species. The present study used PCR and DNA sequence analysis to characterize the structure of these gene cassette arrays. A approximately 4.0 kb integron containing the gene cassette array arr2/cmlA5/bla (OXA10) /aadA1 was found in isolates belonging to serovars Isangi and Typhimurium from South Africa. A approximately 6.0 kb integron containing the gene cassettes aac(6')IIc/ereA2/IS1247/aac/arr/ereA2 was found in isolates belonging to serovar Heidelberg from the Philippines. In this gene cassette array, the insertion sequence, IS1247, and two putative resistance genes, disrupt the erythromycin resistance gene cassette. Finally, a approximately 6.0 kb integron containing the gene cassette qacH/dfrA32/ereA1/aadA2/cmlA/aadA1 was found in serovar Stanley isolates from Taiwan. This integron, which has not been previously reported in any bacterial species, contains a new dihydrofolate reductase gene cassette sequence designated dfrA32, with only 90% sequence similarity to previously reported dfrA cassettes. The S. enterica integrons described in the present study represent novel collections of resistance genes which confer multi-drug resistance and have the potential to be widely disseminated among S. enterica as well as other bacterial species.
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46. |
Schubert S,
Darlu P,
Clermont O,
Wieser A,
Magistro G,
Hoffmann C,
Weinert K,
Tenaillon O,
Matic I,
Denamur E,
( 2009 ) Role of intraspecies recombination in the spread of pathogenicity islands within the Escherichia coli species. PMID : 19132082 : DOI : 10.1371/journal.ppat.1000257 PMC : PMC2606025 Abstract >>
Horizontal gene transfer is a key step in the evolution of bacterial pathogens. Besides phages and plasmids, pathogenicity islands (PAIs) are subjected to horizontal transfer. The transfer mechanisms of PAIs within a certain bacterial species or between different species are still not well understood. This study is focused on the High-Pathogenicity Island (HPI), which is a PAI widely spread among extraintestinal pathogenic Escherichia coli and serves as a model for horizontal transfer of PAIs in general. We applied a phylogenetic approach using multilocus sequence typing on HPI-positive and -negative natural E. coli isolates representative of the species diversity to infer the mechanism of horizontal HPI transfer within the E. coli species. In each strain, the partial nucleotide sequences of 6 HPI-encoded genes and 6 housekeeping genes of the genomic backbone, as well as DNA fragments immediately upstream and downstream of the HPI were compared. This revealed that the HPI is not solely vertically transmitted, but that recombination of large DNA fragments beyond the HPI plays a major role in the spread of the HPI within E. coli species. In support of the results of the phylogenetic analyses, we experimentally demonstrated that HPI can be transferred between different E. coli strains by F-plasmid mediated mobilization. Sequencing of the chromosomal DNA regions immediately upstream and downstream of the HPI in the recipient strain indicated that the HPI was transferred and integrated together with HPI-flanking DNA regions of the donor strain. The results of this study demonstrate for the first time that conjugative transfer and homologous DNA recombination play a major role in horizontal transfer of a pathogenicity island within the species E. coli.
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47. |
Lee K,
Lee M,
Lim J,
Jung J,
Park Y,
Lee Y,
( 2008 ) Contamination of chicken meat with Salmonella enterica Serovar Haardt with nalidixic acid resistance and reduced fluoroquinolone susceptibility. PMID : 19047832 : Abstract >>
Salmonella contamination in chicken meat was studied with 100 chicken meat samples purchased from 55 shops located in various regions. A total of 21 isolates of Salmonella enterica were isolated from 21 chicken meat samples from four shops located at open markets, whereas there were none from supermarkets with well-equipped cold systems. Among these, 18 isolates were identified as Salmonella enterica serotype Haardt (S. Haardt) and three isolates were S. enterica serotype Muenchen. When the minimal inhibitory concentrations of the S. Haardt isolates were assayed with the agar dilution method to determine susceptibility to ampicillin, chloramphenicol, sulfisoxazole, tetracycline, and nalidixic acid, all 18 isolates were resistant to tetracycline and nalidixic acid and nine of these were resistant to ampicillin. These isolates showed reduced susceptibility to eight fluoroquinolones including ciprofloxacin, enrofloxacin, levofloxacin, gatifloxacin, gemifloxacin, moxifloxacin, norfloxacin, and ofloxacin. When quinolone resistance determining regions of gyrA and gyrB were sequenced, every isolate had the same missense mutation Ser83-->Tyr (TCC-->TAC) in gyrA, whereas no mutation was found in gyrB. Pulsed-field gel electrophoresis with XbaI revealed a close relationship among these isolates, suggesting a contamination of raw chicken meat with clonal spread of nalidixic acid-resistant and quinolone-reduced susceptibility S. Haardt in chickens. Results in this study show the importance of a wellequipped cold system and the prudent use of fluoroquinolone in chickens to prevent the occurrence of quinolone resistant isolates.
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48. |
Liu D,
Verma NK,
Romana LK,
Reeves PR,
( 1991 ) Relationships among the rfb regions of Salmonella serovars A, B, and D. PMID : 1856174 : DOI : 10.1128/jb.173.15.4814-4819.1991 PMC : PMC208160 Abstract >>
The O antigens of Salmonella serogroups A, B, and D differ structurally in their side chain sugar residues. The genes encoding O-antigen biosynthesis are clustered in the rfb operon. The gene rfbJ in strain LT2 (serovar typhimurium, group B) and the genes rfbS and rfbE in strain Ty2 (serovar typhi, group D) account for the known differences in the rfb gene clusters used for determination of group specificity. In this paper, we report the nucleotide sequence of 2.9 kb of DNA from the rfb gene cluster of strain Ty2 and the finding of two open reading frames which have limited similarity with the corresponding open reading frames of strain LT2. These two genes complete the sequence of the rfb region of group D strain Ty2 if we use strain LT2 sequence where restriction site data show it to be extremely similar to the strain Ty2 sequence. The restriction map of the rfb gene cluster in group A strain IMVS1316 (serovar paratyphi) is identical to that of the cluster in strain Ty2 except for a frameshift mutation in rfbE and a triplicated region. The rfb gene clusters of these three strains are compared, and the evolutionary origin of these genes is discussed.
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49. |
Chang HW,
Nam YD,
Jung MY,
Kim KH,
Roh SW,
Kim MS,
Jeon CO,
Yoon JH,
Bae JW,
( 2008 ) Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods. PMID : 18782592 : DOI : 10.1016/j.mimet.2008.08.003 Abstract >>
The genomic DNA-DNA hybridization (DDH) method has been widely used as a practical method for the determination of phylogenetic relationships between closely related biological strains. Traditional DDH methods have serious limitations including low reproducibility, a high background and a time-consuming procedure. The DDH method using a genome-probing microarray (GPM) has been recently developed to complement conventional methods and could be used to overcome the limitations that are typically encountered. It is necessary to compare the GPM-based DDH method to the conventional methods before using the GPM for the estimation of genomic similarities since all of the previous scientific data have been entirely dependent on conventional DDH methods. In order to address this issue we compared the DDH values obtained using the GPM, microplate and nylon membrane methods to multi-locus sequence typing (MLST) data for 9 Salmonella genomes and an Escherichia coli type strain. The results showed that the genome similarity values and the degrees of standard deviation obtained using the GPM method were lower than those obtained with the microplate and nylon membrane methods. The dendrogram from the cluster analysis of GPM DDH values was consistent with the phylogenetic tree obtained from the multi-locus sequence typing (MLST) data but was not similar to those obtained using the microplate and nylon membrane methods. Although the signal intensity had to be maximal when the targets were hybridized to their own probe, the methods using membranes and microplates frequently produced higher signals in the heterologous hybridizations than those obtained in the homologous hybridizations. Only the GPM method produced the highest signal intensity in homologous hybridizations. These results show that the GPM method can be used to obtain results that are more accurate than those generated by the other methods tested.
