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1. Escobar-Páramo  P, Giudicelli  C, Parsot  C, Denamur  E,     ( 2003 )

The evolutionary history of Shigella and enteroinvasive Escherichia coli revised.

Journal of molecular evolution 57 (2)
PMID : 14562958  :   DOI  :   10.1007/s00239-003-2460-3    
Abstract >>
In Shigella and enteroinvasive Escherichia coli (EIEC), the etiologic agents of shigellosis in humans, the determinants responsible for entry of bacteria into and dissemination within epithelial cells are encoded by a virulence plasmid. To understand the evolution of the association between the virulence plasmid and the chromosome, we performed a phylogenetic analysis using the sequences of four chromosomal genes (trpA, trpB, pabB, and putP) and three virulence plasmid genes (ipaB, ipaD, and icsA) of a collection of 51 Shigella and EIEC strains. The phylogenetic tree derived from chromosomal genes showed a typical "star" phylogeny, indicating a fast diversification of Shigella and EIEC groups. Phylogenetic groups obtained from the chromosomal and plasmidic genes were similar, suggesting that the virulence plasmid and the chromosome share similar evolutionary histories. The few incongruences between the trees could be attributed to exchanges of fragments of different plasmids and not to the transfer of an entire plasmid. This indicates that the virulence plasmid was not transferred between the different Shigella and EIEC groups. These data support a model of evolution in which the acquisition of the virulence plasmid in an ancestral E. coli strain preceded the diversification by radiation of all Shigella and EIEC groups, which led to highly diversified but highly specialized pathogenic groups.
KeywordMeSH Terms
Evolution, Molecular
Phylogeny
2. DeLappe  N, O'Halloran  F, Fanning  S, Corbett-Feeney  G, Cheasty  T, Cormican  M,     ( 2003 )

Antimicrobial resistance and genetic diversity of Shigella sonnei isolates from western Ireland, an area of low incidence of infection.

Journal of clinical microbiology 41 (5)
PMID : 12734227  :   DOI  :   10.1128/jcm.41.5.1919-1924.2003     PMC  :   PMC154704    
Abstract >>
Shigella sonnei is a significant cause of gastroenteritis in both developing and industrialized countries. Definition of the diversity and antimicrobial susceptibility of S. sonnei isolates may be helpful in the management of individual cases and outbreaks. Antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE) were performed with 67 isolates of S. sonnei predominantly (n = 59) from three counties in the west of Ireland. Phage typing (n = 17), plasmid profiling (n = 28), and integron analysis (n = 24) were performed with subsets of strains. PFGE typing permitted recognition of two major clusters: PFGE type A (n = 53) and PFGE type B (n = 14). PFGE type A was associated with resistance to ampicillin, streptomycin, and sulfonamides (51 of 53 isolates), and those that were phage typed (n = 6) were phage type 3. PFGE type B was associated with resistance to streptomycin, sulfonamides, tetracycline, and trimethoprim (11 of 14 isolates) and phage type 6 (9 of 11 isolates). Fifteen different plasmid profiles were identified among the 28 isolates analyzed. A class 2 integron was present in all 14 PFGE type B isolates. One of these isolates also contained a class 1 integron and showed a unique variant of the PFGE type B pattern. Sequence analysis of the gene cassette structures contained within these integrons identified distinct open reading frames that encoded determinants of resistance to trimethoprim, streptomycin, and streptothricin. Our data demonstrate two predominant PFGE types among S. sonnei isolates circulating in this region. The limited diversity of the S. sonnei isolates in this region means that detection of isolates indistinguishable by PFGE and according to their antibiograms in two or more patients is not persuasive evidence of a common-source food- or waterborne outbreak. Indistinguishable plasmid profiles in addition to indistinguishable PFGE and antibiogram types may be more suggestive of an epidemiologically relevant link between cases.
KeywordMeSH Terms
3. Hartman  AB, Essiet  II, Isenbarger  DW, Lindler  LE,     ( 2003 )

Epidemiology of tetracycline resistance determinants in Shigella spp. and enteroinvasive Escherichia coli: characterization and dissemination of tet(A)-1.

Journal of clinical microbiology 41 (3)
PMID : 12624025  :   DOI  :   10.1128/jcm.41.3.1023-1032.2003     PMC  :   PMC150258    
Abstract >>
To make a comprehensive study of tetracycline resistance determinant distribution in the genus Shigella, a collection of 577 clinical isolates of Shigella spp. and enteroinvasive Escherichia coli (EIEC) from a variety of geographical locations was screened to identify tetracycline-resistant strains. The 459 tetracycline-resistant isolates identified were then screened by PCR analysis to determine the distribution in these strains of tetracycline efflux resistance determinants belonging to classes A to E, G, and H that have been identified in gram-negative bacteria. Only classes A to D were represented in these strains. Although Tet B was the predominant determinant in all geographical locations, there were geographical and species differences in the distribution of resistance determinants. An allele of tet(A), designated tet(A)-1, was identified and sequenced, and the 8.6-kb plasmid containing determinant Tet A-1, designated pSSTA-1, was found to have homologies to portions of a Salmonella enterica cryptic plasmid and the broad-host-range resistance plasmid RSF1010. This allele and pSSTA-1 were used as epidemiological markers to monitor clonal and horizontal transmission of determinant Tet A-1. An analysis of serotype, distribution of tetracycline resistance determinants, and resistance profiles indicated that both clonal spread and horizontal transfer had contributed to the spread of specific tetracycline resistance determinants in these populations and demonstrated the use of these parameters as an epidemiological tool to follow the transmission of determinants and strains.
KeywordMeSH Terms
4. Xu  DQ, Cisar  JO, Ambulos  N, Burr  DH, Kopecko  DJ,     ( 2002 )

Molecular cloning and characterization of genes for Shigella sonnei form I O polysaccharide: proposed biosynthetic pathway and stable expression in a live salmonella vaccine vector.

Infection and immunity 70 (8)
PMID : 12117952  :   DOI  :   10.1128/iai.70.8.4414-4423.2002     PMC  :   PMC128211    
Abstract >>
The gene region for biosynthesis of Shigella sonnei form I O polysaccharide (O-Ps) and flanking sequences, totaling >18 kb, was characterized by deletion analysis to define a minimal construct for development of Salmonella-based live vaccine vector strains. Lipopolysaccharide (LPS) expression and DNA sequence studies of plasmid deletion derivatives indicated form I O-Ps expression from a 12.3-kb region containing a putative promoter and 10 contiguous open reading frames (ORFs), one of which is the transposase of IS630. A detailed biosynthetic pathway, consistent with the predicted functions of eight of the nine essential ORFs and the form I O-Ps structure, is proposed. Further sequencing identified partial IS elements (i.e., IS91 and IS630) and wzz upstream of the form I coding region and a fragment of aqpZ and additional full or partial IS elements (i.e., IS629, IS91, and IS911) downstream of this region. The stability of plasmid-based form I O-Ps expression was greater from low-copy vectors than from high-copy vectors and was enhanced by deletion of the downstream IS91 from plasmid inserts. Both core-linked (i.e., LPS) and non-core-linked (i.e., capsule-like) surface expression of form I O-Ps were detected by Western blotting and silver staining of polyacrylamide gel electrophoresis-separated Shigella and Escherichia coli extracts. However, salmonellae, which have a core that is chemically dissimilar to that of shigellae, expressed only non-core-linked surface-associated form I O-Ps. Finally, attenuated Salmonella enterica serovar Typhi live vaccine vector candidates, containing minimal-sized form I operon constructs, elicited immune protection in mice against virulent S. sonnei challenge, thereby supporting the promise of live, oral vaccines for the prevention of shigellosis.
KeywordMeSH Terms
5. Fukushima  M, Kakinuma  K, Kawaguchi  R,     ( 2002 )

Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence.

Journal of clinical microbiology 40 (8)
PMID : 12149329  :   DOI  :   10.1128/jcm.40.8.2779-2785.2002     PMC  :   PMC120687    
Abstract >>
Phylogenetic analysis of about 200 strains of Salmonella, Shigella, and Escherichia coli was carried out using the nucleotide sequence of the gene for DNA gyrase B (gyrB), which was determined by directly sequencing PCR fragments. The results establish a new phylogenetic tree for the classification of Salmonella, Shigella, and Escherichia coli in which Salmonella forms a cluster separate from but closely related to Shigella and E. coli. In comparison with 16S rRNA analysis, the gyrB sequences indicated a greater evolutionary divergence for the bacteria. Thus, in screening for the presence of bacteria, the gyrB gene might be a useful tool for differentiating between closely related species of bacteria such as Shigella spp. and E. coli. At present, 16S rRNA sequence analysis is an accurate and rapid method for identifying most unknown bacteria to the genus level because the highly conserved 16S rRNA region is easy to amplify; however, analysis of the more variable gyrB sequence region can identify unknown bacteria to the species level. In summary, we have shown that gyrB sequence analysis is a useful alternative to 16S rRNA analysis for constructing the phylogenetic relationships of bacteria, in particular for the classification of closely related bacterial species.
KeywordMeSH Terms
Phylogeny
6. Wong  RS, Chow  AW,     ( 2002 )

Identification of enteric pathogens by heat shock protein 60 kDa (HSP60) gene sequences.

FEMS microbiology letters 206 (1)
PMID : 11786265  :   DOI  :   10.1111/j.1574-6968.2002.tb10994.x    
Abstract >>
A highly specific and reproducible approach for the simultaneous detection of enteric pathogenic bacteria was developed using bacterial hsp60 gene and molecular biological tools. A single pair of universal primers was derived from the highly conserved sequence of hsp60 genes encompassing a 600-bp hypervariable region. PCR amplification followed by either dot blot hybridization or restriction enzyme digestion performed on 38 enteric bacteria indicated that this approach could differentiate not only different genera such as Campylobacter, Yersinia and Vibrio, but also species that are closely related genetically, such as between C. jejuni and C. coli, or between Salmonella and Shigella or Escherichia coli.
KeywordMeSH Terms
Amino Acid Sequence
7. Yokoigawa  K, Hirasawa  R, Ueno  H, Okubo  Y, Umesako  S, Soda  K,     ( 2001 )

Gene cloning and characterization of alanine racemases from Shigella dysenteriae, Shigella boydii, Shigella flexneri, and Shigella sonnei.

Biochemical and biophysical research communications 288 (3)
PMID : 11676496  :   DOI  :   10.1006/bbrc.2001.5817    
Abstract >>
Alanine racemase genes (alr) from Shigella dysenteriae, Shigella boydii, Shigella flexneri, and Shigella sonnei were cloned and expressed in Escherichia coli JM109. All genes encoded a polypeptide of 359 amino acids, and showed more than 99% sequence identities with each other. In particular, the S. dysenteriae alr was identical with the S. flexneri alr. Differences in the amino acid sequences between the four Shigella enzymes were only two residues: Gly138 in S. dysenteriae and S. flexneri (Glu138 in the other) and Ile225 in S. sonnei (Thr225 in the other). The S. boydii enzyme was identical with the E. coli K12 alr enzyme. Each Shigella alr enzyme purified to homogeneity has an apparent molecular mass about 43,000 by SDS-gel electrophoresis, and about 46,000 by gel filtration. However, all enzymes showed an apparent molecular mass about 60,000 by gel filtration in the presence of a substrate, 0.1 M l-alanine. These results suggest that the Shigella alr enzymes having an ordinary monomeric structure interact with other monomer in the presence of the substrate. The enzymes were almost identical in the enzymological properties, and showed lower catalytic activities (about 210 units/mg) than those of homodimeric alanine racemases reported.
KeywordMeSH Terms
8. Smajs  D, Weinstock  GM,     ( 2001 )

Genetic organization of plasmid ColJs, encoding colicin Js activity, immunity, and release genes.

