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1. Pembroke  JT, MacMahon  C, McGrath  B,     ( 2002 )

The role of conjugative transposons in the Enterobacteriaceae.

Cellular and molecular life sciences : CMLS 59 (12)
PMID : 12568331  :  
Abstract >>
Although widely studied in gram-positive Streptococci and in the gram-negative Bacteroides, there is a scarcity of information on the occurrence and nature of conjugative transposon-like elements in the well-studied Enterobacteriaceae. In fact, some of the major reviews on conjugative transposons prior to 1996 failed to mention their occurrence in this group. Recently, their presence has been reported in Salmonella, Vibrio and Proteus species, and in some cases such as the SXT element in Vibrio and the IncJ group element CTnR391, there has been some molecular characterization. The elements thus far examined appear to be larger than the common gram-positive conjugative transposons and to be mosaic in structure, with genes derived from several sources. Recent evidence suggests that in the Enterobacteriaceae the elements may be related to enteric pathogenicity islands. The evolution, distribution and role of these elements in the Enterobacteriaceae is discussed.
KeywordMeSH Terms
Conjugation, Genetic
DNA Transposable Elements
2. Böltner  D, MacMahon  C, Pembroke  JT, Strike  P, Osborn  AM,     ( 2002 )

R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements.

Journal of bacteriology 184 (18)
PMID : 12193633  :   DOI  :   10.1128/jb.184.18.5158-5169.2002     PMC  :   PMC135318    
Abstract >>
The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements. Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair. While initially described as a plasmid, R391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the SXT element from Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence of R391 has revealed a mosaic structure consisting of elements originating in bacteriophages and plasmids and of transposable elements. A total of 96 open reading frames were identified; of these, 30 could not be assigned a function. Sequence similarity suggests a relationship of large sections of R391 to sequences from Salmonella, in particular those corresponding to the putative conjugative transfer proteins, which are related to the IncHI1 plasmid R27. A composite transposon carrying the kanamycin resistance gene and a novel insertion element were identified. Challenging the previous assumption that IncJ elements are plasmids, no plasmid replicon was identified on R391, suggesting that they cannot replicate autonomously.
KeywordMeSH Terms
Conjugation, Genetic
Plasmids
Virus Integration
3. Hochhut  B, Beaber  JW, Woodgate  R, Waldor  MK,     ( 2001 )

Formation of chromosomal tandem arrays of the SXT element and R391, two conjugative chromosomally integrating elements that share an attachment site.

Journal of bacteriology 183 (4)
PMID : 11157923  :   DOI  :   10.1128/JB.183.4.1124-1132.2001     PMC  :   PMC94984    
Abstract >>
The SXT element, a conjugative, self-transmissible, integrating element (a constin) originally derived from a Vibrio cholerae O139 isolate from India, and IncJ element R391, originally derived from a South African Providencia rettgeri isolate, were found to be genetically and functionally related. Both of these constins integrate site specifically into the Escherichia coli chromosome at an identical attachment site within the 5' end of prfC. They encode nearly identical integrases, which are required for chromosomal integration, excision, and extrachromosomal circularization of these elements, and they have similar tra genes. Therefore, these closely related constins have virtually identical mechanisms for chromosomal integration and dissemination. The presence of either element in a recipient cell did not significantly reduce its ability to acquire the other element, indicating that R391 and SXT do not encode surface exclusion determinants. In cells harboring both elements, SXT and R391 were integrated in tandem fashion on the chromosome, and homologous recombination appeared to play little or no role in the formation of these arrays. Interference between R391 and SXT was detected by measuring the frequency of loss of an unselected resident element upon introduction of a second selected element. In these assays, R391 was found to have a stronger effect on SXT stability than vice versa. The level of expression and/or activity of the donor and recipient integrases may play a role in the interference between these two related constins.
KeywordMeSH Terms
Genes, Bacterial
4. Klei  HE, McDonough  MA,     ( 1999 )

Crystal structure of penicillin G acylase from the Bro1 mutant strain of Providencia rettgeri.