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50. |
Luque I,
Echeita A,
León J,
Herrera-León S,
Tarradas C,
González-Sanz R,
Huerta B,
Astorga RJ,
( 2009 ) Salmonella Indiana as a cause of abortion in ewes: Genetic diversity and resistance patterns. PMID : 18823722 : DOI : 10.1016/j.vetmic.2008.08.015 Abstract >>
Salmonella enterica subspecies enterica Indiana, a food-borne serovar uncommon in most countries, was responsible for an outbreak of abortion in a flock of Lacaune dairy ewes in southern Spain. Drinking water and feedstuff samples were analysed in an attempt to determine the source of the infection. Pigeons (Columba livia) and turtledoves (Streptopelia turtur) in close contact with the ewes were captured and examined for the bacterium. Seventeen S. Indiana strains were isolated from the ewes and wild birds and the genetic similarity among them analysed by Pulsed Field Gel Electrophoresis (PFGE) after the digestion of their genomic DNA with the restriction enzyme XbaI. The results suggest the wild birds might be responsible for the outbreak in the ewes. The strains recovered were fully susceptible to 15 out of the 16 antimicrobial agents tested: ampicillin, amoxycillin clavulanate, cephalothin, ceftriaxone, gentamicin, neomycin, streptomycin, tetracycline, ciprofloxacin, enrofloxacin, sulphonamides, trimethoprim-sulphamethoxazole, apramycin, colistin and chloramphenicol. Differences in the resistance pattern to nalidixic acid were observed; 11 strains (64.7%) were nalidixic acid resistant (R-Nx) and 6 (35.3%) sensitive (S-Nx). Among the R-Nx strains, a substitution of Gly to Cys at position 81 (Gly81?Cys) of the gyrA gene in 10 strains isolated from wild birds and ovine foetuses, and of Asp to Tyr at position 87 (Asp87?Tyr) in one strain isolated from ewe faeces, were revealed by sequencing the gene. To control the outbreak, enrofloxacin treatment was administered for 5 days. The same therapy was used to prevent infection during following gestation cycles, administering the antimicrobial agent at presentation and over 4 weeks before birth. Anti-bird meshes and closed drinking and feeding troughs were also installed to prevent further contact of the ewes with wild birds.
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51. |
McQuiston JR,
Herrera-Leon S,
Wertheim BC,
Doyle J,
Fields PI,
Tauxe RV,
Logsdon JM,
( 2008 ) Molecular phylogeny of the salmonellae: relationships among Salmonella species and subspecies determined from four housekeeping genes and evidence of lateral gene transfer events. PMID : 18757540 : DOI : 10.1128/JB.01552-07 PMC : PMC2580703 Abstract >>
The salmonellae are a diverse group of bacteria within the family Enterobacteriaceae that includes two species, Salmonella enterica and Salmonella bongori. In order to characterize the phylogenetic relationships of the species and subspecies of Salmonella, we analyzed four housekeeping genes, gapA, phoP, mdh and recA, comprising 3,459 bp of nucleotide sequence data for each isolate sequenced. Sixty-one isolates representing the most common serotypes of the seven subspecies of Salmonella enterica and six isolates of Salmonella bongori were included in this study. We present a robust phylogeny of the Salmonella species and subspecies that clearly defines the lineages comprising diphasic and monophasic subspecies. Evidence of intersubspecies lateral gene transfer of the housekeeping gene recA, which has not previously been reported, was obtained.
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52. |
García-Fernández A,
Chiaretto G,
Bertini A,
Villa L,
Fortini D,
Ricci A,
Carattoli A,
( 2008 ) Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum beta-lactamases in Escherichia coli and Salmonella of human and animal origin. PMID : 18367460 : DOI : 10.1093/jac/dkn131 Abstract >>
Plasmids belonging to incompatibility group I1 (IncI1) are widespread in Enterobacteriaceae and are characterized by the presence of a cluster of genes encoding the type IV pili, contributing to the virulence of Shiga-toxigenic Escherichia coli. Recently, IncI1 plasmids were identified in E. coli and Salmonella strains of animal origin as responsible for the dissemination of beta-lactamase genes. Plasmid multilocus sequence typing (pMLST) was developed to discern naturally occurring IncI1 plasmids in homogeneous groups according to their allele assortment. pMLST was developed by selecting multiple target genes on the available complete IncI1 plasmid DNA sequences. Sixteen plasmids, all assigned to the IncI1 group by the PCR-based replicon typing method, were included in this study. They were analysed for beta-lactamase genes and typed by restriction fragment length polymorphism (RFLP) and pMLST. Sixteen plasmids identified in E. coli and Salmonella isolated from animals and humans in different countries carried bla(CMY-2), bla(CTX-M-15), bla(CTX-M-1), bla(CTX-M-14), bla(TEM-52), bla(SHV-12) or bla(TEM-1) beta-lactamase genes. These plasmids were classified by RFLP in nine different groups corresponding to the nine sequence types determined by pMLST. The pMLST method was suitable for rapid and easy subtyping of IncI1 plasmids. This study demonstrates that the pMLST method can contribute to the epidemiological description of circulation of specific resistance plasmids among beta-lactamase producers isolated from animals and humans.
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53. |
Hong SF,
Chiu CH,
Chu C,
Feng Y,
Ou JT,
( 2008 ) Complete nucleotide sequence of a virulence plasmid of Salmonella enterica serovar Dublin and its phylogenetic relationship to the virulence plasmids of serovars Choleraesuis, Enteritidis and Typhimurium. PMID : 18336553 : DOI : 10.1111/j.1574-6968.2008.01096.x Abstract >>
The complete nucleotide sequence of pOU1113 (pSDVu), one of the two types of virulence plasmids of Salmonella enterica serovar Dublin, was determined. It contained 80 156 bp with 53.8 mol% G+C content. Approximately 70 genes could be discerned. Compared with pSTV, the virulence plasmid of serovar Typhimurium, pOU1113 was shorter owing to a missing region amounting to c. 10 kb; furthermore, except for a unique 10 849-bp region, the nucleotide as well as deduced amino acid sequences of pOU1113 were nearly identical to the corresponding regions of three S. enterica virulence plasmids, namely pSCV (virulence plasmid of Choleraesuis), pSTV and pSEV (virulence plasmids of Enteritidis), confirming their close phylogenetic relationship. Comparative analysis indicated that these virulence plasmids appeared to have descended by deletion from a relatively large plasmid to smaller ones, with some recombination events occurring over time. From a biological and evolutionary point of view, if the decreasing sizes of pOU1113 and pSCV truly reflect a process in which the virulence plasmid has been shedding unnecessary genes during evolution, our data suggest that some genes in the missing region, such as the pef and tra operons, could have a minimal role in maintaining the survival of the bacteria in their environmental niche.
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54. |
Woodford CR,
Thoden JB,
Holden HM,
( 2017 ) Molecular architecture of an N-formyltransferase from Salmonella enterica O60. PMID : 28263875 : DOI : 10.1016/j.jsb.2017.03.002 PMC : PMC5581740 Abstract >>
N-formylated sugars are found on the lipopolysaccharides of various pathogenic Gram negative bacteria including Campylobacter jejuni 81116, Francisella tularensis, Providencia alcalifaciens O30, and Providencia alcalifaciens O40. The last step in the biosynthetic pathways for these unusual sugars is catalyzed by N-formyltransferases that utilize N10-formyltetrahydrofolate as the carbon source. The substrates are dTDP-linked amino sugars with the functional groups installed at either the C-3' or C-4' positions of the pyranosyl rings. Here we describe a structural and enzymological investigation of the putative N-formyltransferase, FdtF, from Salmonella enterica O60. In keeping with its proposed role in the organism, the kinetic data reveal that the enzyme is more active with dTDP-3-amino-3,6-dideoxy-d-galactose than with dTDP-3-amino-3,6-dideoxy-d-glucose. The structural data demonstrate that the enzyme contains, in addition to the canonical N-formyltransferase fold, an ankyrin repeat moiety that houses a second dTDP-sugar binding pocket. This is only the second time an ankyrin repeat has been shown to be involved in small molecule binding. The research described herein represents the first structural analysis of a sugar N-formyltransferase that specifically functions on dTDP-3-amino-3,6-dideoxy-d-galactose in vivo and thus adds to our understanding of these intriguing enzymes.