Journal of bacteriology 183 (13)
PMID : 11395458  :   DOI  :   10.1128/JB.183.13.3949-3957.2001     PMC  :   PMC95277    
Abstract >>
The 5.2-kb ColJs plasmid of a colicinogenic strain of Shigella sonnei (colicin type 7) was isolated and sequenced. pColJs was partly homologous to pColE1 and to pesticin-encoding plasmid pPCP1, mainly in the rep, mob, and cer regions. A 1.2-kb unique region of pColJs showed significantly different G+C content (34%) compared to the rest of pColJs (53%). Within the unique region, seven open reading frames (ORFs) were identified. ORF94 was shown to code for colicin Js activity (cja), a 94-amino-acid polypeptide (molecular mass, 10.4 kDa); ORF129 (cji) was shown to code for the 129-amino-acid colicin Js immunity protein (molecular mass, 14.3 kDa); and ORF65 was shown to be involved in colicin Js release by producer bacteria (cjl) coding for a 65-amino-acid polypeptide (molecular mass, 7.5 kDa). In contrast to the gene order in other colicin operons, the cjl gene was found upstream from cja. Moreover, the promoter upstream from cjl was similar to promoters described upstream from several colicin activity genes. The cji gene was found to be located downstream from cja with a transcription polarity opposite to that of the cjl and cja genes. The cja, cji, and cjl genes were not similar to other known colicin genes. Colicin Js was purified as an inactive fusion protein with an N-terminal histidine tag. Activity of the purified fusion form of colicin Js was restored after cleavage of the amino acids fused to the colicin Js N terminus.
KeywordMeSH Terms
9. Kharat  AS,     ( 2000 )

Analysis of the beta-glucoside utilization (bgl) genes of Shigella sonnei: evolutionary implications for their maintenance in a cryptic state.

Microbiology (Reading, England) 146 (Pt 8) (N/A)
PMID : 10931908  :   DOI  :   10.1099/00221287-146-8-2039    
Abstract >>
The pattern of expression of the genes involved in the utilization of aryl beta-glucosides such as arbutin and salicin is different in the genus Shigella compared to Escherichia coli. The results presented here indicate that the homologue of the cryptic bgl operon of E. coli is conserved in Shigella sonnei and is the primary system involved in beta-glucoside utilization in the organism. The organization of the bgl genes in S. sonnei is similar to that of E. coli; however there are three major differences in terms of their pattern of expression. (i) The bglB gene, encoding phospho-beta-glucosidase B, is insertionally inactivated in S. sonnei. As a result, mutational activation of the silent bgl promoter confers an Arbutin-positive (Arb(+)) phenotype to the cells in a single step; however, acquiring a Salicin-positive (Sal(+)) phenotype requires the reversion or suppression of the bglB mutation in addition. (ii) Unlike in E. coli, a majority of the activating mutations (conferring the Arb(+) phenotype) map within the unlinked hns locus, whereas activation of the E. coli bgl operon under the same conditions is predominantly due to insertions within the bglR locus. (iii) Although the bgl promoter is silent in the wild-type strain of S. sonnei (as in the case of E. coli), transcriptional and functional analyses indicated a higher basal level of transcription of the downstream genes. This was correlated with a 1 bp deletion within the putative Rho-independent terminator present in the leader sequence preceding the homologue of the bglG gene. The possible evolutionary implications of these differences for the maintenance of the genes in the cryptic state are discussed.
KeywordMeSH Terms
Genes, Bacterial
10. Shepherd  JG, Wang  L, Reeves  PR,     ( 2000 )

Comparison of O-antigen gene clusters of Escherichia coli (Shigella) sonnei and Plesiomonas shigelloides O17: sonnei gained its current plasmid-borne O-antigen genes from P. shigelloides in a recent event.

Infection and immunity 68 (10)
PMID : 10992522  :   DOI  :   10.1128/iai.68.10.6056-6061.2000     PMC  :   PMC101574    
Abstract >>
Escherichia coli Sonnei has an O antigen identical to that of Plesiomonas shigelloides O17, and its O-antigen gene cluster is located on a plasmid. By sequencing the chromosomal O-antigen gene cluster of P. shigelloides O17 and comparing it with that of Sonnei, we showed that Sonnei gained its O-antigen genes recently.
KeywordMeSH Terms
Genes, Bacterial
11. Xiong  Z, Li  T, Xu  Y, Li  J,     ( 2007 )

Detection of CTX-M-14 extended-spectrum beta-lactamase in Shigella sonnei isolates from China.

The Journal of infection 55 (5)
PMID : 17767959  :   DOI  :   10.1016/j.jinf.2007.07.017    
Abstract >>
Shigellosis is an important cause of acute diarrheal disease and multidrug-resistant phenotype has been reported in S. sonnei. In this study, we investigate the resistance and identify extended-spectrum beta-lactamases (ESBLs) gene in 37 S. sonnei isolates by agar dilution procedure and the modified three-dimensional test, respectively. The bla genes of ESBL-producing isolates were detected by polymerase chain reaction (PCR) and sequencing. More than 50% of these strains were resistant to tetracycline, sulfamethoxazole-trimethoprim, ampicillin, ampicillin-sulbactam, or gentamicin. However, they were still susceptible to third generation cephalosporins, fluoroquinolones, and chloramphenicol. A total of 8.1% (3/37) of the isolates with intermediate susceptibility to ceftriaxone and cefotaxime were ESBL-producers, which produced CTX-M-14 ESBLs and TEM-1 beta-lactamases. This is the first report of CTX-M-14 in S. sonnei isolates from China and it is important to closely monitor such strains.
KeywordMeSH Terms
12. Hu  LF, Li  JB, Ye  Y, Li  X,     ( 2007 )

Mutations in the GyrA subunit of DNA gyrase and the ParC subunit of topoisomerase IV in clinical strains of fluoroquinolone-resistant Shigella in Anhui, China.

Journal of microbiology (Seoul, Korea) 45 (2)
PMID : 17483803  :  
Abstract >>
In this research 26 Shigella isolates were examined by PCR and direct nucleotide sequencing for genetic alterations in the quinolone-resistance determining regions (QRDRs). We tested for the presence of qnr genes by PCR in 91 strains, but no qnr genes were found. The results did show, however, some novel mutations at codon 83 of gyrA (Ser-->Ile) and codon 64 of parC (Ala64-->Cys, Ala64-->Asp), which were related to fluroquinolone resistance.
KeywordMeSH Terms
Mutation
13. Pham  HN, Ohkusu  K, Mishima  N, Noda  M, Monir Shah  M, Sun  X, Hayashi  M, Ezaki  T,     ( 2007 )

Phylogeny and species identification of the family Enterobacteriaceae based on dnaJ sequences.

Diagnostic microbiology and infectious disease 58 (2)
PMID : 17368802  :   DOI  :   10.1016/j.diagmicrobio.2006.12.019    
Abstract >>
Phylogenetic relations within the family Enterobacteriaceae were analyzed using partial dnaJ sequences of 165 strains belonging to 93 species from 27 enterobacterial genera. The dnaJ phylogeny was in relative agreement with that constructed by 16S rDNA sequences, but more monophyletic groups were obtained from the dnaJ tree than from the 16S rDNA tree. The degree of divergence of the dnaJ gene was approximately 6 times greater than that of 16S rDNA. Also, the dnaJ gene showed the most discriminatory power in comparison with tuf and atpD genes, facilitating clear differentiation of any 2 enterobacterial species by dnaJ sequence analysis. The application of dnaJ sequences to the identification was confirmed by assigning 72 clinical isolates to the correct enterobacterial species. Our data indicate that analysis of the dnaJ gene sequences can be used as a powerful marker for phylogenetic study and identification at the species level of the family Enterobacteriaceae.
KeywordMeSH Terms
HSP40 Heat-Shock Proteins
Phylogeny
14. Dubois  V, Parizano  MP, Arpin  C, Coulange  L, Bezian  MC, Quentin  C,     ( 2007 )

High genetic stability of integrons in clinical isolates of Shigella spp. of worldwide origin.

Antimicrobial agents and chemotherapy 51 (4)
PMID : 17242143  :   DOI  :   10.1128/AAC.01109-06     PMC  :   PMC1855518    
Abstract >>
Over a 12-year period, 68 Shigella strains (31 S. sonnei, 30 S. flexneri, 4 S. dysenteriae, and 3 S. boydii strains) were collected in a French University Hospital from the stools of patients who generally had a recent history of travel to various parts of the world (91%), particularly Africa (67%). These strains were often resistant (streptomycin, spectinomycin, trimethoprim, tetracycline, and sulfonamides, 66 to 84%; ampicillin and chloramphenicol, 34 to 38%; nalidixic acid, 4%) and even multiresistant (87%), and they generally carried integrons (81%) of class 1 (21%), class 2 (47%), or both (13%). Class 1 integrons were associated with ampicillin resistance due to the production of an OXA-30 beta-lactamase in S. flexneri and S. dysenteriae. Class 2 integrons were associated with trimethoprim resistance in S. sonnei. Class 1 and class 2 integrons were inserted within transposons Tn21 and Tn7, respectively, themselves located on the bacterial chromosome, except in one strain. Class 1 integrons showed an atypical organization consisting of the insertion sequence IS1 at the 3' end instead of the typical 3' conserved segment and two blaOXA-30 and aadA1 gene cassettes, despite the absence of epidemiological relationships between the strains, and an apparently functional integrase. Class 2 integrons showed the same albeit classical organization with the three dfrA1, sat, and aadA1 gene cassettes. Occasionally, the 3' end was deleted and the aadA1 gene cassette was unexpressed. Thus, integrons contributed only in part to the multidrug resistance of the Shigella strains. The highly conserved organization of integrons might be related to their location within mobile genetic superstructures.
KeywordMeSH Terms
15. 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.

Analytical biochemistry 360 (2)
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.
KeywordMeSH Terms
16. Ahmed  AM, Furuta  K, Shimomura  K, Kasama  Y, Shimamoto  T,     ( 2006 )

Genetic characterization of multidrug resistance in Shigella spp. from Japan.

Journal of medical microbiology 55 (Pt 12)
PMID : 17108272  :   DOI  :   10.1099/jmm.0.46725-0    
Abstract >>
This study characterized the genetic basis of antimicrobial resistance of a number of Shigella spp. isolated from humans from 2000 to 2004 in Hiroshima prefecture, Japan. A total of 26 isolates of Shigella spp. were included in this study. Antimicrobial susceptibility tests revealed high levels of resistance, especially to ampicillin, streptomycin, trimethoprim, tetracycline, nalidixic acid and ciprofloxacin. PCR and DNA sequencing were used for screening and characterization of antibiotic-resistance determinants. PCR sequencing analysis revealed the presence of only one type of class 1 integron in one isolate of Shigella sonnei. This class 1 integron was 1904 bp and contained two gene cassettes: a probable esterase/lipase (estX) and aadA1, which confers resistance to streptomycin and spectinomycin. Two types of class 2 integron were identified in this study. One was the classic type (2158 bp) and carried the three conserved resistance gene cassettes of the class 2 integron, dfrA1, sat1 and aadA1, which confer resistance to trimethoprim, streptothricin and streptomycin/spectinomycin, respectively. This type was detected in both Shigella sonnei (14 isolates) and Shigella flexneri (five isolates). The other type was shorter (1313 bp) and carried only two gene cassettes, dfrA1 and sat1. This integron was detected in a single isolate of Shigella sonnei. PFGE patterns showed limited diversity within clusters of the same species. Furthermore, an extended-spectrum beta-lactamase gene, bla(OXA-30), which confers resistance to ampicillin, was characterized in all isolates of Shigella flexneri except the oldest strain, which was isolated in 2000. Southern blot hybridization and conjugation experiments showed that bla(OXA-30) was located in the chromosome.
KeywordMeSH Terms
17. Pan  JC, Ye  R, Meng  DM, Zhang  W, Wang  HQ, Liu  KZ,     ( 2006 )

Molecular characteristics of class 1 and class 2 integrons and their relationships to antibiotic resistance in clinical isolates of Shigella sonnei and Shigella flexneri.