Protein science : a publication of the Protein Society 8 (10)
PMID : 10548042  :   DOI  :   10.1110/ps.8.10.1971     PMC  :   PMC2144132    
Abstract >>
Penicillin G acylase is an important enzyme in the commercial production of semisynthetic penicillins used to combat bacterial infections. Mutant strains of Providencia rettgeri were generated from wild-type cultures subjected to nutritional selective pressure. One such mutant, Bro1, was able to use 6-bromohexanamide as its sole nitrogen source. Penicillin acylase from the Bro1 strain exhibited an altered substrate specificity consistent with the ability of the mutant to process 6-bromohexanamide. The X-ray structure determination of this enzyme was undertaken to understand its altered specificity and to help in the design of site-directed mutants with desired specificities. In this paper, the structure of the Bro1 penicillin G acylase has been solved at 2.5 A resolution by molecular replacement. The R-factor after refinement is 0.154 and R-free is 0.165. Of the 758 residues in the Bro1 penicillin acylase heterodimer (alpha-subunit, 205; beta-subunit, 553), all but the eight C-terminal residues of the alpha-subunit have been modeled based on a partial Bro1 sequence and the complete wild-type P. rettgeri sequence. A tightly bound calcium ion coordinated by one residue from the alpha-subunit and five residues from the beta-subunit has been identified. This enzyme belongs to the superfamily of Ntn hydrolases and uses Ogamma of Ser beta1 as the characteristic N-terminal nucleophile. A mutation of the wild-type Met alpha140 to Leu in the Bro1 acylase hydrophobic specificity pocket is evident from the electron density and is consistent with the observed specificity change for Bro1 acylase. The electron density for the N-terminal Gln of the alpha-subunit is best modeled by the cyclized pyroglutamate form. Examination of aligned penicillin acylase and cephalosporin acylase primary sequences, in conjunction with the P. rettgeri and Escherichia coli penicillin acylase crystal structures, suggests several mutations that could potentially allow penicillin acylase to accept charged beta-lactam R-groups and to function as a cephalosporin acylase and thus be used in the manufacture of semi-synthetic cephalosporins.
KeywordMeSH Terms
5. O'Halloran  JA, McGrath  BM, Pembroke  JT,     ( 2007 )

The orf4 gene of the enterobacterial ICE, R391, encodes a novel UV-inducible recombination directionality factor, Jef, involved in excision and transfer of the ICE.

FEMS microbiology letters 272 (1)
PMID : 17504243  :   DOI  :   10.1111/j.1574-6968.2007.00747.x    
Abstract >>
The enterobacterial mobile genetic element R391, the prototype ICE (integrating-conjugative element) of the SXT/R391 family, shows increased conjugative transfer following UV irradiation. This is dependent on a functioning R391 orf4 gene, which is adjacent to the element encoded integrase gene, int. orf4 mutants fail to form a detectable circular transfer intermediate, do not show UV induced transfer and show a much reduced general transfer ability. The orf4 gene product, termed Jef (IncJ excision factor), shows little homology to anything currently in the nucleotide or protein databases. It is predicted to encode a 66 amino acid, 8.03 kDa, basic, DNA-binding protein with an iso-electric point of pH 8.1: these characteristics being similar to those of recombinational directionality factors involved in excision. Jef expression is up-regulated upon UV irradiation as demonstrated by real-time reverse transcriptase PCR and is controlled by two element encoded genes orf90 and orf91, which show similarity to the transcriptional activator complex FlhC and FlhD. orf4, orf90 and orf91 are conserved in all the SXT/R391-like elements sequenced to date including SXT, ICESpuPO1 and ICEVchMex1. orf4 is also conserved in other SXT/R391 family members such as R997, R392, R705 and pMERPH as shown by sequencing amplicons from these ICEs generated using orf4 specific primers.
KeywordMeSH Terms
Interspersed Repetitive Sequences
Recombination, Genetic
6. 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
7. 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
8. Paradis  S, Boissinot  M, Paquette  N, Bélanger  SD, Martel  EA, Boudreau  DK, Picard  FJ, Ouellette  M, Roy  PH, Bergeron  MG,     ( 2005 )

Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase beta-subunit.