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55. |
Yang YQ,
Zhang AY,
Ma SZ,
Kong LH,
Li YX,
Liu JX,
Davis MA,
Guo XY,
Liu BH,
Lei CW,
Wang HN,
( 2016 ) Co-occurrence of mcr-1 and ESBL on a single plasmid in Salmonella enterica. PMID : 27330065 : DOI : 10.1093/jac/dkw243 Abstract >>
N/A
|
56. |
Norel F,
Pisano MR,
Nicoli J,
Popoff MY,
( 1989 ) Nucleotide sequence of the plasmid-borne virulence gene mkfB from Salmonella typhimurium. PMID : 2696057 : Abstract >>
N/A
|
57. |
Amha YM,
Kumaraswamy R,
Ahmad F,
( 2015 ) A probabilistic QMRA of Salmonella in direct agricultural reuse of treated municipal wastewater. PMID : 25909731 : DOI : 10.2166/wst.2015.093 Abstract >>
Developing reliable quantitative microbial risk assessment (QMRA) procedures aids in setting recommendations on reuse applications of treated wastewater. In this study, a probabilistic QMRA to determine the risk of Salmonella infections resulting from the consumption of edible crops irrigated with treated wastewater was conducted. Quantitative polymerase chain reaction (qPCR) was used to enumerate Salmonella spp. in post-disinfected samples, where they showed concentrations ranging from 90 to 1,600 cells/100 mL. The results were used to construct probabilistic exposure models for the raw consumption of three vegetables (lettuce, cabbage, and cucumber) irrigated with treated wastewater, and to estimate the disease burden using Monte Carlo analysis. The results showed elevated median disease burden, when compared with acceptable disease burden set by the World Health Organization, which is 10?? disability-adjusted life years per person per year. Of the three vegetables considered, lettuce showed the highest risk of infection in all scenarios considered, while cucumber showed the lowest risk. The results of the Salmonella concentration obtained with qPCR were compared with the results of Escherichia coli concentration for samples taken on the same sampling dates.
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58. |
Wong MH,
Liu L,
Yan M,
Chan EW,
Chen S,
( 2015 ) Dissemination of IncI2 Plasmids That Harbor the blaCTX-M Element among Clinical Salmonella Isolates. PMID : 26014934 : DOI : 10.1128/AAC.00775-15 PMC : PMC4505288 Abstract >>
The extended-spectrum-�]-lactamase (ESBL) determinant CTX-M-55 is increasingly prevalent in Escherichia coli but remains extremely rare in Salmonella. This study reports the isolation of a plasmid harboring the blaCTX-M-55 element in a clinical Salmonella enterica serotype Typhimurium strain resistant to multiple antibiotics. This plasmid is genetically identical to several known IncI2-type elements harbored by E. coli strains recovered from animals. This finding indicates that IncI2 plasmids harboring the blaCTX-M genes may undergo cross-species migration among potential bacterial pathogens, with E. coli as the major source of such elements.
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59. |
Mehrane S,
Weill FX,
De Champs C,
Le Magrex-Debar E,
Kermas R,
( 2012 ) Characterization of extended-spectrum beta-lactamase-producing Salmonella enterica serotype Brunei and Heidelberg at the Hussein Dey hospital in Algiers (Algeria). PMID : 22871227 : DOI : 10.1089/fpd.2012.1159 Abstract >>
The purpose of this work was to study the genetic determinants responsible for extended-spectrum cephalosporin (ESC) resistance of Salmonella collected during the period of 1995-2008 at the Hussein Dey hospital in Algiers (Algeria). Fourteen ESC-resistant Salmonella isolates were tested towards 22 antimicrobial agents. Polymerase chain reaction (PCR) and sequencing were used to determine the underlying genetic determinants responsible for the extended-spectrum beta-lactamase (ESBL) phenotypes. Enterobacterial Repetitive Intergenic Consensus PCR was employed to type the isolates. All tested isolates were resistant to ticarcillin, ticarcillin-clavulanate, piperacillin, cefuroxime, aztreonam, ceftazidime, cefotaxime (except two isolates), cefepime, and cefpirome. PCR and DNA sequencing identified these ESBLs as TEM-48 (n=6), TEM-4 (n=3), CTX-M-15 (n=4), and one new TEM, designated TEM-188. Thus, continued surveillance for the presence of ESBL-producing (non-typhoidal) salmonellae in Algeria is essential.
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60. |
Reeves PR,
Cunneen MM,
Liu B,
Wang L,
( 2013 ) Genetics and evolution of the Salmonella galactose-initiated set of o antigens. PMID : 23874940 : DOI : 10.1371/journal.pone.0069306 PMC : PMC3715488 Abstract >>
This paper covers eight Salmonella serogroups, that are defined by O antigens with related structures and gene clusters. They include the serovars that are now most frequently isolated. Serogroups A, B1, B2, C2-C3, D1, D2, D3 and E have O antigens that are distinguished by having galactose as first sugar, and not N-acetyl glucosamine or N-acetyl galactosamine as in the other 38 serogroups, and indeed in most Enterobacteriaceae. The gene clusters for these galactose-initiated appear to have entered S. enterica since its divergence from E. coli, but sequence comparisons show that much of the diversification occurred long before this. We conclude that the gene clusters must have entered S. enterica in a series of parallel events. The individual gene clusters are discussed, followed by analysis of the divergence for those genes shared by two or more gene clusters, and a putative phylogenic tree for the gene clusters is presented. This set of O antigens provides a rare case where it is possible to examine in detail the relationships of a significant number of O antigens. In contrast the more common pattern of O-antigen diversity within a species is for there to be only a few cases of strains having related gene clusters, suggesting that diversity arose through gain of individual O-antigen gene clusters by lateral gene transfer, and under these circumstances the evolution of the diversity is not accessible. This paper on the galactose-initiated set of gene clusters gives new insights into the origins of O-antigen diversity generally.
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61. |
Liu B,
Knirel YA,
Feng L,
Perepelov AV,
Senchenkova SN,
Reeves PR,
Wang L,
( 2014 ) Structural diversity in Salmonella O antigens and its genetic basis. PMID : 23848592 : DOI : 10.1111/1574-6976.12034 Abstract >>
This review covers the structures and genetics of the 46 O antigens of Salmonella, a major pathogen of humans and domestic animals. The variation in structures underpins the serological specificity of the 46 recognized serogroups. The O antigen is important for the full function and virulence of many bacteria, and the considerable diversity of O antigens can confer selective advantage. Salmonella O antigens can be divided into two major groups: those which have N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine (GalNAc) and those which have galactose (Gal) as the first sugar in the O unit. In recent years, we have determined 21 chemical structures and sequenced 28 gene clusters for GlcNAc-/GalNAc-initiated O antigens, thus completing the structure and DNA sequence data for the 46 Salmonella O antigens. The structures and gene clusters of the GlcNAc-/GalNAc-initiated O antigens were found to be highly diverse, and 24 of them were found to be identical or closely related to Escherichia coli O antigens. Sequence comparisons indicate that all or most of the shared gene clusters were probably present in the common ancestor, although alternative explanations are also possible. In contrast, the better-known eight Gal-initiated O antigens are closely related both in structures and gene cluster sequences.
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62. |
Akiyama T,
Khan AA,
( 2012 ) Molecular characterization of strains of fluoroquinolone-resistant Salmonella enterica serovar Schwarzengrund carrying multidrug resistance isolated from imported foods. PMID : 22010209 : DOI : 10.1093/jac/dkr414 Abstract >>
To determine the fluoroquinolone resistance determinants in Salmonella enterica serovar Schwarzengrund from imported foods. Antibiotic susceptibility of Salmonella Schwarzengrund to 16 antibiotics was examined using disc agar diffusion and Etest. Quinolone resistance determinants were examined by sequence analysis of gyrA, gyrB, parC and parE, PCR amplification of qnrA, qnrB and qnrS, and expression of acrB, ramA, marA, soxS and rob using quantitative RT-PCR. The contribution of efflux pump activities to antibiotic resistance was determined by the addition of carbonyl cyanide m-chlorophenylhydrazone (CCCP). The effect of ramR deletion on ciprofloxacin resistance was determined by complementing with wild-type ramR. Salmonella strains 30 and 487 were susceptible to ciprofloxacin and had a single mutation in gyrA as compared with strain 75, which was highly resistant to ciprofloxacin and had a double mutation in gyrA. Increased expression of ramA was associated with high resistance to ciprofloxacin. Strain 75 had a deletion of 315 bp in the ramR gene, which regulates ramA expression. Overexpression of ramA was possibly related to a loss of ramR. Introduction of ramR decreased the MIC of ciprofloxacin from 48 to 24 mg/L. The addition of CCCP did not reduce antibiotic resistance. To our knowledge, this study reports for the first time the natural deletion of ramR in Salmonella Schwarzengrund. This study indicates that fluoroquinolone-resistant Salmonella are prevalent in imported food. Double mutations in gyrA and a loss of ramR were associated with high-level quinolone resistance in multidrug-resistant Salmonella Schwarzengrund strain 75.