The Journal of antimicrobial chemotherapy 58 (2)
PMID : 16766536  :   DOI  :   10.1093/jac/dkl228    
Abstract >>
To analyse the gene cassettes and determine the roles of class 1 and class 2 integrons in antibiotic-resistant strains of Shigella sonnei (n=31) and Shigella flexneri (n=33). Various molecular techniques, including PCR and Southern-blotting analysis, were used to analyse various markers of class 1 and class 2 integrons in these 64 S. sonnei and S. flexneri isolates collected in Hangzhou, China. The gene cassette arrays in integrons were identified by DNA sequencing and/or restriction fragment length polymorphism. Two genomic DNA fragments, one containing intI1 from a S. flexneri isolate that contains intI1 but lacks 3'-conserved region and another containing intI2 from a S. sonnei isolate, were cloned into pUC19 vectors and sequenced. The links between integron gene cassette arrays and antibiotic resistance were analysed. Class 2 integrons were present in 80.6% (25/31) of the S. sonnei isolates and 87.9% (29/33) of the S. flexneri isolates. All of these integron 2-positive isolates contained constant gene cassette arrays of dfrA1+sat1+aadA1 which confer resistance to trimethoprim and streptomycin. It was demonstrated that the class 2 integron was located in the Tn7 region inside the attTn7 locus downstream of glmS in Shigella. Class 1 integrons were found in 9.4% (6/64) of Shigella spp. isolates. An atypical class 1 integron without a 3'-conserved segment on the Shigella chromosome, termed Shigella atypical class 1 integron (SAI), was present in 84.9% (28/33) of S. flexneri isolates. The SAI contained two gene cassettes, bla(OXA30) and aadA1; however, the SAI conferred resistance to ampicillin, but not to streptomycin, in Escherichia coli host. The bla(OXA30) and aadA1 cassettes of the SAI seemed to be always coordinately excised or integrated. Multiple and complex mechanisms involving mobile genetic elements in class 1 and class 2 integrons and antibiotic resistance have been developed in the evolution of Shigella strains.
KeywordMeSH Terms
18. Miura  M, Terajima  J, Izumiya  H, Mitobe  J, Komano  T, Watanabe  H,     ( 2006 )

OspE2 of Shigella sonnei is required for the maintenance of cell architecture of bacterium-infected cells.

Infection and immunity 74 (5)
PMID : 16622194  :   DOI  :   10.1128/IAI.74.5.2587-2595.2006     PMC  :   PMC1459745    
Abstract >>
The OspE2 product of Shigella spp., the expression of which is regulated by the mxiE gene, is secreted through a type III secretion system into host cells. We investigated the function of OspE2 of Shigella sonnei by using cultured epithelial cells. Cells invaded by an ospE2 deletion mutant altered their morphology into the rounding shape, which was not due to cell death, whereas cells invaded by the wild-type strain kept their cell shape intact. The ospE2 mutation did not affect initial cell entry and multiplication in cells, but the mutant formed smaller-than-normal plaques on cell monolayers, indicating a deficiency in cell-to-cell spread by the bacteria. An mxiE deletion mutant also showed changes in cell morphology and deficiency in bacterial spread to adjacent cells. In cells invaded by the ospE2 mutant, disturbance of actin stress fibers was prominent at 3 h after invasion. Analysis of OspE2 localization indicated that the OspE2 protein accumulated on focal contact-like structures in the infected host cells. These results suggest that colocalization of the OspE2 protein in the focal contacts of infected cells may function to maintain an intact cell morphology. The morphological change induced by invasion of the ospE2 mutant may affect secondary bacterial transmission.
KeywordMeSH Terms
19. Watanabe  H, Arakawa  E, Ito  K, Kato  J, Nakamura  A,     ( 1990 )

Genetic analysis of an invasion region by use of a Tn3-lac transposon and identification of a second positive regulator gene, invE, for cell invasion of Shigella sonnei: significant homology of invE with ParB of plasmid P1.

Journal of bacteriology 172 (2)
PMID : 1688841  :   DOI  :   10.1128/jb.172.2.619-629.1990     PMC  :   PMC208485    
Abstract >>
We have previously cloned two distinct regions of the Shigella sonnei form I plasmid pSS120, a 37-kilobase-pair DNA region and a virF region, which were found to be essential for cell invasion in Escherichia coli K-12 (J. Kato, K. Ito, A. Nakamura, and H. Watanabe, Infect. Immun. 57:1391-1398, 1989). The 37-kilobase-pair DNA region was randomly inserted by use of transposon Tn3-lac. At least eight genes were found to be located within the region, as determined by analysis of Tn3-lac-generated lac fusions. Expression of six genes, ipaB, ipaC, invE, invG, invJ, and invK, was apparently regulated by the positive regulator virF. IpaB and IpaC proteins could not found in invE mutants even if the virF gene was present. This observation suggested that the invE region encoded a positive regulator different from the virF gene. The functional relationship between the invE and virF genes was then examined. Translational fusions ipaB::Tn3-lac and invJ::Tn3-lac were used as indicators for gene expression, and the following results were obtained. Full expression of the ipaB and invJ genes required the presence of both the invE and virF regions. virF positively regulated the expression of invE at the transcriptional level. An increase in the copy number of invE enhanced the expression of ipaB and invJ in the absence of virF. These findings strongly indicate that the invE gene product, whose expression is regulated by virF, acts positively on the invasion-associated genes. InvE is a 35,407-dalton protein and has significant homologies with ParB of plasmid P1 and SopB of plasmid F, which are DNA-binding proteins involved in plasmid partitioning.
KeywordMeSH Terms
DNA Transposable Elements
Genes, Bacterial
Genes, Regulator
20. Delmas  J, Breysse  F, Devulder  G, Flandrois  JP, Chomarat  M,     ( 2006 )

Rapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene.

Diagnostic microbiology and infectious disease 55 (4)
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.
KeywordMeSH Terms
21. Hama  C, Takizawa  T, Moriwaki  H, Urasaki  Y, Mizobuchi  K,     ( 1990 )

Organization of the replication control region of plasmid ColIb-P9.

Journal of bacteriology 172 (4)
PMID : 1690704  :   DOI  :   10.1128/jb.172.4.1983-1991.1990     PMC  :   PMC208695    
Abstract >>
We identified a 1,845-base-pair sequence that contains essential information for the autonomous replication and regulation of the 93-kilobase-pair IncI alpha group ColIb-P9 plasmid. Biochemical and genetic analyses revealed that this sequence specifies at least two structural genes, designated repZ and inc. The repZ gene encodes a protein with a molecular weight of 39,000, which probably functions as an initiator for the ColIb-P9 replicon. The inc gene that phenotypically governs the incompatibility encodes an RNA with a size of about 70 bases. This small RNA acts in trans to repress the expression of repZ, thereby functioning to maintain a constant copy number of the ColIb-P9 replicon in host cells.
KeywordMeSH Terms
DNA Replication
Plasmids
22. Andrews  GP, Maurelli  AT,     ( 1992 )

mxiA of Shigella flexneri 2a, which facilitates export of invasion plasmid antigens, encodes a homolog of the low-calcium-response protein, LcrD, of Yersinia pestis.

Infection and immunity 60 (8)
PMID : 1639496  :   PMC  :   PMC257313    
Abstract >>
The plasmid-encoded invasion plasmid antigen (Ipa) export accessory locus of Shigella flexneri 2a, mxiA, was cloned, and the complete DNA sequence of the gene was determined. The mixA open reading frame was found to encode a polypeptide of 74.03 kDa with a pI of 5.02. A hydropathy analysis of the predicted protein revealed a hydrophilic C terminus and an extremely hydrophobic N terminus without a cleavable signal sequence but with several potential membrane-spanning regions. While a homology search did not reveal any significant relatedness of the mxiA DNA sequence to any known bacterial gene sequences, the derived amino acid sequence of MxiA was found to be highly homologous (68%) to the sequence of the protein encoded by the low-calcium-response locus, lcrD, of Yersinia pestis. The lcrD encodes an inner membrane regulatory protein that has an N-terminal membrane anchor and that is implicated in facilitating the export of Y. pestis outer membrane proteins (G. V. Plano, S. S. Barve, and S. C. Straley, J. Bacteriol. 173:7293-7303, 1991). Congo red binding, HeLa cell invasion, and Ipa excretion were restored in two avirulent mxiA fusion mutants when they were transformed with a cloned copy of the mxiA gene. Furthermore, the expression of the cloned mxiA gene was independent of any vector-specified promoter, suggesting that the transcription of mxiA is driven by its own promoter in this clone. In contrast, the overexpression of mxiA that resulted when it was placed under the control of the lac promoter was found to be deleterious in Escherichia coli. We conclude that mxiA is a homolog of the Y. pestis lcrD locus and may function similarly in S. flexneri, either by directly affecting the excretion of virulence factors or by regulating the expression of export accessory genes.
KeywordMeSH Terms
Bacterial Proteins
Genes, Bacterial
Plasmids
Sequence Homology, Nucleic Acid
23. Tominaga  A, Lan  R, Reeves  PR,     ( 2005 )

Evolutionary changes of the flhDC flagellar master operon in Shigella strains.

Journal of bacteriology 187 (12)
PMID : 15937193  :   DOI  :   10.1128/JB.187.12.4295-4302.2005     PMC  :   PMC1151726    
Abstract >>
Shigella strains are nonmotile. The master operon of flagellar synthesis, flhDC, was analyzed for genetic damage in 46 Shigella strains representing all known serotypes. In 11 strains (B1, B3, B6, B8, B10, B18, D5, F1B, D10, F3A, and F3C) the flhDC operon was completely deleted. PCR and sequence analysis of the flhDC region of the remaining 35 strains revealed many insertions or deletions associated with insertion sequences, and the majority of the strains were found to be defective in their flhDC genes. As these genes also play a role in regulation of non-flagellar genes, the loss may have other consequences or be driven by selection pressures other than those against flagellar motility. It has been suggested that Shigella strains fall mostly into three clusters within Escherichia coli, with five outlier strains, four of which are also within E. coli (G. M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567-10572, 2000). The distribution of genetic changes in the flhDC region correlated very well with the three clusters and outlier strains found using housekeeping gene DNA sequences, enabling us to follow the sequence of mutational change in the flhDC locus. Two cluster 2 strains were found to have unique flhDC sequences, which are most probably due to recombination during the exchange of the adjacent O-antigen gene clusters.
KeywordMeSH Terms
24. Li  B, Brown  EW, D'Agostino  C, Leclerc  JE, Cebula  TA,     ( 2005 )

Structure and distribution of the phosphoprotein phosphatase genes, prpA and prpB, among Shigella subgroups.