International journal of systematic and evolutionary microbiology 55 (Pt 5)
PMID : 16166704  :   DOI  :   10.1099/ijs.0.63539-0    
Abstract >>
The phylogeny of enterobacterial species commonly found in clinical samples was analysed by comparing partial sequences of their elongation factor Tu gene (tuf) and of their F-ATPase beta-subunit gene (atpD). An 884 bp fragment for tuf and an 884 or 871 bp fragment for atpD were sequenced for 96 strains representing 78 species from 31 enterobacterial genera. The atpD sequence analysis exhibited an indel specific to Pantoea and Tatumella species, showing, for the first time, a tight phylogenetic affiliation between these two genera. Comprehensive tuf and atpD phylogenetic trees were constructed and are in agreement with each other. Monophyletic genera are Cedecea, Edwardsiella, Proteus, Providencia, Salmonella, Serratia, Raoultella and Yersinia. Analogous trees based on 16S rRNA gene sequences available from databases were also reconstructed. The tuf and atpD phylogenies are in agreement with the 16S rRNA gene sequence analysis, and distance comparisons revealed that the tuf and atpD genes provide better discrimination for pairs of species belonging to the family Enterobacteriaceae. In conclusion, phylogeny based on tuf and atpD conserved genes allows discrimination between species of the Enterobacteriaceae.
KeywordMeSH Terms
Phylogeny
9. McGrath  BM, Pembroke  JT,     ( 2004 )

Detailed analysis of the insertion site of the mobile elements R997, pMERPH, R392, R705 and R391 in E. coli K12.

FEMS microbiology letters 237 (1)
PMID : 15268933  :   DOI  :   10.1016/j.femsle.2004.06.009    
Abstract >>
The IncJ group of mobile elements have not been extensively studied until recently, due to the inability to isolate extrachromosomal DNA from IncJ-strains. Sequence analysis of the prototype IncJ element, R391, revealed it to be a mosaic structure, integrated into the prfC gene in E. coli. Using inverse PCR (iPCR), we localised the other available IncJ elements (R392, R705, R997 and pMERPH) site of insertion to a 17-bp sequence, within the 5' end of prfC at 99.31 min on the E. coli chromosome, and confirmed this for R391. Despite disrupting prfC, the IncJ's encode novel promoter and 5' sequences, restoring function of the disrupted prfC. Sequence analysis of the elements ends revealed that they contain integrase genes, which share extensive homologies among the group, despite being isolated from broad geographic locations. The elements excise from the host chromosome by recombination between their attL and attR sites, with subsequent recombination between the attP sites on the circular forms and the attB sites in the host genomes. The attB site is highly conserved and found in many different bacteria, suggesting a possible broad host range.
KeywordMeSH Terms
Recombination, Genetic
10. Ljubijanki?  G, Konstantinovi?  M, Glisin  V,     ( 1992 )

The primary structure of Providencia rettgeri penicillin G amidase gene and its relationship to other gram negative amidases.

DNA sequence : the journal of DNA sequencing and mapping 3 (3)
PMID : 1472713  :  
Abstract >>
The nucleotide sequence of Penicillin G amidase (PA,E.C.3.5.1.11) of Providencia rettgeri was determined. We aligned our P. rettgeri PA with other known Gram negative periplasmically located beta-lactam amidases. The analysis revealed a high homology with other Enterobacteric amidases (60%-65%), while with similar Pseudomonas sp. amidases the homology exceeded 25%. These homologies indicate their common ancestry.
KeywordMeSH Terms
Genes, Bacterial
11. 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
12. Giammanco  GM, Grimont  PA, Grimont  F, Lefevre  M, Giammanco  G, Pignato  S,     ( 2011 )

Phylogenetic analysis of the genera Proteus, Morganella and Providencia by comparison of rpoB gene sequences of type and clinical strains suggests the reclassification of Proteus myxofaciens in a new genus, Cosenzaea gen. nov., as Cosenzaea myxofaciens comb. nov.