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63. |
( 1997 ) A secreted Salmonella protein with homology to an avirulence determinant of plant pathogenic bacteria. PMID : 9275221 : DOI : 10.1073/pnas.94.18.9887 PMC : PMC23287 Abstract >>
Bacterial pathogens have evolved sophisticated mechanisms to interact with their hosts. A specialized type III protein secretion system capable of translocating bacterial proteins into host cells has emerged as a central factor in the interaction between a variety of mammalian and plant pathogenic bacteria with their hosts. Here we describe AvrA, a novel target of the centisome 63 type III protein secretion system of Salmonella enterica. AvrA shares sequence similarity with YopJ of the animal pathogen Yersinia pseudotuberculosis and AvrRxv of the plant pathogen Xanthomonas campestris pv. vesicatoria. These proteins are the first examples of putative targets of type III secretion systems in animal and plant pathogenic bacteria that share sequence similarity. They may therefore constitute a novel family of effector proteins with related functions in the cross-talk of these pathogens with their hosts.
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64. |
( 1997 ) Fluorescence-based isolation of bacterial genes expressed within host cells. PMID : 9302299 : DOI : 10.1126/science.277.5334.2007 Abstract >>
A selection strategy was devised to identify bacterial genes preferentially expressed when a bacterium associates with its host cell. Fourteen Salmonella typhimurium genes, which were under the control of at least four independent regulatory circuits, were identified to be selectively induced in host macrophages. Four genes encode virulence factors, including a component of a type III secretory apparatus. This selection methodology should be generally applicable to the identification of genes from pathogenic organisms that are induced upon association with host cells or tissues.
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65. |
( 1997 ) The specificity of sty SKI, a type I restriction enzyme, implies a structure with rotational symmetry. PMID : 9108149 : DOI : 10.1093/nar/25.9.1694 PMC : PMC146652 Abstract >>
The type I restriction and modification (R-M) enzyme from Salmonella enterica serovar kaduna (Sty SKI) recognises the DNA sequence 5'-CGAT(N)7GTTA, an unusual target for a type I R-M system in that it comprises two tetranucleotide components. The amino target recognition domain (TRD) of Sty SKI recognises 5'-CGAT and shows 36% amino acid identity with the carboxy TRD of Eco R124I which recognises the complementary, but degenerate, sequence 5'-RTCG. Current models predict that the amino and carboxy TRDs of the specificity subunit are in inverted orientations within a structure with 2-fold rotational symmetry. The complementary target sequences recognised by the amino TRD of Sty SKI and the carboxy TRD of Eco R124I are consistent with the predicted inverted positions of the TRDs. Amino TRDs of similar amino acid sequence have been shown to recognise the same nucleotide sequence. The similarity reported here, the first example of one between amino and carboxy TRDs, while consistent with a conserved mechanism of target recognition, offers additional flexibility in the evolution of sequence specificity by increasing the potential diversity of DNA targets for a given number of TRDs. Sty SKI identifies the first member of the IB family in Salmonella species.
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66. |
( 1997 ) Comparative genetics of the inv-spa invasion gene complex of Salmonella enterica. PMID : 9068645 : DOI : 10.1128/jb.179.6.1985-1991.1997 PMC : PMC178923 Abstract >>
The chromosomal region containing the Salmonella enterica pathogenic island inv-spa was present in the last common ancestor of all the contemporary lineages of salmonellae. For multiple strains of S. enterica, representing all eight subspecies, nucleotide sequences were obtained for five genes of the inv-spa invasion complex, invH, invE, invA, spaM, and spaN, al of which encode proteins that are required for entry of the bacteria into cultured epithelial cells. The invE, invA, spaM, and spaN genes were present in all eight subspecies of S. enterica, and for invE and invA and their products, levels of sequence variation among strains were within the ranges reported for housekeeping genes. In contrast, the InvH, SpaM, and SpaN proteins were unusually variable in amino acid sequence. Furthermore, invH was absent from the subspecies V isolates examined. The SpaM and SpaN proteins provide further evidence of a relationship (first detected by Li et al. [J. Li, H. Ochman, E. A. Groisman, E. F. Boyd, F. Solomon, K. Nelson, and R. K. Selander, Proc. Natl. Acad. Sci. USA 92:7252-7256, 1995]) between the cellular location of the products of the inv-spa genes and evolutionary rate, as reflected in the level of polymorphism within S. enterica. Invasion proteins that are membrane bound or membrane associated are relatively conserved in amino acid sequence, whereas those that are exported to the extracellular environment are hypervariable, possibly reflecting the action of diversifying selection.
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67. |
( 1993 ) Molecular mechanism of the regulation of expression of plasmid-encoded mouse bacteremia (mba) genes in Salmonella serovar Choleraesuis. PMID : 8437568 : DOI : 10.1007/bf00277116 Abstract >>
The regulation of mouse bacteremia genes (mba genes) encoded by a 6.4 kb region on the 50 kb virulence plasmid (pKDSC50) of Salmonella serovar Choleraesuis was analyzed. The genes mba1, mba2, mba3, and mba4, are arranged in this order, and form a cluster located in the 6.4 kb mba region. We prepared four antibodies, each specific for an individual Mba protein, using synthetic peptides as antigens. Their amino acid sequences were deduced from the DNA sequence of the corresponding mba genes. Each Mba peptide antiserum was able to recognize the corresponding Mba protein produced by Escherichia coli carrying a recombinant plasmid containing individual mba genes. When the recombinant plasmid contained all four mba genes (pMKD601), three Mba proteins (Mba2, Mba3, and Mba4) were identified by Western blotting analysis using Mba antisera. These proteins could not be detected when the recombinant plasmid lacked mba1 (pMKD201). Three species of mRNA for mba2, mba3, and mba4 with different chain length were detected from pMKD601 by Northern blot hybridization, and two start sites were identified by primer extension assay. Gel mobility shift assays demonstrated that Mba1 specifically bound to a fragment containing the start sites of mRNAs. The amino acid sequence of Mba1 had significant homology to the LysR family of DNA binding proteins, possessing a characteristic helix-turn-helix DNA binding motif. The present study provides clear evidence to show that the Mba1 protein binds to the promoter region of mba2, and positively regulates the expression of mba2, mba3, and mba4 genes.
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68. |
( 1993 ) Evolution of Salmonella O antigen variation by interspecific gene transfer on a large scale. PMID : 8434412 : DOI : 10.1016/0168-9525(93)90067-R Abstract >>
The O antigen is a bacterial surface polysaccharide made up of repeats of a short oligosaccharide. There are about 60 forms of O antigen in Salmonella, and genetic analysis indicates that these were acquired by interspecific gene transfer.
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69. |
( 1996 ) Molecular genetic relationships of the salmonellae. PMID : 8975610 : PMC : PMC167847 Abstract >>
A multilocus enzyme electrophoresis analysis of 96 strains of the salmonellae distinguished 80 electrophoretic types (ETs) and placed them in eight groups, seven of which correspond precisely to the seven taxonomic groups (I, II, IIIa, IIIb, IV, V, and VI) previously defined on the basis of biotype and genomic DNA hybridization. In addition, multilocus enzyme electrophoresis identified an eighth distinctive group (designated VII) composed of five strains that had been assigned to group IV on the basis of biotype. An analysis of variation in the combined nucleotide sequences of five housekeeping genes among 16 strains representing all eight groups yielded estimates of overall genetic relationships that are fully consistent with those indicated by DNA hybridization. However, the nucleotide sequences of seven invasion genes (inv/spa) in the strains of group VII were closely similar to those of strains of group IV. These findings are interpreted as evidence that group VII represents an old, differentiated lineage to which one or more large parts of the chromosomal genome of the group IV lineage, including the 40-kb segment on which the invasion genes are located, have been horizontally transferred. All lines of molecular genetic evidence indicate that group V is very strongly differentiated from all other groups, thus supporting its current taxonomic treatment as a species, Salmonella bongori, separate from S. enterica. The Salmonella Reference Collection C, composed of the 16 strains used in DNA sequence studies, has been established for research on variation in natural populations.