Microbiology (Reading, England) 151 (Pt 8)
PMID : 16079345  :   DOI  :   10.1099/mic.0.27990-0    
Abstract >>
Phosphoprotein phosphatases encoded by the prpA and prpB genes function in signal transduction pathways for degradation of misfolded proteins in the extracytoplasmic compartments of Escherichia coli. In order to trace the evolution of prp genes and assess their roles in other enteric pathogens, the structure and distribution of these genes among closely related Shigella subgroups were studied. PCR amplification, probe hybridization studies and DNA sequencing were used to determine the prp genotypes of 58 strains from the four Shigella subgroups, Dysenteriae, Boydii, Sonnei and Flexneri. It was found that the prp alleles among Shigella subgroups were extremely susceptible to gene inactivation and that the mutations involved in prp allele inactivation were varied. They included IS insertions, gene replacement by an IS element, a small deletion within the gene or large deletion engulfing the entire gene region, and base substitutions that generated premature termination codons. As a result, of 58 strains studied, only eight (14 %) possessed intact prpA and prpB genes. Of the Shigella strains examined, 76 % (44/58) showed at least one of the prp alleles inactivated by one or more IS elements, including IS1, IS4, IS600 and IS629. Phylogenetic analysis revealed that IS elements have been independently acquired in multiple lineages of Shigella, suggesting that loss of functional alleles has been advantageous during Shigella strain evolution.
KeywordMeSH Terms
Signal Transduction
25. Mitobe  J, Arakawa  E, Watanabe  H,     ( 2005 )

A sensor of the two-component system CpxA affects expression of the type III secretion system through posttranscriptional processing of InvE.

Journal of bacteriology 187 (1)
PMID : 15601694  :   DOI  :   10.1128/JB.187.1.107-113.2005     PMC  :   PMC538841    
Abstract >>
The chief function of the Cpx two-component system is perceiving various cell envelope stresses, but CpxR is also known to regulate the expression of the type III secretion system (TTSS) of Shigella sonnei through transcription of the primary regulator virF. Here, we have isolated novel cpxA mutants that exhibited decreased TTSS expression from Escherichia coli HW1273, which carries the virulence plasmid of S. sonnei. The cpxA deletion strain of HW1273 expressed beta-galactosidase activity levels from the virF-lacZ fusion similar to those of HW1273. However, the second regulator InvE (VirB) and the TTSS component IpaB proteins were apparently expressed at a low level. In the cpxA strain, beta-galactosidase activity levels from the invE-lacZ transcriptional fusion remained similar to those of HW1273, whereas the beta-galactosidase activity level from the translational fusion of invE-lacZ was reduced to 21% of that of HW1273. Therefore, the deletion of the cpxA gene influenced TTSS expression chiefly at the posttranscriptional processing of InvE. In addition, the cpxA deletion strain of S. sonnei showed the same phenotype. These results indicate that the Cpx two-component system is involved in virulence expression through posttranscriptional processing of the regulatory protein InvE, a novel feature of the Cpx two-component system in posttranscriptional processing and virulence expression of Shigella.
KeywordMeSH Terms
26. Jones  AL, Barth  PT, Wilkins  BM,     ( 1992 )

Zygotic induction of plasmid ssb and psiB genes following conjugative transfer of Incl1 plasmid Collb-P9.

Molecular microbiology 6 (5)
PMID : 1552860  :   DOI  :   10.1111/j.1365-2958.1992.tb01507.x    
Abstract >>
The Incl1 conjugative plasmid Collb-P9 carries a psiB gene that prevents induction of the SOS response in host bacteria. This locus is located 2.5 kb downstream of the ssb (single-stranded DNA-binding protein) gene in the leading region. This portion of Collb is strikingly similar to part of the leading region of the otherwise distinct F plasmid. Expression of psiB and ssb is increased when the host cell is exposed to an SOS-inducing treatment or the Collb transfer system is derepressed. Moreover, expression of both genes on a derepressed plasmid is strongly enhanced in conjugatively infected recipient cells. Carriage of the psiB gene by Collb is shown to prevent a low level of SOS induction following conjugation. Plasmid ssb and psiB genes may function to promote installation of the replicon in the new cell.
KeywordMeSH Terms
Plasmids
27. Hill  JE, Penny  SL, Crowell  KG, Goh  SH, Hemmingsen  SM,     ( 2004 )

cpnDB: a chaperonin sequence database.

Genome research 14 (8)
PMID : 15289485  :   DOI  :   10.1101/gr.2649204     PMC  :   PMC509277    
Abstract >>
Type I chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. Sequences of cpn60 genes, encoding 60-kDa chaperonin protein subunits (CPN60, also known as GroEL or HSP60), are useful for phylogenetic studies and as targets for detection and identification of organisms. Conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal PCR primers. Here, we introduce cpnDB, a curated collection of cpn60 sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic, and microbial ecology studies. The growing database currently contains approximately 2000 records covering over 240 genera of bacteria, eukaryotes, and archaea. The database also contains over 60 sequences for the archaeal Type II chaperonin (thermosome, a homolog of eukaryotic cytoplasmic chaperonin) from 19 archaeal genera. As the largest curated collection of sequences available for a protein-encoding gene, cpnDB provides a resource for researchers interested in exploiting the power of cpn60 as a diagnostic or as a target for phylogenetic or microbial ecology studies, as well as those interested in broader subjects such as lateral gene transfer and codon usage. We built cpnDB from open source tools and it is available at http://cpndb.cbr.nrc.ca.
KeywordMeSH Terms
28. Gueneau de Novoa  P, Williams  KP,     ( 2004 )

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts.

Nucleic acids research 32 (Database issue)
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.
KeywordMeSH Terms
Databases, Nucleic Acid
Evolution, Molecular
Internet
29. Yang  J, Wang  J, Chen  L, Yu  J, Dong  J, Yao  ZJ, Shen  Y, Jin  Q, Chen  R,     ( 2003 )

Identification and characterization of simple sequence repeats in the genomes of Shigella species.

Gene 322 (N/A)
PMID : 14644500  :   DOI  :   10.1016/j.gene.2003.09.017    
Abstract >>
A variety of simple sequence repeats (SSRs) have been identified in the genome of Shigella flexneri serotype 2a (strain Sf301), an enteric pathogen that causes bacillary dysentery in man. The distribution of SSRs, with unit length ranging from 1 to 9 nucleotides, was biased in different regions of the genome. The tri-, tetra- and hexanucleotide SSRs prevailed in the coding regions while the mono- and dinucleotide SSRs were more common in the noncoding regions. Many intergenic SSRs are less than 30 bp away from the downstream open reading frames (ORFs), suggesting a potential role in transcriptional regulation. To study polymorphism of SSRs, we compared 17 coding-region SSRs from strain Sf301 with the corresponding sequences from 23 other strains of four Shigella species. Five chromosomal loci were found to be polymorphic, of which those from S. flexneri strains were most variable. Particularly interesting is the C5-1 locus in the coding sequence of the hcaD gene encoding a subunit of ferredoxin reductase. Depending on the insertion of variable numbers of the unit sequence (CGCAG), the Shigella hcaD genes can encode truncated products due to premature stop codons or frame shifts, or products with extended core alpha helices that leads to radical alterations in the predicted tertiary structure. Hence, SSRs may serve as genotyping markers for epidemiological investigations, and may offer insights into evolutionary adaptation of the pathogens.
KeywordMeSH Terms
Genome, Bacterial
30. Matsutani  S, Ohtsubo  E,     ( 1990 )

Complete sequence of IS629.

Nucleic acids research 18 (7)
PMID : 2159625  :   DOI  :   10.1093/nar/18.7.1899     PMC  :   PMC330622    
Abstract >>
N/A
KeywordMeSH Terms
DNA Transposable Elements
31. Tominaga  A, Ikemizu  S, Enomoto  M,     ( 1991 )

Site-specific recombinase genes in three Shigella subgroups and nucleotide sequences of a pinB gene and an invertible B segment from Shigella boydii.

Journal of bacteriology 173 (13)
PMID : 2061288  :   DOI  :   10.1128/jb.173.13.4079-4087.1991     PMC  :   PMC208056    
Abstract >>
Inversional switching systems in procaryotes are composed of an invertible DNA segment and a site-specific recombinase gene adjacent to or contained in the segment. Four related but functionally distinct systems have previously been characterized in detail: the Salmonella typhimurium H segment-hin gene (H-hin), phage Mu G-gin, phage P1 C-cin, and Escherichia coli e14 P-pin. In this article we report the isolation and characterization of three new recombinase genes: pinB, pinD, and defective pinF from Shigella boydii, Shigella dysenteriae, and Shigella flexneri, respectively. The genes pinB and pinD were detected by the complementation of a hin mutation of Salmonella and were able to mediate inversion of the H, P, and C segments. pinB mediated H inversion as efficiently as the hin gene did and mediated C inversion with a frequency three orders of magnitude lower than that of the cin gene. pinD mediated inversion of H and P segments with frequencies ten times as high as those for the genes intrinsic to each segment and mediated C inversion with a frequency ten times lower than that for cin. Therefore, the pinB and pinD genes were inferred to be different from each other. The invertible B segment-pinB gene cloned from S. boydii is highly homologous to the G-gin in size, organization, and nucleotide sequence of open reading frames, but the 5' constant region outside the segment is quite different in size and predicted amino acid sequence. The B segment underwent inversion in the presence of hin, pin, or cin. The defective pinF gene is suggested to hae the same origin as P-pin on e14 by the restriction map of the fragment cloned from a Pin+ transductant that was obtained in transduction from S. flexneri to E. coli delta pin.
KeywordMeSH Terms
Chromosome Inversion
Genes, Bacterial
Integrases
32. Chang  CY, Lu  PL, Lin  CC, Lee  TM, Tsai  MY, Chang  LL,     ( 2011 )

Integron types, gene cassettes, antimicrobial resistance genes and plasmids of Shigella sonnei isolates from outbreaks and sporadic cases in Taiwan.

Journal of medical microbiology 60 (Pt 2)
PMID : 20947666  :   DOI  :   10.1099/jmm.0.022517-0    
Abstract >>
This study analysed the presence, location and transferability of integrons and antibiotic resistance genes in 103 Shigella sonnei outbreak isolates and in 32 sporadic isolates from Taiwan. Multiple antimicrobial resistance was common in both outbreak (95 %) and sporadic (97 %) isolates. Class 1 integrons were present in 34 outbreak isolates (33 %) and in six sporadic isolates (19 %). This study is the first, to our knowledge, to identify an atypical sul3-associated class 1 integron carrying the estX-psp-aadA2-cmlA-aadA1-qacH cassette array in Shigella. Class 2 integrons carrying the dfr1-sat2-aadA1 cassette array were predominant in outbreak isolates (90 %) but were not present in sporadic isolates. Other antimicrobial resistance genes not associated with integrons were found to encode resistance to ampicillin (bla(TEM)), chloramphenicol (cat1), sulfonamide (sul2) and tetracycline (tetA and tetB). The most common plasmid size was 130 kb (observed in 43 and 97 % of 1998 outbreak and sporadic isolates, respectively). In conclusion, the plasmid location of resistance genes and horizontal plasmid transfer promote the spread of multiple resistance genes in outbreak and sporadic isolates of S. sonnei.
KeywordMeSH Terms
Genes, Bacterial
Integrons
Plasmids
33. Nagano  Y, Nagano  N, Wachino  J, Ishikawa  K, Arakawa  Y,     ( 2009 )

Novel chimeric beta-lactamase CTX-M-64, a hybrid of CTX-M-15-like and CTX-M-14 beta-lactamases, found in a Shigella sonnei strain resistant to various oxyimino-cephalosporins, including ceftazidime.