International journal of systematic and evolutionary microbiology 61 (Pt 7)
PMID : 20709916  :   DOI  :   10.1099/ijs.0.021964-0    
Abstract >>
Phylogenetic analysis of partial rpoB gene sequences of type and clinical strains belonging to different 16S rRNA gene-fingerprinting ribogroups within 11 species of enterobacteria of the genera Proteus, Morganella and Providencia was performed and allowed the definition of rpoB clades, supported by high bootstrap values and confirmed by ?2.5 % nucleotide divergence. None of the resulting clades included strains belonging to different species and the majority of the species were confirmed as discrete and homogeneous. However, more than one distinct rpoB clade could be defined among strains belonging to the species Proteus vulgaris (two clades), Providencia alcalifaciens (two clades) and Providencia rettgeri (three clades), suggesting that some strains represent novel species according to the genotypes outlined by rpoB gene sequence analysis. Percentage differences between the rpoB gene sequence of the type strain of Proteus myxofaciens and other members of the same genus (17.3-18.9 %) were similar to those calculated amongst strains of the genus Providencia (16.4-18.7 %), suggesting a genetic distance at the genus-level between Proteus myxofaciens and the rest of the Proteus-Providencia group. Proteus myxofaciens therefore represents a member of a new genus, for which the name Cosenzaea gen. nov., is proposed.
KeywordMeSH Terms
Phylogeny
13. Juneja  P, Lazzaro  BP,     ( 2009 )

Providencia sneebia sp. nov. and Providencia burhodogranariea sp. nov., isolated from wild Drosophila melanogaster.

International journal of systematic and evolutionary microbiology 59 (Pt 5)
PMID : 19406801  :   DOI  :   10.1099/ijs.0.000117-0    
Abstract >>
Multiple isolates of the genus Providencia were obtained from the haemolymph of wild-caught Drosophila melanogaster fruit flies. Sixteen isolates were distinguished from the six previously described species based on 16S rRNA gene sequences. These isolates belonged to two distinct groups, which we propose each comprise previously undescribed species. Two isolates, designated A(T) and B(T), were characterized by DNA sequences of the fusA, lepA, leuS, gyrB and ileS housekeeping genes, whole-genome DNA-DNA hybridizations with their nearest relatives and utilization of substrates for metabolism. The closest phylogenetic relatives of strain A(T) are strain B(T) (86.9 % identity for the housekeeping genes) and Providencia stuartii DSM 4539(T) (86.0 % identity). The closest phylogenetic relatives of strain B(T) are strain A(T) (86.9 % identity) and P. stuartii DSM 4539(T) (86.6 % identity). The type strains of described species in this genus shared between 84.1 and 90.1 % identity for these sequences. DNA-DNA hybridization between the strain pairs A(T)-B(T), A(T)-P. stuartii DSM 4539(T) and B(T)-P. stuartii DSM 4539(T) all resulted in less than 25 % relatedness. In addition, patterns of utilization of amygdalin, arbutin, aesculin, salicin, d-sorbitol, trehalose, inositol, d-adonitol and d-galactose distinguish strains A(T) and B(T) from other members of this genus. Strains A(T) and B(T) therefore represent novel species, for which the names Providencia sneebia sp. nov. (type strain A(T) =DSM 19967(T) =ATCC BAA-1589(T)) and Providencia burhodogranariea sp. nov. (type strain B(T) =DSM 19968(T) =ATCC BAA-1590(T)) are proposed.
KeywordMeSH Terms
14. Revilla  C, Garcillán-Barcia  MP, Fernández-López  R, Thomson  NR, Sanders  M, Cheung  M, Thomas  CM, de la Cruz  F,     ( 2008 )

Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids.