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70. |
( 1996 ) A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA. PMID : 8939428 : Abstract >>
Salmonella enterica serovar blegdam has a restriction and modification system encoded by genes linked to serB. We have cloned these genes, putative alleles of the hsd locus of Escherichia coli K-12, and confirmed by the sequence similarities of flanking DNA that the hsd genes of S. enterica serovar blegdam have the same chromosomal location as those of E. coli K-12 and Salmonella enterica serovar typhimurium LT2. There is, however, no obvious similarity in their nucleotide sequences, and while the gene order in S. enterica serovar blegdam is serB hsdM, S and R, that in E. coli K-12 and S. enterica serovar typhimurium LT2 is serB hsdR, M and S. The hsd genes of S. enterica serovar blegdam identify a third family of serB-linked hsd genes (type ID). The polypeptide sequence predicted from the three hsd genes show some similarities (18-50% identity) with the polypeptides of known and putative type I restriction and modification systems; the highest levels of identity are with sequences of Haemophilus influenzae Rd. The HsdM polypeptide has the motifs characteristic of adenine methyltransferases. Comparisons of the HsdR sequence with those for three other families of type I systems and three putative HsdR polypeptides identify two highly conserved regions in addition to the seven proposed DEAD-box motifs.
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71. |
( 1997 ) Recent horizontal transmission of plasmids between natural populations of Escherichia coli and Salmonella enterica. PMID : 9045822 : DOI : 10.1128/jb.179.5.1622-1627.1997 PMC : PMC178875 Abstract >>
Seventy-one natural isolates obtained from a Salmonella reference collection were examined for the presence of plasmids closely related to the Escherichia coli F plasmid. The collection consists of several serovars of the S. enterica Typhimurium complex, subspecies I, to which 99% of pathogenic salmonellae belong. Molecular genetic techniques of DNA hybridization, along with PCR and DNA sequencing, were used to examine the occurrence, distribution, and genetic diversity of F-like plasmids among Salmonella strains. The F plasmid genes examined were finO, traD, traY, and repA, which map at dispersed positions on the F plasmid of E. coli. Comparative sequence analysis of each of the four genes in Salmonella plasmids showed them to be homologous (in some cases, virtually identical) to those found in F plasmids of E. coli natural isolates. Furthermore, the frequency of F-like plasmids in Salmonella strains was approximately the same as that observed in the E. coli Reference Collection. However, in Salmonella, the distribution was confined predominately to the serovars Typhimurium and Muenchen. The unexpected finding of a shared pool of F-like plasmids between S. enterica and E. coli demonstrates the significant role of conjugation in the histories of these important bacterial species.
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72. |
( 1996 ) Bacterial polysaccharide synthesis and gene nomenclature. PMID : 9004408 : Abstract >>
Gene nomenclature for bacterial surface polysaccharides is complicated by the large number of structures and genes. We propose a scheme applicable to all species that distinguishes different classes of genes, provides a single name for all genes of a given function and greatly facilitates comparative studies.
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73. |
( 1996 ) Distribution, gene sequence and expression in vivo of the plasmid encoded fimbrial antigen of Salmonella serotype Enteritidis. PMID : 8760946 : DOI : 10.1017/s0950268800001084 PMC : PMC2271688 Abstract >>
The pefA gene which encoded the serotype associated plasmid (SAP) mediated fimbrial major subunit antigen of Salmonella enterica serotype Typhimurium shared genetic identity with 128 of 706 salmonella isolates as demonstrated by dot (colony) hybridization. Seventy-seven of 113 isolates of Typhimurium and individual isolates of serotypes Bovis-morbificans, Cholerae-suis and Enteritidis phage type 9b hybridized pefA strongly, whereas 48 isolates of Enteritidis hybridized pefA weakly and one Enteritidis isolate of phage type 14b failed to hybridize. Individual isolates of 294 serotypes and 247 individual isolates of serotype Dublin did not hybridize pefA. Southern hybridization of plasmids extracted from Enteritidis demonstrated that the pefA gene probe hybridized strongly an atypical SAP of 80 kb in size harboured by one Enteritidis isolate of phage-type 9b, whereas the typical SAP of 58 kb in size harboured by 48 Enteritidis isolates hybridized weakly. One Enteritidis isolate of phage type 14b which failed to hybridize pefA in dot (colony) hybridization experiments was demonstrated to be plasmid free. A cosmid library of Enteritidis phage type 4 expressed in Escherichia coli K12 was screened by hybridization for the presence of pef sequences. Recombinant clones which were deduced to harbour the entire pef operon elaborated a PEF-like fimbrial structure at the cell surface. The PEF-like fimbrial antigen was purified from one cosmid clone and used in western blot experiments with sera from chickens infected with Enteritidis phage-type 4. Seroconversion to the fimbrial antigen was observed which indicated that the Enteritidis PEF-like fimbrial structure was expressed at some stage during infection. Nucleotide sequence analysis demonstrated that the pefA alleles of Typhimurium and Enteritidis phage-type 4 shared 76% DNA nucleotide and 82% deduced amino acid sequence identity.
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74. |
( 1996 ) The GalF protein of Escherichia coli is not a UDP-glucose pyrophosphorylase but interacts with the GalU protein possibly to regulate cellular levels of UDP-glucose. PMID : 8971705 : DOI : 10.1046/j.1365-2958.1996.01531.x Abstract >>
We report the functional characterization of the galF gene of strain VW187 (Escherichia coli O7:K1), which encodes a polypeptide displaying structural features common to bacterial UDP-glucose pyrophosphorylases, including the E. coli GalU protein. These enzymes catalyse a reversible reaction converting UTP and glucose-1-phosphate into UDP-glucose and PPi. We show that, although the GalF protein is expressed in vivo, GalF-expressing plasmids cannot complement the phenotype of a galU mutant and extracts from this mutant which only produces GalF are enzymatically inactive. In contrast, the presence of GalU and GalF proteins in the same cell-free extract caused a significant reduction in the rate of pyrophosphorolysis (conversion of UDP-glucose into glucose-1-phosphate) but no significant effect on the kinetics of synthesis of UDP-glucose. The presence of GalF also increased the thermal stability of the enzyme in vitro. The effect of GalF in the biochemical properties of the UDP-glucose pyrophosphorylase required the co-synthesis of GalF and GalU, suggesting that they could interact as components of the oligomeric enzyme. The physical interaction of GalU and GalF was demonstrated in vivo by the co-expression of both proteins as fusion products using a yeast two-hybrid system. Furthermore, using a pair of galF-/galU+ and galF/galU+ isogenic strains, we demonstrated that the presence of GalF is associated with an increased concentration of intracellular UDP-glucose as well as with an enhancement of the thermal stability of the UDP-glucose pyrophosphorylase in vivo. We propose that GalF is a non-catalytic subunit of the UDP-glucose pyrophosphorylase modulating the enzyme activity to increase the formation of UDP-glucose, and this function is important for bacterial adaptation to conditions of stress.
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75. |
( 1996 ) C-terminal half of Salmonella enterica WbaP (RfbP) is the galactosyl-1-phosphate transferase domain catalyzing the first step of O-antigen synthesis. PMID : 8626328 : DOI : 10.1128/jb.178.9.2598-2604.1996 PMC : PMC177985 Abstract >>
We previously showed that the product of the wbaP gene of Salmonella enterica serovar Typhimurium has two functions: it is involved in the first step of O-antigen synthesis (the galactosyltransferase [GT] function) and in a later step (the T function), first thought to be the flipping of the O-antigen subunit on undecaprenyl pyrophosphate from the cytoplasmic face to the periplasmic face of the cytoplasmic membrane. We now locate two wbaP(T) mutations within the first half of the wbaP gene by sequencing. Both mutants retain GT activity, although one was a frameshift mutation resulting in a stop codon 10 codons after the frameshift to give an open reading frame containing only 138 of the 476 codons in WbaP. We also show that there is a secondary translation starting within the wbaP gene resulting in the synthesis of a polypeptide with GT activity. These results indicate that the N- and C-terminal halves of WbaP are the T and GT functional domains, respectively. We now propose that the T block operates prior to the flippase function, probably at the release of undecaprenyl pyrophosphate-linked galactose from WbaP.