Antimicrobial agents and chemotherapy 53 (1)
PMID : 18955524  :   DOI  :   10.1128/AAC.00227-08     PMC  :   PMC2612187    
Abstract >>
The plasmid-mediated novel beta-lactamase CTX-M-64 was first identified in Shigella sonnei strain UIH-1, which exhibited resistance to cefotaxime (MIC, 1,024 microg/ml) and ceftazidime (MIC, 32 microg/ml). The amino acid sequence of CTX-M-64 showed a chimeric structure of a CTX-M-15-like beta-lactamase (N- and C-terminal moieties) and a CTX-M-14-like beta-lactamase (central portion, amino acids 63 to 226), suggesting that it originated by homologous recombination between the corresponding genes. The introduction of a recombinant plasmid carrying bla(CTX-M-64) conferred resistance to cefotaxime in Escherichia coli, and the activities of cefotaxime and ceftazidime were restored in the presence of clavulanic acid. Of note, CTX-M-64 production could also confer consistent resistance to ceftazidime, which differs from the majority of CTX-M-type enzymes, which poorly hydrolyze ceftazidime. These results were consistent with the kinetic parameters determined with the purified CTX-M-64 enzyme. The bla(CTX-M-64) gene was flanked upstream by an ISEcp1 sequence and downstream by an orf477 sequence. The sequence of the 45-bp spacer region between the right inverted repeat (IRR) of ISEcp1 and bla(CTX-M-64) was exactly identical to that of ISEcp1-bla(CTX-M-15-like). Moreover, the presence of a putative IRR of ISEcp1 at the right end of truncated orf477 is indicative of an ISEcp1-mediated transposition event in the bla(CTX-M-64) gene. The emergence of CTX-M-64 by probable homologous recombination would suggest the natural potential of an alternative mechanism for the diversification of CTX-M-type beta-lactamases.
KeywordMeSH Terms
34. Gassama Sow  A, Diallo  MH, Gatet  M, Denis  F, Aïdara-Kane  A, Ploy  MC,     ( 2008 )

Description of an unusual class 2 integron in Shigella sonnei isolates in Senegal (sub-Saharan Africa).

The Journal of antimicrobial chemotherapy 62 (4)
PMID : 18565971  :   DOI  :   10.1093/jac/dkn264    
Abstract >>
N/A
KeywordMeSH Terms
Integrons
35. von Rhein  C, Bauer  S, Simon  V, Ludwig  A,     ( 2008 )

Occurrence and characteristics of the cytolysin A gene in Shigella strains and other members of the family Enterobacteriaceae.

FEMS microbiology letters 287 (2)
PMID : 18754791  :   DOI  :   10.1111/j.1574-6968.2008.01290.x    
Abstract >>
Cytolysin A (ClyA, HlyE, SheA) is a hemolytic pore-forming toxin found in Escherichia coli and Salmonella enterica serovars Typhi and Paratyphi A. In the present study, analysis of several Shigella strains revealed that they harbor only nonfunctional clyA gene copies that have been inactivated either by the integration of insertion sequence (IS) elements (Shigella dysenteriae, Shigella boydii, and Shigella sonnei strains) or by a frameshift mutation (Shigella flexneri). Shigella dysenteriae and S. boydii strains also exhibited IS-associated deletions at the clyA locus. PCR and Southern blot analyses as well as database searches indicated that clyA-related DNA sequences are completely absent in strains belonging to various other genera of the family Enterobacteriaceae. According to these data, ClyA may play a role only for a rather small subset of the enteric bacteria.
KeywordMeSH Terms
36. Mitobe  J, Morita-Ishihara  T, Ishihama  A, Watanabe  H,     ( 2008 )

Involvement of RNA-binding protein Hfq in the post-transcriptional regulation of invE gene expression in Shigella sonnei.

The Journal of biological chemistry 283 (9)
PMID : 18156173  :   DOI  :   10.1074/jbc.M710108200    
Abstract >>
The temperature-dependent regulation of Shigella virulence genes is believed to be accomplished at the transcriptional stage by the regulators VirF and InvE. Several lines of evidence herein described indicate that post-transcriptional regulation of InvE expression plays a key role in the temperature-dependent regulation of virulence gene expression: (i) a considerable amount of invE mRNA continues to be transcribed under low temperature conditions, where the production of InvE protein is tightly repressed; (ii) the stability of invE mRNA markedly decreases, because its decay rate is significantly increased under the repressing conditions. Strikingly, in the hfq mutant of Shigella sonnei, a considerable amount of InvE protein was produced even at low temperature. This increase in the InvE level was found to be associated with the improved stability of invE mRNA, in agreement with the finding that the RNA chaperon Hfq influences post-transcriptional regulations of various genes. Consistently, overexpression of the Hfq protein decreased the production of InvE protein even under the expressing condition at 37 degrees C. The binding in vitro of purified Hfq protein to invE RNA was shown to be stronger at 30 degrees C than at 37 degrees C in two experiments, gel shift analysis and surface plasmon resonance (Biacore) analysis. These results altogether suggest that Hfq plays an important role in the temperature-dependent regulation of invE expression at the post-transcriptional step.
KeywordMeSH Terms
37. Lefort  A, Arlet  G, Join-Lambert  OF, Lecuit  M, Lortholary  O,     ( 2007 )

Novel extended-spectrum beta-lactamase in Shigella sonnei.

Emerging infectious diseases 13 (4)
PMID : 17561568  :   DOI  :   10.3201/eid1304.061160     PMC  :   PMC2725971    
Abstract >>
N/A
KeywordMeSH Terms
38. Matsutani  S, Ohtsubo  H, Maeda  Y, Ohtsubo  E,     ( 1987 )

Isolation and characterization of IS elements repeated in the bacterial chromosome.

Journal of molecular biology 196 (3)
PMID : 2824781  :   DOI  :   10.1016/0022-2836(87)90023-4    
Abstract >>
Shigella sonnei contains repetitive sequences, including an insertion element IS1, which can be isolated as double-stranded DNA fragments by DNA denaturation and renaturation and by treatment with S1 nuclease. In this paper, we describe a method of cloning the IS1 fragments prepared by the S1 nuclease digestion technique into phage M13mp8 RFI DNA. Several clones contained IS1, usually with a few additional bases. We isolated and characterized five other repetitive sequences using this method. One sequence, 1264 base-pairs in length, had terminal inverted repeats and contained two open reading frames. This sequence, called IS600, showed about 44% sequence homology with IS3 and was repeated more than 20 times in the Sh. sonnei chromosome. Another sequence (named IS629, 1310 base-pairs in length), which was repeated six times, was found also to be related to IS3 and thus IS600. Two other sequences (named IS630 and IS640, 1159 and 1092 base-pairs in length, respectively), which were repeated approximately ten times, had characteristic terminal inverted repeats and contained a large open reading frame coding for a protein. The inverted repeat sequences of IS630 were similar to the sequence at one end of IS200, a Salmonella-specific IS element. The fifth sequence, repeated ten times in Sh. sonnei, had about 98% sequence homology with a portion of IS2. The method described here can be applied to the isolation of IS or iso-IS elements present in any other bacterial chromosome.
KeywordMeSH Terms
Chromosomes, Bacterial
DNA Transposable Elements
Repetitive Sequences, Nucleic Acid
39. Tenover  FC, Filpula  D, Phillips  KL, Plorde  JJ,     ( 1988 )

Cloning and sequencing of a gene encoding an aminoglycoside 6'-N-acetyltransferase from an R factor of Citrobacter diversus.

Journal of bacteriology 170 (1)
PMID : 2826403  :   DOI  :   10.1128/jb.170.1.471-473.1988     PMC  :   PMC210671    
Abstract >>
The aacA1 gene, which encodes a 6'-N-acetyltransferase [AAC(6')-I] mediating resistance to kanamycin, tobramycin, and amikacin, was cloned from the Citrobacter diversus R plasmid pBWH100 into the Escherichia coli vector pBR322. The complete nucleotide sequence of the gene and flanking regions was determined. A protein of approximately 21 kilodaltons was identified when the chimeric plasmid encoding the aacA1 gene was introduced into E. coli maxicells. This value is consistent with the size predicted for a protein translated from the open reading frame of the gene.
KeywordMeSH Terms
R Factors
40. Kato  J, Ito  K, Nakamura  A, Watanabe  H,     ( 1989 )

Cloning of regions required for contact hemolysis and entry into LLC-MK2 cells from Shigella sonnei form I plasmid: virF is a positive regulator gene for these phenotypes.

Infection and immunity 57 (5)
PMID : 2651305  :   PMC  :   PMC313288    
Abstract >>
Two distinct regions required for both contact hemolysis and entry into LLC-MK2 cells were cloned into Escherichia coli from the Shigella sonnei form I plasmid, pSS120. The first region was cloned into an E. coli HB101 strain containing noninvasive Tn1 insertion mutants of the form I plasmid, and expression of ipa (invasion plasmid antigen) gene products was restored. The plasmid carrying the first region was then transformed into E. coli lacking the form I plasmid, and additional DNA fragments from the form I plasmid were cloned into the same recipient on compatible vectors. Five of these double transformants were found to be positive for contact hemolysis activity. Restriction analysis of these five clones indicated that the previously reported ipa locus and the invA locus were present on the second plasmid region. Only the strains carrying both of these regions were active in contact hemolysis and cell invasion assays. Several proteins, including the a, b, c, and d proteins encoded by the ipa genes, were detected in the double transformants by Western blot (immunoblot) analysis with serum of a monkey convalescing from shigellosis. A positive regulator was suggested to exist in the first region, since the amounts of most of these proteins were simultaneously increased in the presence of this region. Subcloning and nucleotide sequencing indicated that this positive regulator gene was virF. Product analysis of the virF gene with minicells showed that two peptides (30 and 21 kilodaltons) were synthesized and that at least the 30-kilodalton protein was essential for regulation of the ipa genes.
KeywordMeSH Terms
Genes, Bacterial
Genes, Regulator
Hemolysis
41. Kim  SR, Komano  T,     ( 1989 )

Cloning and nucleotide sequence of the ColIb shufflon.

Plasmid 22 (2)
PMID : 2623084  :  
Abstract >>
The R64 shufflon is a novel type of DNA rearrangement in which four DNA segments invert independently or in groups. The related plasmid ColIb carries a variant shufflon. The present sequence analysis shows that the ColIb shufflon consists of three DNA segments that are highly homologous to the A, B, and C segments of the R64 shufflon. The 329-bp D segment of R64 is not present in the ColIb shufflon. As in the case of R64, the ColIb shufflon may act as a biological switch to select one of the six open reading frames in which the N-terminal region is constant while the C-terminal region is variable.
KeywordMeSH Terms
Plasmids
Recombination, Genetic
42. Calcuttawala  F, Hariharan  C, Pazhani  GP, Ghosh  S, Ramamurthy  T,     ( 2015 )

Activity spectrum of colicins produced by Shigella sonnei and genetic mechanism of colicin resistance in conspecific S. sonnei strains and Escherichia coli.

Antimicrobial agents and chemotherapy 59 (1)
PMID : 25331695  :   DOI  :   10.1128/AAC.04122-14     PMC  :   PMC4291344    
Abstract >>
Colicin-mediated killing is an example of allelopathy, which has been found among several bacteria. Screening of 42 strains of Shigella sonnei isolated from diarrheal patients revealed that 39 (93%) S. sonnei strains were positive for colicin production against Escherichia coli DH5�\. In the PCR-based detection of the colicin types, 36 (92.3%) were identified as E3, 2 (5.1%) as E3 and E8, and 1 (2.6%) as E3 and E2. Representative S. sonnei strains producing heterologous colicins exhibited antagonism against diarrheagenic Escherichia coli (DEC) groups. Although it is known that mutation in the colicin receptor renders the host resistant to colicin, there is a dearth of information on the genetic characterization of such mutants. In the fluctuation test, colicin-resistant E. coli mutants were found to occur spontaneously at the rates of 2.51 �� 10(-8) and 5.52 �� 10(-8) per generation when exposed to colicins E3 and E8 and colicins E3 and E2, respectively. Genotypic characterization of colicin-resistant E. coli (EC(Cr)) and S. sonnei (SS(Cr)) strains displayed mutations in the btuB gene, which encodes the receptor for vitamin B12 uptake. This gene was interrupted by various insertion sequences, such as IS1, IS2, and IS911. Complementation of EC(Cr) and SS(Cr) with plasmid-borne btuB (pbtuB) accomplished restoration of the colicin-susceptible phenotype. The vitamin B12 uptake assay gave an insight into the physiological relevance of the btuB mutation. Our studies provide insights into the latent influence of S. sonnei colicins in governing the existence of some of the shigellae and all of the DEC and the genetic mechanism underlying the emergence of resistance.
KeywordMeSH Terms
43. Ud-Din  AI, Wahid  SU, Latif  HA, Shahnaij  M, Akter  M, Azmi  IJ, Hasan  TN, Ahmed  D, Hossain  MA, Faruque  AS, Faruque  SM, Talukder  KA,     ( 2013 )

Changing trends in the prevalence of Shigella species: emergence of multi-drug resistant Shigella sonnei biotype g in Bangladesh.