Antimicrobial agents and chemotherapy 52 (4)
PMID : 18268088  :   DOI  :   10.1128/AAC.00982-07     PMC  :   PMC2292564    
Abstract >>
DNA sequence analysis of five IncW plasmids (R388, pSa, R7K, pIE321, and pIE522) demonstrated that they share a considerable portion of their genomes and allowed us to define the IncW backbone. Among these plasmids, the backbone is stable and seems to have diverged recently, since the overall identity among its members is higher than 95%. The only gene in which significant variation was observed was trwA; the changes in the coding sequence correlated with parallel changes in the corresponding TrwA binding sites at oriT, suggesting a functional connection between both sets of changes. The present IncW plasmid diversity is shaped by the acquisition of antibiotic resistance genes as a consequence of the pressure exerted by antibiotic usage. Sequence comparisons pinpointed the insertion events that differentiated the five plasmids analyzed. Of greatest interest is that a single acquisition of a class I integron platform, into which different gene cassettes were later incorporated, gave rise to plasmids R388, pIE522, and pSa, while plasmids R7K and pIE321 do not contain the integron platform and arose in the antibiotic world because of the insertion of several antibiotic resistance transposons.
KeywordMeSH Terms
Evolution, Molecular
15. Paiva  MC, Reis  MP, Costa  PS, Dias  MF, Bleicher  L, Scholte  LLS, Nardi  RMD, Nascimento  AMA,     ( 2017 )

Identification of new bacteria harboring qnrS and aac(6')-Ib/cr and mutations possibly involved in fluoroquinolone resistance in raw sewage and activated sludge samples from a full-scale WWTP.

Water research 110 (N/A)
PMID : 27984803  :   DOI  :   10.1016/j.watres.2016.11.056    
Abstract >>
Wastewater treatment plants (WWTPs) harbor bacteria and antimicrobial resistance genes, favoring gene exchange events and resistance dissemination. Here, a culture-based and metagenomic survey of qnrA, qnrB, qnrS, and aac(6')-Ib genes from raw sewage (RS) and activated sludge (AS) of a full-scale municipal WWTP was performed. A total of 96 bacterial isolates were recovered from nalidixic acid-enrichment cultures. Bacteria harboring the aac(6')-Ib gene predominated in RS, whereas qnrS-positive isolates were specific to AS. Novel qnrS- and aac(6')-Ib-cr positive species were identified: Morganella morganii, Providencia rettgeri, and Pseudomonas guangdongensis (qnrS), and Alcaligenes faecalis and P. rettgeri (aac(6')-Ib-cr). Analysis of qnrS and aac(6')-Ib sequences from isolates and clone libraries suggested that the diversity of qnrS is wider than that of aac(6')-Ib. A large number of amino acid mutations were observed in the QnrS and AAC(6')-Ib proteins at previously undetected positions, whose structural implications are not clear. An accumulation of mutations at the C72, Q73, L74, A75 and M76 positions of QnrS, and D181 of AAC(6')-Ib might be important for resistance. These findings add significant information on bacteria harboring qnrS and aac(6')-Ib genes, and the presence of novel mutations that may eventually emerge in clinical isolates.
KeywordMeSH Terms
Activated sludge
Bacteria
Quinolone
Raw sewage
aac(6′)Ib
aac(6′)Ib-cr
qnrS
Activated sludge
Bacteria
Quinolone
Raw sewage
aac(6′)Ib
aac(6′)Ib-cr
qnrS
Activated sludge
Bacteria
Quinolone
Raw sewage
aac(6′)Ib
aac(6′)Ib-cr
qnrS
Activated sludge
Bacteria
Quinolone
Raw sewage
aac(6′)Ib
aac(6′)Ib-cr
qnrS
Activated sludge
Bacteria
Quinolone
Raw sewage
aac(6′)Ib
aac(6′)Ib-cr
qnrS
Sewage
16. Yugendran  T, Harish  BN,     ( 2016 )

High incidence of plasmid-mediated quinolone resistance genes among ciprofloxacin-resistant clinical isolates of Enterobacteriaceae at a tertiary care hospital in Puducherry, India.