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76. |
( 1994 ) Recombinational basis of serovar diversity in Salmonella enterica. PMID : 8146152 : DOI : 10.1073/pnas.91.7.2552 PMC : PMC43407 Abstract >>
The fliC gene, which encodes phase 1 flagellin, was sequenced in strains of 15 Salmonella enterica serovars expressing flagellar antigenic factors of the g series. The occurrence of each of the flagellin serotypes g,m, m,t, and g,z51 in distantly related strains is the result of horizontal exchange of DNA, as indicated by identity or close similarity in nucleotide sequence of all or parts of the antigenic factor-determining central region of fliC. The flagellin genes of some serovars are complex mosaic structures composed of diverse segments derived through multiple recombination events. Thus, recombination of horizontally transferred segments (intragenic) or entire genes (assortative) within and among subspecies is identified as a major evolutionary mechanism generating both allelic variation at the fliC locus and serovar diversity in natural populations. Evidence that flagellar serological diversity is promoted by diversifying selection in adaptation to host immune defense system or flagellotropic phage is discussed.
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77. |
( 1994 ) Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria. PMID : 7937867 : DOI : 10.1073/pnas.91.21.10227 PMC : PMC44991 Abstract >>
The gnd gene, encoding 6-phosphogluconate dehydrogenase (EC 1.1.1.44), was sequenced in 87 strains of 15 species assigned to five nominal genera of the Enterobacteriaceae, including 36 isolates of Salmonella enterica and 32 strains of Escherichia coli. In S. enterica, the effective (realized) rate of recombination of horizontally transferred gnd sequences is only moderately higher than the rates for other chromosomal housekeeping genes. In contrast, recombination at gnd has occurred with such high frequency in Escherichia coli that the indicated evolutionary relationships among strains are not congruent with those estimated by sequence analysis of other genes and by multilocus enzyme electrophoresis. E. coli and S. enterica apparently have not exchanged gnd sequences, but those of several strains of E. coli have been imported from species of Citrobacter and Klebsiella. The relatively frequent exchange of gnd within and among taxonomic groups of the Enterobacteriaceae, compared with other housekeeping genes, apparently results from its close linkage with genes that are subject to diversifying selection, including those of the rfb region determining the structure of the O antigen polysaccharide.
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78. |
( 1994 ) Molecular analysis of the rfb gene cluster of a group D2 Salmonella enterica strain: evidence for its origin from an insertion sequence-mediated recombination event between group E and D1 strains. PMID : 8021222 : DOI : 10.1128/jb.176.14.4357-4365.1994 PMC : PMC205649 Abstract >>
The Salmonella enterica O antigen is a highly variable surface polysaccharide composed of a repeated oligosaccharide (the O unit). The O unit produced by serogroup D2 has structural features in common with those of groups D1 and E1, and hybridization studies had previously suggested that the D2 rfb gene cluster responsible for O-unit biosynthesis is indeed a hybrid of the two. In this study, the rfb gene cluster was cloned from a group D2 strain of S. enterica sv. Strasbourg. Mapping, hybridization, and DNA sequencing showed that the organization of the D2 rfb genes is similar to that of group D1, with the alpha-mannosyl transferase gene rfbU replaced by rfbO, the E1-specific beta-mannosyl transferase gene. The E1-specific polymerase gene (rfc) has also been acquired. Interestingly, the D1-like and E1-like rfb regions are separated by an additional sequence closely related to an element (Hinc repeat [H-rpt]) associated with the Rhs loci of Escherichia coli. The H-rpt resembles an insertion sequence and possibly mediated the intraspecific recombination events which produced the group D2 rfb gene organization.
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79. |
( 1994 ) Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica. PMID : 8108402 : DOI : 10.1073/pnas.91.4.1280 PMC : PMC43141 Abstract >>
Nucleotide sequences of the mdh gene encoding the metabolic enzyme malate dehydrogenase (MDH) were determined for 44 strains representing the major lineages of Escherichia coli and the eight subspecies of Salmonella enterica. Sequence diversity was four times greater in S. enterica than in E. coli, and in both species the rate of amino acid substitution was lower in the NAD(+)-binding domain than in the catalytic domain. Divergence of the mdh genes of the two species apparently has not involved excess nonsynonymous substitutions resulting from the fixation of adaptive amino acid mutations. Allozyme analysis detected 57% of the distinctive amino acid sequences. Statistical tests of the distribution of polymorphic synonymous nucleotide sites identified four possible intragenic recombination events, one involving a single allele of E. coli and three involving alleles of the three subspecies of S. enterica. But recombination at mdh has not occurred with sufficient frequency to obscure the phylogenetic relationships among strains indicated by multilocus enzyme electrophoresis, total DNA hybridization, and sequence analysis of the gapA and putP genes. These findings provide further evidence that the effective (realized) rates of horizontal transfer and recombination for metabolic enzyme and other housekeeping genes are generally low in these species, in contrast to those for loci encoding or mediating the structure of cell-surface and other macromolecules for which recombinants may be subject to strong balancing, directional, or diversifying selection.
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80. |
Li J,
Ochman H,
Groisman EA,
Boyd EF,
Solomon F,
Nelson K,
Selander RK,
( 1995 ) Relationship between evolutionary rate and cellular location among the Inv/Spa invasion proteins of Salmonella enterica. PMID : 7638176 : DOI : 10.1073/pnas.92.16.7252 PMC : PMC41317 Abstract >>
For 21 strains of Salmonella enterica, nucleotide sequences were obtained for three invasion genes, spaO, spaP, and spaQ, of the chromosomal inv/spa complex, the products of which form a protein export system required for entry of the bacteria into nonphagocytic host cells. These genes are present in all eight subspecies of the salmonellae, and homologues occur in a variety of other bacteria, including the enteric pathogens Shigella and Yersinia, in which they are plasmid borne. Evolutionary diversification of the invasion genes among the subspecies of S. enterica has been generally similar in pattern and average rate to that of housekeeping genes. However, the range of variation in evolutionary rate among the invasion genes is unusually large, and there is a relationship between the evolutionary rate and cellular location of the invasion proteins, possibly reflecting diversifying selection on exported proteins in adaptation to variable host factors in extracellular environments. The SpaO protein, which is hypervariable in S. enterica and exhibits only 24% sequence identity with its homologues in Shigella and Yersinia, is secreted. In contrast, the membrane-associated proteins SpaP, SpaQ, and InvA are weakly polymorphic and have > 60% sequence identity with the corresponding proteins of other enteric bacteria. Acquisition of the inv/spa genes may have been a key event in the evolution of the salmonellae as pathogens, following which the invention of flagellar phase shifting facilitated niche expansion to include warm-blooded vertebrates.
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81. |
Liu D,
Haase AM,
Lindqvist L,
Lindberg AA,
Reeves PR,
( 1993 ) Glycosyl transferases of O-antigen biosynthesis in Salmonella enterica: identification and characterization of transferase genes of groups B, C2, and E1. PMID : 7684736 : DOI : 10.1128/jb.175.11.3408-3413.1993 PMC : PMC204739 Abstract >>
In Salmonella enterica, there is a great variety of O antigens, each consisting of a short oligosaccharide (the repeating unit) repeated many times. The O antigens differ in their sugar composition and glycosidic linkages. The genetic determinants of the O antigen are located in an rfb gene cluster, and some, including those of S. enterica O serogroups B, C2, and E1, have been cloned and sequenced. In this study of the glycosyltransferases which form the glycosidic linkages, we identify and characterize the four mannosyl and three rhamnosyl transferase genes of the three rfb gene clusters.
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82. |
Vanegas RA,
Joys TM,
( 1995 ) Molecular analyses of the phase-2 antigen complex 1,2,.. of Salmonella spp. PMID : 7541401 : DOI : 10.1128/jb.177.13.3863-3864.1995 PMC : PMC177107 Abstract >>
The nucleotide sequences of the structural genes (fljB) for salmonellar flagellins representative of the phase-2 flagellar antigens 1,2.., 1,5.., 1,6.., and 1,7.. were determined. The results did not indicate linear epitopes for the antigen 1 subfactors, suggesting that conformational aspects are involved in determining these antigenic specificities.