PloS one 8 (12)
PMID : 24367527  :   DOI  :   10.1371/journal.pone.0082601     PMC  :   PMC3867351    
Abstract >>
Shigellosis, caused by Shigella species, is a major public health problem in Bangladesh. To determine the prevalence and distribution of different Shigella species, we analyzed 10,827 Shigella isolates from patients between 2001 and 2011. S. flexneri was the predominant species isolated throughout the period. However, the prevalence of S. flexneri decreased from 65.7% in 2001 to 47% in 2011, whereas the prevalence of S. sonnei increased from 7.2% in 2001 to 25% in 2011. S. boydii and S. dysenteriae accounted for 17.3% and 7.7% of the isolates respectively throughout the period. Of 200 randomly selected S. sonnei isolates for extensive characterization, biotype g strains were predominant (95%) followed by biotype a (5%). Resistance to commonly used antibiotics including trimethoprim-sulfamethoxazole, nalidixic acid, ciprofloxacin, mecillinam and ampicillin was 89.5%, 86.5%, 17%, 10.5%, and 9.5%, respectively. All isolates were susceptible to ceftriaxone, cefotaxime, ceftazidime and imipenem. Ninety-eight percent of the strains had integrons belonging to class 1, 2 or both. The class 1 integron contained only dfrA5 gene, whereas among class 2 integron, 16% contained dhfrAI-sat1-aadA1-orfX gene cassettes and 84% harbored dhfrA1-sat2 gene cassettes. Plasmids of ?5, ?1.8 and ?1.4 MDa in size were found in 92% of the strains, whereas only 33% of the strains carried the 120 MDa plasmid. PFGE analysis showed that strains having different integron patterns belonged to different clusters. These results show a changing trend in the prevalence of Shigella species with the emergence of multidrug resistant S. sonnei. Although S. flexneri continues to be the predominant species albeit with reduced prevalence, S. sonnei has emerged as the second most prevalent species replacing the earlier dominance by S. boydii and S. dysenteriae in Bangladesh.
KeywordMeSH Terms
44. Holt  KE, Thieu Nga  TV, Thanh  DP, Vinh  H, Kim  DW, Vu Tra  MP, Campbell  JI, Hoang  NV, Vinh  NT, Minh  PV, Thuy  CT, Nga  TT, Thompson  C, Dung  TT, Nhu  NT, Vinh  PV, Tuyet  PT, Phuc  HL, Lien  NT, Phu  BD, Ai  NT, Tien  NM, Dong  N, Parry  CM, Hien  TT, Farrar  JJ, Parkhill  J, Dougan  G, Thomson  NR, Baker  S,     ( 2013 )

Tracking the establishment of local endemic populations of an emergent enteric pathogen.

Proceedings of the National Academy of Sciences of the United States of America 110 (43)
PMID : 24082120  :   DOI  :   10.1073/pnas.1308632110     PMC  :   PMC3808646    
Abstract >>
Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.
KeywordMeSH Terms
drug resistance
enteric disease
genomics
phylogeography
Endemic Diseases
Genetic Variation
45. Mercier  J, Lachapelle  J, Couture  F, Lafond  M, Vézina  G, Boissinot  M, Levesque  RC,     ( 1990 )

Structural and functional characterization of tnpI, a recombinase locus in Tn21 and related beta-lactamase transposons.

Journal of bacteriology 172 (7)
PMID : 2163386  :   DOI  :   10.1128/jb.172.7.3745-3757.1990     PMC  :   PMC213353    
Abstract >>
A novel discrete mobile DNA element from Tn21 from the plasmid R100.1 is described, and its mobilization function was confirmed experimentally. In addition, the element behaves as a recombinase-active locus (tnpI) which facilitates insertions of antibiotic resistance genes as modules or cassettes at defined hot spots or integration sites. A similar tnpI sequence was detected by DNA hybridization in a series of beta-lactamase transposons and plasmids and localized on their physical maps. The genetic function of the locus cloned from Tn21 into pACYC184 was tested for conduction and integration into the plasmids R388 and pOX38Km, and the results suggested recombinase-integrase activity and recA independence. DNA sequence analysis of the tnpI locus revealed no inverted or direct terminal repeats or transposition features of class I and class II transposons. The coding capacity revealed three putative open reading frames encoding 131, 134, and 337 amino acids. Orf3 encoded a putative polypeptide product of 337 amino acids that shared highly significant identity with the carboxyl region of integrase proteins. A comparison and an alignment of the tnpI locus from Tn21 and its flanking sequences identified similar sequences in plasmids and in transposons. The alignment revealed discrete nucleotide changes in these tnpI-like loci and a conserved 3' and 5' GTTA/G hot spot as a duplicated target site. Our data confirm the remarkable ubiquity of tnpI associated with antibiotic resistance genes. We present a model of transposon modular evolution into more complex multiresistant units via tnpI and site-specific insertions, deletions, and DNA rearrangements at this locus.
KeywordMeSH Terms
DNA Transposable Elements
46. Thomson  CJ, Barg  N, Amyes  SG,     ( 1990 )

N-terminal amino acid sequence of the novel type IIIb trimethoprim-resistant plasmid-encoded dihydrofolate reductase from Shigella sonnei.

Journal of general microbiology 136 (4)
PMID : 2204677  :   DOI  :   10.1099/00221287-136-4-673    
Abstract >>
The type IIIb dihydrofolate reductase, a novel plasmid-encoded enzyme recently identified in Shigella sonnei, has been shown to have some similar biochemical properties to the type IIIa dihydrofolate reductase which was first identified in New Zealand in 1979. However, the type IIIb enzyme has a Ki for trimethoprim of 0.4 microM, and a pI of 5.35 (as compared to 19 nM and 6.1 for the type IIIa); both these results suggest that it is a different enzyme from the prototype type IIIa. The type IIIb dihydrofolate reductase was purified by methotrexate agarose affinity chromatography, yielding a pure protein as determined by HPLC. Automatic amino acid analysis of the purified enzyme showed it to be distinct from all other known plasmid-encoded dihydrofolate reductases and quite different from the type IIIa enzyme. The purified enzyme was examined by SDS-PAGE, which revealed that the type IIIb dihydrofolate reductase was a monomeric protein of Mr 17,200.
KeywordMeSH Terms
Plasmids
47. Bhattacharya  D, Bhattacharjee  H, Thamizhmani  R, Sayi  DS, Bharadwaj  AP, Singhania  M, Sugunan  AP, Roy  S,     ( 2011 )

Prevalence of the plasmid-mediated quinolone resistance determinants among clinical isolates of Shigella sp. in Andaman & Nicobar Islands, India.

Letters in applied microbiology 53 (2)
PMID : 21615433  :   DOI  :   10.1111/j.1472-765X.2011.03092.x    
Abstract >>
This study was carried out to find the prevalence of various plasmid-mediated quinolone-resistant (PMQR) determinants among the quinolone-resistant clinical isolates of Shigella sp. from paediatric patients in Andaman & Nicobar Islands. A total of 106 quinolone-resistant Shigella isolates obtained from paediatric patients during hospital-based surveillance from January 2003 to June 2010 were screened for the presence of various PMQR determinants. Of 106 isolates, 8 (7.5%) showed the presence of aac (6')-Ib-cr and 3 (2.8%) harboured the qnrB genes with 2 (1.9%) of these isolates showing the presence of both. All the 9 isolates had uniform mutations in gyrA (S83L) and in parC (S80I). The prevalence of fluoroquinolone-acetylating aminoglycoside acetyltransferase {aac (6')-Ib-cr} gene is higher than qnrB gene among the clinical Shigella isolates. These PMQR determinants were detected in the Shigella isolates obtained from 2008-2010, indicating that it happens in a stepwise manner following the multiple mutations in quinolone resistance-determining regions increase or extend resistance to quinolones or fluoroquinolones. The prevalence of these genes are of grave concern as it may be horizontally transferred to other human pathogenic bacteria and can lead to therapeutic failure as a consequence of antimicrobial resistance, not only for the islands but also for the entire south-east region. The results obtained should encourage further studies on the implications of the presence, distribution, association and variation of these determinants in our quest for understanding PMQR.
KeywordMeSH Terms
48.     ( 1993 )

MxiD, an outer membrane protein necessary for the secretion of the Shigella flexneri lpa invasins.

Molecular microbiology 7 (1)
PMID : 8437520  :   DOI  :   10.1111/j.1365-2958.1993.tb01097.x    
Abstract >>
The invasive phenotype of Shigella flexneri is conferred by a 220 kb virulence plasmid, pWR100, that encodes both the lpa proteins, which are involved in the entry process, and factors which are required for the export and correct localization of the lpa proteins. We have characterized the mxiD gene, whose expression, like that of the ipa operon, is regulated by temperature. After inactivation of mxiD, the mutant strain was unable to invade HeLa cells and to provoke keratoconjunctivitis in guinea-pigs. Analysis of culture supernatants indicated that wild-type S. flexneri secretes about nine polypeptides and that secretion of several of these, including lpaA, lpaB, and lpaC, is abolished in the mxiD mutant. Examination of the membrane proteins of the wild-type and mxiD strains suggested that MxiD is an outer membrane protein. Amino acid sequence comparison revealed that MxiD is homologous to the YscC protein of Yersinia enterocolitica and to the C-terminal region of the PulD protein of Klebsiella pneumoniae. Both YscC and PulD are involved in extracellular protein secretion. These results indicate that MxiD is an essential component of the lpa secretion apparatus.
KeywordMeSH Terms
Adhesins, Bacterial
DNA-Binding Proteins
Genes, Bacterial
Transcription Factors
49.     ( 1993 )

Functional and physiological characterization of the Tn21 cassette for resistance genes in Tn2426.

Journal of general microbiology 139 (5)
PMID : 8393071  :   DOI  :   10.1099/00221287-139-5-995    
Abstract >>
The Tn21 subgroup of class II transposons plays an important role in the dissemination of resistance genes and especially in the epidemic spread of multi-resistance. This ability reflects the variety of resistance genes that associate with the streptomycin/spectinomycin-resistance gene (aadA) of Tn21. Deletion experiments with Tn2426, a typical member of the Tn21 subgroup, and sequencing of the region that accommodates additional resistance genes revealed significant structural characteristics. Each resistance gene was flanked by short, directly repeated recombinationally active sequences with unexpected variability in their sequence and length. The consensus for a recombinationally active sequence appeared to be 13 bp in length (TAAAACAANGNNA), compared to previous estimates of 54 bp. This sequence, in combination with the product of the integrase gene, is responsible for the genetic variability of members of the Tn21 family of transposable elements and the dissemination of multi-resistance.
KeywordMeSH Terms
Recombination, Genetic
50.     ( 1993 )

Characterization of the Shigella flexneri ipgD and ipgF genes, which are located in the proximal part of the mxi locus.