PeerJ 4 (N/A)
PMID : 27168994  :   DOI  :   10.7717/peerj.1995     PMC  :   PMC4860338    
Abstract >>
Background. Plasmid-mediated quinolone resistance (PMQR) has received considerable attention recently. Data analysis in Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER) revealed 75% of the Enterobacteriaceae isolates to be ciprofloxacin-resistant in 2012. Few reports regarding the prevalence of PMQR are available from India. Hence, the present study was carried out to ascertain the prevalence of PMQR genes among clinical isolates of ciprofloxacin-resistant Enterobacteriaceae in JIPMER. Methods. The study included 642 ciprofloxacin-resistant clinical Enterobacteriaceae isolates. JIPMER hospital's annual consumption data for fluoroquinolones were retrieved from the Department of Pharmacy. The test isolates were screened for the presence of qnr A, B, D, S and aac(6')-Ib-cr genes. PMQR-positive isolates alone were tested for the presence of class I (intI1) and class II (intI2) integrons. Randomly selected PCR amplicons were sequenced and analysed using MEGA software. A total of 30 PMQR strains chosen at random were assessed for the transferability of the PMQR genes. Results. A majority of the strains exhibited high MIC values with 106 strains exhibiting MIC values >256 ?g/mL. The aac(6')-Ib-cr gene had the highest prevalence at 64% (414) while, qnrB and qnrS genes were present in 15% (97) and 10% (64) of the isolates respectively. None of the strains were positive for qnrA and qnrD. All PMQR-positive isolates were screened for class I (intI1) and class II (intI2) integrons. Class I integron was found to be predominant among the test isolates with a few of them carrying both the classes of integrons. Transferability of PMQR genes to transconjugants was identified. Conclusion. The incidence of PMQR genes in the tertiary-care setup of the JIPMER hospital was found to be high which could be probably due to the increased prescription of fluoroquinolones. Thus, there is a need for rational usage of fluoroquinolones.
KeywordMeSH Terms
Enterobacteriaceae
Fluoroquinolone resistance
PMQR
aac(6’)-Ib-cr
qnr
Enterobacteriaceae
Fluoroquinolone resistance
PMQR
aac(6’)-Ib-cr
qnr
Enterobacteriaceae
Fluoroquinolone resistance
PMQR
aac(6’)-Ib-cr
qnr
Enterobacteriaceae
Fluoroquinolone resistance
PMQR
aac(6’)-Ib-cr
qnr
Enterobacteriaceae
Fluoroquinolone resistance
PMQR
aac(6’)-Ib-cr
qnr
Enterobacteriaceae
Fluoroquinolone resistance
PMQR
aac(6’)-Ib-cr
qnr
Enterobacteriaceae
Fluoroquinolone resistance
PMQR
aac(6’)-Ib-cr
qnr
Enterobacteriaceae
Fluoroquinolone resistance
PMQR
aac(6’)-Ib-cr
qnr
Enterobacteriaceae
Fluoroquinolone resistance
PMQR
aac(6’)-Ib-cr
qnr
17. Dropa  M, Ghiglione  B, Matté  MH, Balsalobre  LC, Lincopan  N, Matté  GR, Gutkind  G, Power  P,     ( 2015 )

Molecular and biochemical characterization of CTX-M-131, a natural Asp240Gly variant derived from CTX-M-2, produced by a Providencia rettgeri clinical strain in S?o Paulo, Brazil.

Antimicrobial agents and chemotherapy 59 (3)
PMID : 25583719  :   DOI  :   10.1128/AAC.04116-14     PMC  :   PMC4325771    
Abstract >>
CTX-M-131 is a natural Asp240Gly variant from the CTX-M-2 group detected in a Providencia rettgeri clinical strain from Brazil. Molecular analysis showed that blaCTX-M-131 was inserted in a complex class 1 integron harbored by a 112-kb plasmid, which has not been previously described as a platform for CTX-M-encoding genes with the Asp240Gly mutation. Steady-state kinetic parameters showed that the enzyme has a typical cefotaximase catalytic profile and an enhanced activity against ceftazidime.
KeywordMeSH Terms
18. Mataseje  LF, Boyd  DA, Lefebvre  B, Bryce  E, Embree  J, Gravel  D, Katz  K, Kibsey  P, Kuhn  M, Langley  J, Mitchell  R, Roscoe  D, Simor  A, Taylor  G, Thomas  E, Turgeon  N, Mulvey  MR, N/A  N/A,     ( 2014 )

Complete sequences of a novel blaNDM-1-harbouring plasmid from Providencia rettgeri and an FII-type plasmid from Klebsiella pneumoniae identified in Canada.