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83. |
Bastin DA,
Stevenson G,
Brown PK,
Haase A,
Reeves PR,
( 1993 ) Repeat unit polysaccharides of bacteria: a model for polymerization resembling that of ribosomes and fatty acid synthetase, with a novel mechanism for determining chain length. PMID : 7682279 : DOI : 10.1111/j.1365-2958.1993.tb01163.x Abstract >>
We report the identification and sequence from Escherichia coli and Salmonella enterica strains of the cld gene, encoding the chain-length determinant (CLD) which confers a modal distribution of chain length on the O-antigen component of lipopolysaccharide (LPS). The distribution of chain lengths in the absence of this gene fits a model in which as the chain is extended there is a constant probability of 0.165 of transfer of growing chain to LPS core, with termination of chain extension. The data for E. coli O111 fit a model in which the CLD reduces this probability for short chains and increases it to 0.4 for longer chains, leading to a reduced number of short chain molecules but an increase in numbers of longer molecules and transfer of essentially all molecules by chain length 21. We put forward a model for O-antigen polymerase which resembles the ribosome and fatty acid synthetase in having two sites, with the growing chain being transferred from a D site onto the new unit at the R site to extend the chain and then back to the D site to repeat the process. It is proposed that the CLD protein and polymerase form a complex which has two states: 'E' facilitating extension and 'T' facilitating transfer to core. The complex is postulated to enter the E state as O-antigen polymerization starts, and to shift to the T state after a predetermined time, the CLD acting as a molecular clock. The CLD is not O-antigen or species-specific but the modal value does depend on the source of the cld gene.
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84. |
Mulvey MR,
Bharat A,
Boyd DA,
Irwin RJ,
Wylie J,
( 2018 ) Characterization of a colistin-resistant Salmonella enterica 4,[5],12:i:- harbouring mcr-3.2 on a variant IncHI-2 plasmid identified in Canada. PMID : 30351266 : DOI : 10.1099/jmm.0.000854 Abstract >>
We have identified a Salmonella enterica serotype 4,[5],12:i:- containing a mcr-3.2 in a patient who travelled to Thailand 1 month prior to the identification of it in Canada. The isolate was multidrug resistant, but remained susceptible to the carbapenems, amikacin and piperacillin/tazobactam. The mcr-3.2 was carried on a 261 Kb variant of the IncHI2 pWJ1. This report provides further evidence of the emergence of a ST34 colistin-resistant clone.
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85. |
Wachtel R,
Bräuning B,
Mader SL,
Ecker F,
Kaila VRI,
Groll M,
Itzen A,
( 2018 ) The protease GtgE from Salmonella exclusively targets inactive Rab GTPases. PMID : 29298974 : DOI : 10.1038/s41467-017-02110-1 PMC : PMC5752668 Abstract >>
Salmonella infections require the delivery of bacterial effectors into the host cell that alter the regulation of host defense mechanisms. The secreted cysteine protease GtgE from S. Typhimurium manipulates vesicular trafficking by modifying the Rab32 subfamily via cleaving the regulatory switch I region. Here we present a comprehensive biochemical, structural, and computational characterization of GtgE in complex with Rab32. Interestingly, GtgE solely processes the inactive GDP-bound GTPase. The crystal structure of the Rab32:GDP substrate in complex with the inactive mutant GtgEC45A reveals the molecular basis of substrate recognition. In combination with atomistic molecular dynamics simulations, the structural determinants for protein and activity-state specificity are identified. Mutations in a central interaction hub lead to loss of the strict GDP specificity. Our findings shed light on the sequence of host cell manipulation events during Salmonella infection and provide an explanation for the dependence on the co-secreted GTPase activating protein SopD2.
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86. |
Tagg KA,
Francois Watkins L,
Moore MD,
Bennett C,
Joung YJ,
Chen JC,
Folster JP,
( 2019 ) Novel trimethoprim resistance gene dfrA34 identified in Salmonella Heidelberg in the USA. PMID : 30202900 : DOI : 10.1093/jac/dky373 Abstract >>
Trimethoprim/sulfamethoxazole is a synthetic antibiotic combination recommended for the treatment of complicated non-typhoidal Salmonella infections in humans. Resistance to trimethoprim/sulfamethoxazole is mediated by the acquisition of mobile genes, requiring both a dfr gene (trimethoprim resistance) and a sul gene (sulfamethoxazole resistance) for a clinical resistance phenotype (MIC ?4/76 mg/L). In 2017, the CDC investigated a multistate outbreak caused by a Salmonella enterica serotype Heidelberg strain with trimethoprim/sulfamethoxazole resistance, in which sul genes but no known dfr genes were detected. To characterize and describe the molecular mechanism of trimethoprim resistance in a Salmonella Heidelberg outbreak isolate. Illumina sequencing data for one outbreak isolate revealed a 588 bp ORF encoding a putative dfr gene. This gene was cloned into Escherichia coli and resistance to trimethoprim was measured by broth dilution and Etest. Phylogenetic analysis of previously reported dfrA genes was performed using MEGA. Long-read sequencing was conducted to determine the context of the novel dfr gene. The novel dfr gene, named dfrA34, conferred trimethoprim resistance (MIC ?32 mg/L) when cloned into E. coli. Based on predicted amino acid sequences, dfrA34 shares less than 50% identity with other known dfrA genes. The dfrA34 gene is located in a class 1 integron in a multiresistance region of an IncC plasmid, adjacent to a sul gene, thus conferring clinical trimethoprim/sulfamethoxazole resistance. Additionally, dfrA34 is associated with ISCR1, enabling easy transmission between other plasmids and bacterial strains.
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87. |
( 2013 ) Salmonella enterica diversity in central Californian coastal waterways. PMID : 23624479 : DOI : 10.1128/AEM.00930-13 PMC : PMC3697486 Abstract >>
Salmonella enterica is one of the most important bacterial enteric pathogens worldwide. However, little is known about its distribution and diversity in the environment. The present study explored the diversity of 104 strains of Salmonella enterica isolated over 2 years from 12 coastal waterways in central California. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing were used to probe species diversity. Seventy-four PFGE patterns and 38 sequence types (STs) were found, including 18 newly described STs. Nineteen of 25 PFGE patterns were indistinguishable from those of clinical isolates in PulseNet. The most common ST was consistent with S. enterica serovar Typhimurium, and other frequently detected STs were associated with the serovars Heidelberg and Enteritidis; all of these serovars are important etiologies of salmonellosis. An investigation into S. enterica biogeography was conducted at the level of ST and subspecies. At the ST and subspecies level, we found a taxon-time relationship but no taxon-area or taxon-environmental distance relationships. STs collected during wet versus dry conditions tended to be more similar; however, STs collected from waterways adjacent to watersheds with similar land covers did not tend to be similar. The results suggest that the lack of dispersal limitation may be an important factor affecting the diversity of S. enterica in the region.
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88. |
Wang Y,
Zhang A,
Yang Y,
Lei C,
Jiang W,
Liu B,
Shi H,
Kong L,
Cheng G,
Zhang X,
Yang X,
Wang H,
( 2017 ) Emergence of Salmonella enterica serovar Indiana and California isolates with concurrent resistance to cefotaxime, amikacin and ciprofloxacin from chickens in China. PMID : 28957726 : DOI : 10.1016/j.ijfoodmicro.2017.09.012 Abstract >>
The aim of this study was to investigate the prevalence and characterization of Salmonella concerning the poultry industry in China. A total of 170 non-duplicate Salmonella isolates were recovered from the 1540 chicken samples. Among the Salmonella isolates from chickens, the predominant serovars were S. enterica serovar Enteritidis (S. Enteritidis) (49/170, 28.8%), S. enterica serovar Indiana (S. Indiana) (37/170, 21.8%) and S. enterica serovar California (S. California) (34/170, 20.0%). High antimicrobial resistance was observed for ciprofloxacin (68.2%), amikacin (48.2%) and cefotaxime (44.7%). Of particular concerns were the 18 S. Indiana and 17 S. California isolates, which were concurrently resistant to cefotaxime, amikacin and ciprofloxacin. The blaCTX-M genes, 16S rRNA methylase genes (armA, rmtD or rmtC) and five plasmid-mediated quinolone resistance (PMQR) determinants (aac(6')-Ib-cr, oqxAB, qnrB, qepA and qnrD) were identified in 18 S. Indiana and 17 S. California isolates. To clarify their genetic correlation, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were further conducted. PFGE profiles showed that the majority of S. Indiana and S. California isolates were clonally unrelated with a standard cut-off of 85%. The results of MLST demonstrated that ST17 and ST40 were the most common ST types in S. Indiana and S. California isolates, respectively. Our findings indicated that the multiple antibiotic resistant S. Indiana and S. California isolates were widespread in chicken in China and might pose a potential threat to public health.
