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PubMed1999

Transposon Tn21, flagship of the floating genome.

The transposon Tn21 and a group of closely related transposons (the Tn21 family) are involved in the global dissemination of antibiotic resistance determinants in gram-negative facultative bacteria. The molecular basis for their involvement is carriage by the Tn21 family of a mobile DNA element (the integron) encoding a site-specific system for the acquisition of multiple antibiotic resistance genes. The paradigm example, Tn21, also carries genes for its own transposition and a mercury resistance (mer) operon. We have compiled the entire 19,671-bp sequence of Tn21 and assessed the possible origins and functions of the genes it contains. Our assessment adds molecular detail to previous models of the evolution of Tn21 and is consistent with the insertion of the integron In2 into an ancestral Tn501-like mer transposon. Codon usage analysis indicates distinct host origins for the ancestral mer operon, the integron, and the gene cassette and two insertion sequences which lie within the integron. The sole gene of unknown function in the integron, orf5, resembles a puromycin-modifying enzyme from an antibiotic producing bacterium. A possible seventh gene in the mer operon (merE), perhaps with a role in Hg(II) transport, lies in the junction between the integron and the mer operon. Analysis of the region interrupted by insertion of the integron suggests that the putative transposition regulator, tnpM, is the C-terminal vestige of a tyrosine kinase sensor present in the ancestral mer transposon. The extensive dissemination of the Tn21 family may have resulted from the fortuitous association of a genetic element for accumulating multiple antibiotic resistances (the integron) with one conferring resistance to a toxic metal at a time when clinical, agricultural, and industrial practices were rapidly increasing the exposure to both types of selective agents. The compendium offered here will provide a reference point for ongoing observations of related elements in multiply resistant strains emerging worldwide.

Base Sequence↗
PubMed2005

Molecular mechanisms of resistance in multidrug-resistant serovars of Salmonella enterica isolated from foods in Germany.

OBJECTIVES: The objectives of this study were to determine antimicrobial susceptibility and to characterize the molecular mechanisms of multidrug resistance among German food-borne Salmonella isolates of different serovars. METHODS: A total of 319 epidemiologically independent multidrug-resistant isolates from German foodstuffs comprising 25 different serovars were tested for their antimicrobial susceptibility by broth microdilution. The presence of antimicrobial resistance genes, integrons of classes 1 and 2 and their integrated resistance gene cassettes as well as the Salmonella genomic island 1 (SGI1) was investigated by PCR and DNA sequencing. Localization of integrons and relevant resistance genes was done by Southern hybridization. Sequence analysis revealed mutations in the quinolone resistance-determining region of the gyrA gene. RESULTS: The most prevalent resistances found in the multidrug-resistant serovars of Salmonella enterica from foods were to streptomycin (94%), sulfamethoxazole (92%), tetracycline (81%), ampicillin (73%), spectinomycin (72%), chloramphenicol (48%) and trimethoprim (27%). Twenty-four resistance genes covering six antimicrobial families (beta-lactams, aminoglycosides, phenicols, sulphonamides, tetracycline, and trimethoprim) were identified in the food isolates, many of them integrated as gene cassettes in class 1 and class 2 integrons. Class 1 integrons were detected in 65% of the multidrug-resistant Salmonella isolates comprising 16 different serovars, while class 2 integrons were found in 10% of the isolates belonging to two serovars only. The results demonstrate a clear predominance of both SGI1-borne resistance genes and class 1 integrons in Salmonella serovar Typhimurium DT104 and of class 2 integrons in Salmonella serovar Paratyphi B (d-tartrate positive). Nalidixic acid resistance found in 15% of the isolates was associated with single mutations in the gyrA gene. CONCLUSIONS: This study confirms the role of foods of animal and other origin as a reservoir of multidrug-resistant Salmonella and underlines the need for continuing surveillance of food-borne zoonotic bacterial pathogens along the food chain.

Anti-Bacterial Agents↗
PubMed2003

Antibiotic selective pressure for the maintenance of antibiotic resistant genes in coliform bacteria isolated from the aquatic environment.