The Journal of antimicrobial chemotherapy 69 (3)
PMID : 24275114  :   DOI  :   10.1093/jac/dkt445    
Abstract >>
Emergence of plasmids harbouring bla(NDM-1) is a major public health concern due to their association with multidrug resistance and their potential mobility. PCR was used to detect bla(NDM-1) from clinical isolates of Providencia rettgeri (PR) and Klebsiella pneumoniae (KP). Antimicrobial susceptibilities were determined using Vitek 2. The complete DNA sequence of two bla(NDM-1) plasmids (pPrY2001 and pKp11-42) was obtained using a 454-Genome Sequencer FLX. Contig assembly and gap closures were confirmed by PCR-based sequencing. Comparative analysis was done using BLASTn and BLASTp algorithms. Both clinical isolates were resistant to all �]-lactams, carbapenems, aminoglycosides, ciprofloxacin and trimethoprim/sulfamethoxazole, and susceptible to tigecycline. Plasmid pPrY2001 (113 295 bp) was isolated from PR. It did not show significant homology to any known plasmid backbone and contained a truncated repA and novel repB. Two bla(NDM-1)-harbouring plasmids from Acinetobacter lwoffii (JQ001791 and JQ060896) shared 100% similarity to a 15 kb region that contained bla(NDM-1). pPrY2001 also contained a type II toxin/antitoxin system. pKp11-42 (146 695 bp) was isolated from KP. It contained multiple repA genes. The plasmid backbone had the highest homology to the IncFIIk plasmid type (51% coverage, 100% nucleotide identity). The bla(NDM-1) region was unique in that it was flanked upstream by IS3000 and downstream by a novel transposon designated Tn6229. pKp11-42 also contained a number of mutagenesis and plasmid stability proteins. pPrY2001 differed from all known plasmids due to its novel backbone and repB. pKp11-42 was similar to IncFIIk plasmids and contained a number of genes that aid in plasmid persistence.
KeywordMeSH Terms
Enterobacteriaceae
carbapenemases
replicon type
Enterobacteriaceae
carbapenemases
replicon type
Plasmids
19. Tada  T, Miyoshi-Akiyama  T, Dahal  RK, Sah  MK, Ohara  H, Shimada  K, Kirikae  T, Pokhrel  BM,     ( 2014 )

NDM-1 Metallo-�]-Lactamase and ArmA 16S rRNA methylase producing Providencia rettgeri clinical isolates in Nepal.

BMC infectious diseases 14 (N/A)
PMID : 24484534  :   DOI  :   10.1186/1471-2334-14-56     PMC  :   PMC3922589    
Abstract >>
Drug-resistant Providencia rettgeri producing metallo-�]-lactamase and 16S rRNA methylase has been reported in several countries. We analyzed P. rettgeri clinical isolates with resistance to carbapenems and aminoglycosides in a hospital in Nepal. Five clinical isolates of multidrug-resistant P. rettgeri were obtained in a hospital in Nepal. Antimicrobial susceptibilities were determined using the microdilution method and entire genomes were sequenced to determine drug-resistant genes. Epidemiological analysis was performed by pulsed-field gel electrophoresis. Four of the 5 isolates were resistant to carbapenems (imipenem and meropenem), with MICs ?16 mg/L, with the remaining isolate showing intermediate resistance to imipenem, with an MIC of 2 mg/L and susceptibility to meropenem with an MIC ?1 mg/L. All 5 isolates had blaVEB-1. Of the 4 carbapenem-resistant strains, 3 had blaNDM-1 and 1 had blaOXA-72. All isolates were highly resistant to aminoglycosides (MICs ?1,024 mg/L) and harbored armA. As the result of pulsed-field gel electrophoresis pattern analysis in the 5 P. rettgeri isolates, 4 had identical PFGE patterns and the fifth showed 95.7% similarity. This is the first report describing multidrug-resistant P. rettgeri strains harboring blaNDM-1 or blaOXA-72 and armA isolated from patients in Nepal.
KeywordMeSH Terms
20. Guillard  T, Cambau  E, Neuwirth  C, Nenninger  T, Mbadi  A, Brasme  L, Vernet-Garnier  V, Bajolet  O, de Champs  C,     ( 2012 )

Description of a 2,683-base-pair plasmid containing qnrD in two Providencia rettgeri isolates.