Infection and immunity 61 (5)
PMID : 8478058  :   PMC  :   PMC280755    
Abstract >>
The Shigella flexneri invasion process requires the synthesis of the Ipa proteins and their secretion by specific factors encoded by the mxi and spa genes, which are clustered upstream from the ipa operon. We report here the characterization of the ipgD, ipgE, and ipgF genes, which are located in the 5' end of the mxi locus. Analysis of IpgF-PhoA fusions endowed with high levels of alkaline phosphatase activity confirmed the functionality of a classical signal sequence detected in the sequence of IpgF. The ipgD and ipgF genes were each inactivated on the large virulence plasmid by insertion of a nonpolar cassette; each of the ipgD and ipgF mutants thus constructed showed the same invasive phenotype as the wild-type strain and was able to provoke keratoconjunctivitis in guinea pigs. It thus appears that two genes located at the ipa-proximal part of the mxi locus are not directly involved in invasion. Analysis of concentrated culture supernatants of the wild-type and ipgD strains indicated that secretion of one polypeptide, whose size was consistent with that predicted for the IpgD protein (60 kDa), was abolished in the ipgD mutant.
KeywordMeSH Terms
Bacterial Proteins
Genes, Bacterial
51.     ( 1994 )

A mutant hook-associated protein (HAP3) facilitates torsionally induced transformations of the flagellar filament of Escherichia coli.

Journal of molecular biology 238 (2)
PMID : 8158647  :   DOI  :   10.1006/jmbi.1994.1279    
Abstract >>
Two mutants with defects in hook-associated protein 3 (HAP3) were isolated that exhibit impaired swimming only when they interact with a solid surface or a semisolid matrix. Motility and chemotaxis were normal in liquid media, even in media containing viscous agents, but cells failed to swarm in 0.28% agar. Mutants appeared to carry a full complement of flagella of normal configuration and length. However, filaments rotating counterclockwise close to a glass surface transformed from normal to straight, while filaments rotating clockwise transformed from curly to straight. Both transformations propagated from base to tip, as expected if torsionally induced. The mutations mapped to the middle of flgL, to structural gene for HAP3, and sequence analysis revealed the same coding change in both mutants: a substitution of cysteine for arginine 168. Our results show that the ability of a filament composed of normal flagellin subunits to resist mechanical stress depends on the structure of the protein (HAP3) to which it is attached at its base. The N-terminal sequence of HAP3 was found to be similar to the N-terminal sequence of flagellin, and the possibility that it provides a nucleation site for the C-terminal region of flagellin is discussed.
KeywordMeSH Terms
52.     ( 1994 )

Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria.

Proceedings of the National Academy of Sciences of the United States of America 91 (21)
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.
KeywordMeSH Terms
Biological Evolution
Gene Transfer Techniques
Genes, Bacterial
53.     ( 1994 )

Molecular characterization of intact, but cryptic, flagellin genes in the genus Shigella.

Molecular microbiology 12 (2)
PMID : 8057852  :   DOI  :   10.1111/j.1365-2958.1994.tb01016.x    
Abstract >>
Flagellin genes (fliC) were detected in two species of the genus Shigella. The fliCSF gene cloned from Shigella flexneri produced normal-type flagella in an Escherichia coli delta fliC strain while the fliCSS genes from two Shigella sonnei strains produced curly-type flagella and their expression is repressible by Salmonella FljA repressor. The fliCSF gene (1650 bp) shared high similarity with the E. coli fliCE gene not only in the 5' and 3' constant sequences but also in the upstream and downstream sequences. The fliCSS genes (1572 bp) shared high similarity with the Salmonella typhimurium fliCS gene in the operator and 3' constant sequences and also shared high similarity with the fliCE gene in the downstream sequence, suggesting that the fliCSS gene has undergone horizontal transfer and recombination. Differences in nucleotide sequences of the central variable regions among the four fliC genes, including fliCE and fliCS, suggest that they started differentiation in each lineage approximately 80 million years ago. Loss of motility in Shigella seems to be evolutionarily a recent event.
KeywordMeSH Terms
Genes, Bacterial
54.     ( 1993 )

Analysis of the nucleotide and derived amino acid sequences of the SsoII restriction endonuclease and methyltransferase.

Gene 124 (1)
PMID : 7916706  :   DOI  :   10.1016/0378-1119(93)90756-s    
Abstract >>
A 2648-bp fragment from the P4 plasmid of Shigella sonnei strain 47 coding for the SsoII restriction endonuclease (ENase) and methyltransferase (MTase) (recognition sequence 5'-CCNGG) was sequenced. Two divergently arranged open reading frames of 905 bp for the SsoII ENase (R.SsoII) and 1137 bp for the MTase (M.SsoII) were identified. The coding regions are separated by 110 bp. The calculated M(r) of R.SsoII (35937) and M.SsoII (42887) are in good agreement with values previously obtained by in vitro transcription-translation experiments, i.e., 35 and 43 kDa for the ENase and MTase, respectively. The M.SsoII amino acid (aa) sequence revealed a considerable similarity to m5C-MTases recognizing the related sequences--M.EcoRII, M.dcm, M.MspI, M.BsuFI, M.HpaII, and M.HhaI. Surprisingly, the greatest degree of homology has been observed between the aa sequences of M.SsoII and M.NlaX, with an unidentified recognition sequence. The multiple alignment of aa sequences helps to identify the blocks of conserved aa in variable regions of MTases. These conserved aa can play a key role in target recognition. Some aspects of evolution of m5C-MTases are discussed.
KeywordMeSH Terms
Genes, Bacterial
55. Barg  NL, Register  S, Thomson  C, Amyes  S,     ( 1995 )

Sequence identity with type VIII and association with IS176 of type IIIc dihydrofolate reductase from Shigella sonnei.

Antimicrobial agents and chemotherapy 39 (1)
PMID : 7695291  :   DOI  :   10.1128/aac.39.1.112     PMC  :   PMC162495    
Abstract >>
An uncommon dihydrofolate reductase (DHFR), type IIIc, was coded for by Shigella sonnei that harbors plasmid pBH700 and that was isolated in North Carolina. The trimethoprim resistance gene carried on pBH700 was subcloned and sequenced. The nucleotide sequence of the gene encoding type IIIc DHFR was identical to the gene encoding type VIII DHFR. The type IIIc amino acid sequence was approximately 50% similar to those of DHFRs commonly found in enteric bacteria. Furthermore, this gene was flanked by IS176 (IS26), an insertion sequence usually associated with those of aminoglycoside resistance genes. The gene for type IIIc DHFR was located by hybridization within a 1,993-bp PstI fragment in each of eight conjugative plasmids from geographically diverse strains of S. sonnei. Each plasmid also conferred resistance to ampicillin, streptomycin, and sulfamethoxazole and belonged to incompatibility group M. Plasmids carrying this new trimethoprim resistance gene, which is uniquely associated with IS176, have disseminated throughout the United States.
KeywordMeSH Terms
56. Olsson  O, Bergström  S, Lindberg  FP, Normark  S,     ( 1983 )

ampC beta-lactamase hyperproduction in Escherichia coli: natural ampicillin resistance generated by horizontal chromosomal DNA transfer from Shigella.

Proceedings of the National Academy of Sciences of the United States of America 80 (24)
PMID : 6369321  :   DOI  :   10.1073/pnas.80.24.7556     PMC  :   PMC534379    
Abstract >>
Six ampicillin-resistant clinical isolates of Escherichia coli that hyperproduced the chromosomal ampC beta-lactamase were studied. By DNA sequence analysis, we found that five of them were identical over an entire 449-base-pair sequence and carried a novel strong ampC promoter [Olsson, O., Bergstr?m, S. & Normark, S. (1982) EMBO J. 1, 1411-1416]. Except for one base pair this sequence was identical to that of a low beta-lactamase-producing clinical isolate of Shigella sonnei. Spontaneous one-step mutants of S. sonnei that overproduced the ampC beta-lactamase by 45-fold were characterized and found to be mutated at the single base that distinguishes S. sonnei from the five E. coli hyperproducers. The most likely explanation for this result is that chromosomal DNA was transferred in vivo from Shigella to E. coli across the species barrier.
KeywordMeSH Terms
Genes
Genes, Bacterial
57. Kato  A, Mizobuchi  K,     ( 1994 )

Evolution of the replication regions of IncI alpha and IncFII plasmids by exchanging their replication control systems.

DNA research : an international journal for rapid publication of reports on genes and genomes 1 (5)
PMID : 7584042  :   DOI  :   10.1093/dnares/1.5.201    
Abstract >>
The basic replicons of bacterial plasmids consist of two sets of genetic systems, the replication-structural system and the replication control system. Comparison of nucleotide sequences suggested that the basic replicons of plasmids P307 (IncFI) and pMU2200 (IncZ) were generated by reciprocal recombination between ancestors of R100 (IncFII) and ColIb-P9 (IncI alpha), or vice versa. The plasmids of each pair, P307/pMU2200 and R100/ColIb-P9, are structurally unrelated to each other. Based on this information, we constructed in vitro and analyzed P307-like chimeric replicons from ColIb-P9 and R100. When the replication-structural region of ColIb-P9 was combined with the whole replication control region of R100, the resultant replicon replicated stably as R100 did. These results revealed that the basic replicons of the plasmids diverged by exchanging their replication control systems. Thus, we propose that the replication control systems of plasmids, in some cases, evolved independently of their structural systems, although these two systems work together to maintain the replication functions. We also showed that the reciprocal recombination was specified by the unique secondary structures of RNA involved in the control of expression of the genes encoding the replication initiator proteins.
KeywordMeSH Terms
Evolution, Molecular
58. Hiraga  S, Sugiyama  T, Itoh  T,     ( 1994 )

Comparative analysis of the replicon regions of eleven ColE2-related plasmids.

Journal of bacteriology 176 (23)
PMID : 7525540  :   DOI  :   10.1128/jb.176.23.7233-7243.1994     PMC  :   PMC197111    
Abstract >>
The incA gene product of ColE2-P9 and ColE3-CA38 plasmids is an antisense RNA that regulates the production of the plasmid-coded Rep protein essential for replication. The Rep protein specifically binds to the origin and synthesizes a unique primer RNA at the origin. The IncB incompatibility is due to competition for the Rep protein among the origins of the same binding specificity. We localized the regions sufficient for autonomous replication of 15 ColE plasmids related to ColE2-P9 and ColE3-CA38 (ColE2-related plasmids), analyzed their incompatibility properties, and determined the nucleotide sequences of the replicon regions of 9 representative plasmids. The results suggest that all of these plasmids share common mechanisms for initiation of DNA replication and its control. Five IncA specificity types, 4 IncB specificity types, and 9 of the 20 possible combinations of the IncA and IncB types were found. The specificity of interaction of the Rep proteins and the origins might be determined by insertion or deletion of single nucleotides and substitution of several nucleotides at specific sites in the origins and by apparently corresponding insertion or deletion and substitution of amino acid sequences at specific regions in the C-terminal portions of the Rep proteins. For plasmids of four IncA specificity types, the nine-nucleotide sequences at the loop regions of the stem-loop structures of antisense RNAs are identical, suggesting an evolutionary significance of the sequence. The mosaic structures of the replicon regions with homologous and nonhomologous segments suggest that some of them were generated by exchanging functional parts through homologous recombination.
KeywordMeSH Terms
DNA Helicases
59. Nakayama  S, Watanabe  H,     ( 1995 )

Involvement of cpxA, a sensor of a two-component regulatory system, in the pH-dependent regulation of expression of Shigella sonnei virF gene.