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89. |
( 2012 ) An allele of an ancestral transcription factor dependent on a horizontally acquired gene product. PMID : 23300460 : DOI : 10.1371/journal.pgen.1003060 PMC : PMC3531487 Abstract >>
Changes in gene regulatory circuits often give rise to phenotypic differences among closely related organisms. In bacteria, these changes can result from alterations in the ancestral genome and/or be brought about by genes acquired by horizontal transfer. Here, we identify an allele of the ancestral transcription factor PmrA that requires the horizontally acquired pmrD gene product to promote gene expression. We determined that a single amino acid difference between the PmrA proteins from the human adapted Salmonella enterica serovar Paratyphi B and the broad host range S. enterica serovar Typhimurium rendered transcription of PmrA-activated genes dependent on the PmrD protein in the former but not the latter serovar. Bacteria harboring the serovar Typhimurium allele exhibited polymyxin B resistance under PmrA- or under PmrA- and PmrD-inducing conditions. By contrast, isogenic strains with the serovar Paratyphi B allele displayed PmrA-regulated polymyxin B resistance only when experiencing activating conditions for both PmrA and PmrD. We establish that the two PmrA orthologs display quantitative differences in several biochemical properties. Strains harboring the serovar Paratyphi B allele showed enhanced biofilm formation, a property that might promote serovar Paratyphi B's chronic infection of the gallbladder. Our findings illustrate how subtle differences in ancestral genes can impact the ability of horizontally acquired genes to confer new properties.
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90. |
( N/A ) Rapid identification of Salmonella spp. phase 2 antigens of the H1 antigenic complex using "multiplex PCR". PMID : 9921582 : Abstract >>
N/A
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91. |
( 1998 ) Relationships among the O-antigen gene clusters of Salmonella enterica groups B, D1, D2, and D3. PMID : 9473060 : PMC : PMC106985 Abstract >>
The O antigen is an important cell wall antigen of gram-negative bacteria, and the genes responsible for its biosynthesis are located in a gene cluster. We have cloned and sequenced the DNA segment unique to the O-antigen gene cluster of Salmonella enterica group D3. This segment includes a novel O-antigen polymerase gene (wzyD3). The polymerase gives alpha(1-->6) linkages but has no detectable sequence similarity to that of group D2, which confers the same linkage. We find the remnant of a D3-like wzy gene in the O-antigen gene clusters of groups D1 and B and suggest that this is the original wzy gene of these O-antigen gene clusters.
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92. |
( 1998 ) Phylogenetic relationships of Salmonella based on DNA sequence comparison of atpD encoding the beta subunit of ATP synthase. PMID : 9561735 : DOI : 10.1111/j.1574-6968.1998.tb12933.x Abstract >>
DNA sequences covering 57% of atpD encoding the beta subunit of ATP synthase were determined for 16 strains of Salmonella enterica, two strains of S. bongori, and one strain each of Citrobacter freundii and Yersinia enterocolitica, and comparison was made with the published Escherichia coli and Enterobacter aerogenes sequences. The phylogenetic tree based on maximum-likelihood analysis showed separation of the subspecies of S. enterica except for two serotypes of subspecies II which were unsupported by a common node. The two serotypes of S. bongori were separated from S. enterica and related to the serotypes of subspecies II. A tight relationship was found between S. enterica subspecies IIIa consisting of monophasic serotypes and subspecies IIIb consisting of diphasic serotypes. This is in conflict with results obtained for most other housekeeping genes and the 23S rRNA gene separating mono- from diphasic subspecies.
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93. |
( 1997 ) Size and sequence polymorphism in the isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella enterica and Escherichia coli. PMID : 9409817 : PMC : PMC1208327 Abstract >>
The sequence of aceK, which codes for the regulatory catalytic enzyme isocitrate dehydrogenase kinase/phosphatase (IDH K/P), and sequences of the 5' flanking region and part or all of the 3' flanking region were determined for 32 strains of Salmonella enterica and Escherichia coli. In E. coli, the aceK gene was 1734 bp long in 13 strains, but in three strains it was 12 bp shorter and the stop codon was TAA rather than TGA. Strains with the shorter aceK lacked an open reading frame (f728) downstream between aceK and iclR that was present, in variable length, in the other strains. Among the 72 ECOR strains, the truncated aceK gene was present in all isolates of the B2 group and half of those of the D group. Other variant conditions included the presence of IS1 elements in two strains and large deletions in two strains. The aceK-aceA intergenic region varied in length from 48 to 280 bp in E. coli, depending largely on the number of repetitive extragenic palindromic (REP) sequences present. Among the ECOR strains, the number of REP elements showed a high degree of phylogenetic association, and sequencing of the region in the ECOR strains permitted partial reconstruction of its evolutionary history. In S. entica, the normal length of aceK was 1752 bp, but three other length variants, ranging from 1746 to 1785 bp, were represented in five of the 16 strains examined. The flanking intergenic regions showed relatively minor variation in length and sequence. The occurrence of several nonrandom patterns of distribution of polymorphic synonymous nucleotide sites indicated that intragenic recombination of horizontally exchanged DNA has contributed to the generation of allelic diversity at the aceK locus in both species.
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94. |
( 1998 ) Salmonella virulence plasmid. Modular acquisition of the spv virulence region by an F-plasmid in Salmonella enterica subspecies I and insertion into the chromosome of subspecies II, IIIa, IV and VII isolates. PMID : 9649513 : PMC : PMC1460215 Abstract >>
The spv operon is common to all Salmonella virulence plasmids. DNA hybridization analysis indicates that the spv region is limited in distribution to serovars of Salmonella enterica subspecies I, II, IIIa, IV, and VII and is absent from Salmonella bongori isolates. Among strains of subspecies II, IIIa, and VII, all isolates examined contained sequences that hybridized with the spv region. However, among isolates of subspecies I, DNA sequences capable of hybridizing with the spv region were found in some isolates of certain serovars. Furthermore, in isolates of subspecies I, the virulence plasmid was found in the same set of isolates as an F-related plasmid, as determined by the presence of the spv region of the virulence plasmid and the finO, traD, and repA sequences of the F-plasmid. The concordance of the virulence plasmid and all three F-plasmid sequences in subspecies I serovar Choleraesuis, Paratyphi, and Typhimurium is most easily explained if the spv region is carried in an F-related plasmid in these isolates. In contrast, among S. enterica subspecies II, IIIa, IV, and VII, the isolates that contain spv sequences did not hybridize with an F-related plasmid or any other identifiable plasmid. With the use of pulse-field gel electrophoresis, the spv region in subspecies II, IIIa, and VII was found to be encoded on the chromosome. Analysis of the phylogenetic distribution of spv among Salmonella isolates and comparative nucleotide sequence analysis of spvA and spvC suggests that the spv region was acquired very recently, after speciation of the salmonellae.
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95. |
( 1998 ) Tetracycline resistance in Salmonella enterica subsp. enterica serovar Dublin. PMID : 9593170 : PMC : PMC105809 Abstract >>
The 47-kbp plasmid pGFT1 from Salmonella enterica subsp. enterica serovar Dublin mediated tetracycline resistance via a tet(A) gene located on an integrated copy of a Tn1721-analogous transposon. The integration site of the transposon was located within the reading frame of a fip gene. Plasmid pGFT1 was shown to be conjugative and to be able to replicate and express tetracycline resistance in Escherichia coli.
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96. |
( 1998 ) IroN, a novel outer membrane siderophore receptor characteristic of Salmonella enterica. PMID : 9515912 : PMC : PMC107043 Abstract >>
Speciation in enterobacteria involved horizontal gene transfer. Therefore, analysis of genes acquired by horizontal transfer that are present in one species but not its close relatives is expected to give insights into how new bacterial species were formed. In this study we characterize iroN, a gene located downstream of the iroBC operon in the iroA locus of Salmonella enterica serotype Typhi. Like iroBC, the iroN gene is present in all phylogenetic lineages of S. enterica but is absent from closely related species such as Salmonella bongori or Escherichia coli. Comparison of the deduced amino acid sequence of iroN with other proteins suggested that this gene encodes an outer membrane siderophore receptor protein. Mutational analysis in S. enterica and expression in E. coli identified a 78-kDa outer membrane protein as the iroN gene product. When introduced into an E. coli fepA cir fiu aroB mutant on a cosmid, iroN mediated utilization of structurally related catecholate siderophores, including N-(2,3-dihydroxybenzoyl)-L-serine, myxochelin A, benzaldehyde-2,3-dihydroxybenzhydrazone, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine amide, and enterochelin. These results suggest that the iroA locus functions in iron acquisition in S. enterica.
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