Antimicrobial agents and chemotherapy 56 (1)
PMID : 21986831  :   DOI  :   10.1128/AAC.00081-11     PMC  :   PMC3256040    
Abstract >>
qnr genes are plasmid-mediated quinolone resistance genes mainly harbored on large conjugative multiresistant plasmids. The qnrD gene was recently observed in Salmonella enterica on a small nonconjugative plasmid (p2007057). We describe two strains of Providencia rettgeri harboring qnrD on nonconjugative plasmids. The plasmids were 99% identical, with 2,683 bp and four open reading frames, including qnrD, but exhibited only 53% identity with the plasmid found in S. enterica.
KeywordMeSH Terms
21. Aibinu  IE, Pfeifer  Y, Ogunsola  F, Odugbemi  T, Koenig  W, Ghebremedhin  B,     ( 2011 )

Emergence of �]-lactamases OXA-10, VEB-1 and CMY in Providencia spp. from Nigeria.

The Journal of antimicrobial chemotherapy 66 (8)
PMID : 21609982  :   DOI  :   10.1093/jac/dkr197    
Abstract >>
N/A
KeywordMeSH Terms
beta-Lactam Resistance
22.     ( 1993 )

Sequence of the Providencia rettgeri lexA gene and its control region.

Nucleic acids research 21 (9)
PMID : 8502572  :   DOI  :   10.1093/nar/21.9.2256     PMC  :   PMC309499    
Abstract >>
N/A
KeywordMeSH Terms
Genes, Bacterial
Serine Endopeptidases
23. Shin  S, Jeong  SH, Lee  H, Hong  JS, Park  MJ, Song  W,     ( 2018 )

Emergence of multidrug-resistant Providencia rettgeri isolates co-producing NDM-1 carbapenemase and PER-1 extended-spectrum �]-lactamase causing a first outbreak in Korea.

Annals of clinical microbiology and antimicrobials 17 (1)
PMID : 29728111  :   DOI  :   10.1186/s12941-018-0272-y     PMC  :   PMC5935979    
Abstract >>
Nosocomial outbreak due to carbapenem-resistant Enterobacteriaceae has become serious challenge to patient treatment and infection control. We describe an outbreak due to a multidrug-resistant Providencia rettgeri from January 2016 to January 2017 at a University Hospital in Seoul, Korea. A total of eight non-duplicate P. rettgeri isolates were discovered from urine samples from eight patients having a urinary catheter and admitted in a surgical intensive care unit. The �]-lactamase genes were identified using polymerase chain reaction and direct sequencing, and strain typing was done with pulsed-field gel electrophoresis (PFGE). All isolates showed high-level resistance to extended-spectrum cephalosporins, aztreonam, meropenem, ertapenem, ciprofloxacin, and amikacin. They harbored the blaNDM-1 carbapenemase and the blaPER-1 type extended-spectrum �]-lactamases genes. PFGE revealed that all isolates from eight patients were closely related strains. The 13-month outbreak ended following reinforcement of infection control measures, including contact isolation precautions and environmental disinfection. This is the first report of an outbreak of a P. rettgeri clinical isolates co-producing NDM-1 and PER-1 �]-lactamase.
KeywordMeSH Terms
NDM-1
Outbreak
PER-1
Providencia rettgeri
Urinary tract infection
Disease Outbreaks
24.     ( 2012 )

Emergence of New Delhi metallo-�]-lactamase in Jerusalem, Israel.

International journal of antimicrobial agents 40 (6)
PMID : 22951226  :   DOI  :   10.1016/j.ijantimicag.2012.07.011    
Abstract >>
N/A
KeywordMeSH Terms

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