Journal of bacteriology 177 (17)
PMID : 7665485  :   DOI  :   10.1128/jb.177.17.5062-5069.1995     PMC  :   PMC177285    
Abstract >>
In Shigella species, IpaBCD proteins encoded on the virulence plasmid direct the entry of this bacterium into host epithelial cells. Expression of the ipaBCD genes is under the control of several environmental conditions, such as temperature and osmolarity. Extracellular pH also controlled the the expression of the genes, and this regulation occurred mainly at the step of expression of virF, a plasmid-encoded positive regulator of ipaBCD. The expression of virF was activated at high pH (pH 7.4) and repressed at low pH (pH 6.0). We isolated a Tn10 transposon mutant in Escherichia coli K-12 which altered this regulation at the transcriptional level. The Tn10 in the mutant inserted within a reading frame of the cpxA gene, whose product belongs to a family of sensor proteins of two-component signal transduction systems. Complementation analysis showed that cpxA was involved in the pH-dependent regulation of virF gene expression. A gene homologous to cpxA was conserved in Shigella spp. as well as in E. coli. These results may indicate that CpxA senses directly or indirectly a change in extracellular pH and influences the expression of virF in E. coli and Shigella spp.
KeywordMeSH Terms
Escherichia coli Proteins
Gene Expression Regulation, Bacterial
Protein Kinases
Virulence Factors
60. Hirose  T, Sugiura  S, Shibata  H, Hase  T, Nakanishi  Y, Masamune  Y,     ( 1988 )

[Total nucleotide sequence of plasmid pKYM and its replication origin].

Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan 108 (9)
PMID : 3073212  :   DOI  :   10.1248/yakushi1947.108.9_886    
Abstract >>
N/A
KeywordMeSH Terms
DNA Replication
Plasmids
61. Mankovich  JA, Hsu  CH, Konisky  J,     ( 1986 )

DNA and amino acid sequence analysis of structural and immunity genes of colicins Ia and Ib.

Journal of bacteriology 168 (1)
PMID : 3531169  :   DOI  :   10.1128/jb.168.1.228-236.1986     PMC  :   PMC213442    
Abstract >>
The nucleotide sequences for colicin Ia and colicin Ib structural and immunity genes were determined. The two colicins each consist of 626 amino acid residues. Comparison of the two sequences along their lengths revealed that the two colicins are nearly identical in the N-terminal 426 amino acid residues. The C-terminal 220 amino acid residues of the colicins are only 60% identical, suggesting that this is the region most likely recognized by their cognate immunity proteins. The predicted proteins for the colicin immunity proteins would contain 111 amino acids for the colicin Ia immunity protein and 115 amino acids for the colicin Ib immunity protein. The colicin immunity proteins have no detectable DNA or amino acid homology but do exhibit a conservation of overall hydrophobicity. The colicin immunity genes lie distal to and in opposite orientation to the colicin structural genes. The colicin Ia immunity protein was purified to apparent homogeneity by a combination of isoelectric focusing and preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The N-terminal amino acid sequence of the purified Ia immunity protein was determined and was found to be in perfect agreement with that predicted from the DNA sequence of its structural gene. The Ia immunity protein is not a processed membrane protein.
KeywordMeSH Terms
Bacteriocin Plasmids
Genes
Plasmids
62. Fling  ME, Kopf  J, Richards  C,     ( 1985 )

Nucleotide sequence of the transposon Tn7 gene encoding an aminoglycoside-modifying enzyme, 3"(9)-O-nucleotidyltransferase.

Nucleic acids research 13 (19)
PMID : 2997737  :   DOI  :   10.1093/nar/13.19.7095     PMC  :   PMC322025    
Abstract >>
The nucleotide sequence of a transposon Tn7 DNA fragment encoding a 3"(9)-O-nucleotidyltransferase, an aminoglycoside-modifying enzyme, which mediates bacterial resistance to spectinomycin and streptomycin, was determined. The aadA structural gene was 786 bases long and predicted a polypeptide of 262 amino acids with a calculated molecular weight of 29,207. Comparison of the DNA sequences of Tn7 and plasmid R538-1 indicated that their aadA genes were nearly identical. Comparison of the polypeptides predicted by the aadA genes of Tn7 and Tn554 indicated that the genes were related.
KeywordMeSH Terms
DNA Transposable Elements
Drug Resistance, Microbial
63. Cameron  FH, Groot Obbink  DJ, Ackerman  VP, Hall  RM,     ( 1986 )

Nucleotide sequence of the AAD(2'') aminoglycoside adenylyltransferase determinant aadB. Evolutionary relationship of this region with those surrounding aadA in R538-1 and dhfrII in R388.

Nucleic acids research 14 (21)
PMID : 3024112  :   DOI  :   10.1093/nar/14.21.8625     PMC  :   PMC311882    
Abstract >>
The nucleotide sequence of the aadB gene which confers resistance to kanamycin, gentamicin, and tobramycin has been determined. The size of the longest reading frame is 747 bases encoding a protein of predicted size 27,992 daltons. A segment of the aadB gene sequence (including the promoter region) was found upstream of the aadA gene in R538-1 and of the dhfrII gene in R388 and the proposed promoters for these genes coincide with the aadB promoter region. The sequence homology extends upstream to the end of the sequenced regions of R388 and R538-1. Almost perfect homology was also found between the sequences 3'- to the aadB gene and 3'- to the aadA genes of R538-1 and pSa. This segment includes a 59 base element previously found flanking the Tn7 aadA gene. A model is presented for the evolution of this region of the plasmid genomes in which the 59- base element functions as an insertional "hot spot" and the possibility that this region is analogous to the aadA/aadB region of the Tn21- like transposon family is considered.
KeywordMeSH Terms
Biological Evolution
Genes
Genes, Bacterial
64.     ( 2013 )

Genetic diversity of Shigella spp. and their integron content.

Foodborne pathogens and disease 10 (3)
PMID : 23489046  :   DOI  :   10.1089/fpd.2012.1250    
Abstract >>
The aim of this study was to investigate the occurrence and resistance gene content of class 1 and 2 integrons among Shigella spp. and to study the genetic diversity of isolates using the pulsed-field gel electrophoresis (PFGE) method. A total of 32 Shigella spp. were identified from 700 stool samples of patients with diarrhea from two provinces in Iran. S. sonnei (70.8%) and S. flexneri (62.5%) were the most frequent serogroups in Tehran and Razavi Khorasan provinces, respectively. Class 2 integrons were more frequent among Shigella spp. in comparison with class 1 integrons. Three different resistance gene arrays were identified among class 1 integrons. Dihydrofolate reductase (dfrA) gene cassette was detected in 78.9% of total integrons (class 1 and 2). PFGE analysis revealed clonal dissemination (62.5%) of a single clone with identical class 2 resistance gene content in Tehran province. Comparison of our Shigella pulsotypes with those published from other countries showed similar pulsotypes in India and Korea, with identical resistance profiles, which suggests dissemination of this (these) clone(s) in Asian countries. Class 2 integrons were found to be predominant among our Shigella spp. This reflects the need to monitor the acquisition and dissemination of different resistant gene cassettes among integrons. Comparison of PFGE pattern through standard procedures promoted the molecular epidemiological surveys and identification of clonal isolates in Iran and other Asian countries.
KeywordMeSH Terms
Genetic Variation
Integrons
65. Yaghoubi  S, Ranjbar  R, Soltan Dallal  MM, Shirazi  MH, Sharifi-Yazdi  MK,     ( N/A )

Frequency of Mutations in Quinolone Resistance-Determining Regions and Plasmid-Mediated Quinolone Resistance in Shigella Isolates Recovered from Pediatric Patients in Tehran, Iran: An Overlooked Problem.

Microbial drug resistance (Larchmont, N.Y.) 24 (6)
PMID : 29148915  :   DOI  :   10.1089/mdr.2017.0155    
Abstract >>
Fluoroquinolone (FQ) resistance in clinical isolates of Shigella species has been increasing reported in recent years. This study was carried out to find the mutations within the quinolone resistance-determining regions (QRDRs) and the prevalence of plasmid-mediated quinolone resistance (PMQR) determinants among the clinical isolates of Shigella sp. in Tehran, Iran. A total of 50 Shigella isolates were collected from five teaching therapeutic centers in Tehran, Iran and analyzed for antibiotic susceptibility over a period of 20 months from July 2015 to January 2017. The PCR and direct nucleotide sequencing were used for genetic alterations in the QRDRs. The PMQR genes were detected using PCR. The results revealed four types of mutations in the QRDR of gyrA: 20 (40%) had a S83L mutation, 1 (2%) had a S83A mutation, 2 (4%) had a D87G mutation, and 1 (2%) isolate had a D87Y mutation. Mutations were also found at codon N57D, D200N, and E210K in three isolates. Seven hospitalized children had qnrS determinants, and one isolates had the mutation S83A, while two isolates had double mutations at S83L and/or D87G (Ser83Leu and Asp-87Gly). The PMQR gene-positive isolates had the single replacement of serine with leucine. In hospitalized children, two isolates had two types of PMQR determinants (qnrS and qnrA) and (qnrS and qnrB) at once. The results of this study indicate that the emergence of strains with mutations in the QRDR regions and the capture of PMQR determinants in strains may lead to failure in therapy with FQ and the widespread emergence of strains with high-level FQ resistance.
KeywordMeSH Terms
DNA gyrase
qnr gene
shigellosis
topoisomerase IV
DNA gyrase
qnr gene
shigellosis
topoisomerase IV
66.     ( 1998 )

Escherichia coli clone Sonnei (Shigella sonnei) had a chromosomal O-antigen gene cluster prior to gaining its current plasmid-borne O-antigen genes.

Journal of bacteriology 180 (11)
PMID : 9603891  :   PMC  :   PMC107268    
Abstract >>
O antigen is part of the lipopolysaccharide present in the outer membrane of gram-negative bacteria. The surface-exposed O antigen is subject to selection by the host immune system, which may account for the maintenance of many different O-antigen forms. Characteristically, all genes specific to O-antigen synthesis are clustered in a region close to the his and gnd genes on the chromosome of Escherichia coli and related species. Shigella sonnei, essentially a clone of E. coli (E. coli clone Sonnei), is an important human pathogen and is unusual in that its O-antigen gene cluster is located on a plasmid. Our results suggest that it once had a normal chromosomal O-antigen gene cluster which has been largely deleted. We suggest that the O antigen encoded by the plasmid-borne genes offered a selective advantage in adapting to a new environment and that the chromosomal O-antigen genes were eventually inactivated. We also identified, by PCR and sequencing, a potential ancestor of E. coli Sonnei among the 166 known E. coli serotype strains.
KeywordMeSH Terms
Bacterial Proteins
67.     ( 1998 )

Genetic analysis of Shigella sonnei form I antigen: identification of a novel IS630 as an essential element for the form I antigen expression.

Microbial pathogenesis 25 (4)
PMID : 9817819  :   DOI  :   10.1006/mpat.1998.0222    
Abstract >>
The form I coding region of Shigella sonnei was cloned and shown to have an operon-like rfb organization. It was found that the 11.0 kb HindIII-XbaI fragment of pHH201 encoding the form I antigen contains 10 contiguous open reading frames (ORF), ORF1 to ORF10. Deletions from either end of pHH201, within ORF1 or ORF10, eliminated form I expression. ORF1 and ORF2 share significant nucleic and amino acids homologies to two ORF's of the Salmonella typhi Vi antigen genes. ORF5 in pHH201 is identical to IS630. pHH2064, derived from pHH201, lacks the IS630 element and can stably express the form I antigen inE. coli HB101. However, pHH2064 is structurally unstable in a S. sonnei form II host. This indicates that the presence of the IS630 gene within the S. sonnei rfb operon may be necessary for the stability of form I expression in S. sonnei. This finding is substantiated by the observation that all virulent S. sonnei isolates examined in this study retained the IS630 element within their rfb operon.
KeywordMeSH Terms

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