Coliform bacteria isolated from the aquatic environment were investigated for antibiotic susceptibility and detailed structures of class 1 integrons. A high proportion of isolates were found to be resistant to sulfamethoxazole, aminoglycosides, and beta-lactams. The 750 (53.6%) isolates were resistant to one or more of the antibiotics tested out of 1,400 coliform bacteria. Based on the MIC of antibiotics and antibiogram, 150 isolates were selected and further studied for class 1 integrons. The intI1 gene was found in 36 (24.0%) of the 150 isolates. Twelve isolates carried the gene cassettes responsible for antibiotic resistance, while no gene cassettes were found in 24 isolates. Seven different genes, dfrA5, dfrA7, dfrA12, dfrA17, aaA2, aaA5, and aad(3'), were detected in gene cassettes. The dfrA and aad genes located on class 1 integrons were responsible for resistance to trimethoprim and aminoglycosides. The remaining 24 coliform bacteria had the incomplete or non-functional class 1 integrons. These results indicated that antibiotic selective pressures may play an important role to maintain gene cassettes of class 1 integrons and in the absence of sustained antibiotic pressures, such as the aquatic environment, coliform bacteria may carry empty or non-functional class 1 integrons.

Drug Resistance, Microbial↗
PubMed2006

[Bacterial superintegrons, a source of new genes with adaptive functions].

Data on the structural organization of the platform of integrons, gene cassettes, and integrons with integrated cassettes of genes encoding drug resistance are briefly summarized. Data obtained during recent years about superintegrons or chromosomal integrons, characteristics of their organization, the presence of genes with known adaptive and unidentified functions in them, as well as data on the differences between superintegrons and previously described multiple resistance integrons, are considered in more detail. Studies that provide evidence for translocations of gene cassettes from stationary chromosomal integrons into integrons associated with mobile elements resulting in gene flows in natural bacterial populations, which favors their survival and adaptation to changing environment, are also reviewed.

Adaptation, Biological↗
PubMed2002

Evolution of multiresistance in nontyphoid salmonella serovars from 1984 to 1998 in Argentina.

Molecular evolution of multiresistance in nontyphoid Salmonella spp. was investigated with 155 isolates obtained in Argentina from 1984 to 1998. In 74 isolates obtained from 1984 to 1988 resistance was associated with the presence of Tn3, Tn9, class I (In0) and II (Tn7) integrons, and the aac(3)-IIa gene. Extended-spectrum cephalosporin (ESC) resistance in Salmonella spp. emerged in 1989, and 81 isolates resistant to at least one ESC and one aminoglycoside were collected thereafter. Among these, two patterns of antimicrobial resistance mechanisms were found: from 1989 to 1992, resistance was related to the spreading of Tn1331 and bla(CTX-M-2), in addition to the persistence of In0 and Tn7. From 1993 to 1998, several integrons were added to the first pattern and three integron groups (IG), namely, IG1 (38% of the isolates), IG2 (51%), and IG3 (11%), were identified. At least two beta-lactamase genes were detected in 65% of the isolates (after 1989) by PCR analysis. Furthermore, five beta-lactamase genes, bla(CTX-M-(2)), bla(OXA-9), bla(OXA-2), bla(TEM-1), and bla(PER-2), were found in two isolates. The bla(CTX-M-2) gene was found in several complex sulI-type integrons with different rearrays within the variable region of class I integrons, suggesting evolution of these integrons in nontyphoid Salmonella. In conclusion, progressive acquisition and accumulation of plasmid-mediated resistance determinants occurred from 1984 to 1998 in nontyphoid Salmonella isolates of the most prevalent serovars from Argentina. It is suggested that antimicrobial resistance mechanisms in these bacteria may have been the consequence of plasmid exchange between Salmonella enterica serovar Typhimurium and Escherichia coli or Shigella flexneri and/or spreading of mobile elements from the nosocomial environment.

Argentina↗
PubMed2001

Identification of epidemic strains of Acinetobacter baumannii by integrase gene PCR.

Forty-eight clinical Acinetobacter isolates with different epidemic behavior were investigated for the presence of integrons and plasmids and for antibiotic susceptibility. Integrons were demonstrated in 50% of the strains by an integrase gene PCR. Epidemic strains of Acinetobacter baumannii were found to contain significantly more integrons than nonepidemic strains. Also, the presence of integrons was significantly correlated with simultaneous resistance to several antibiotics. Plasmids were detected in 42% of the strains. However, there was no significant correlation between the numbers of plasmids and integrons in Acinetobacter species strains, no significant difference in the number of plasmids between epidemic and nonepidemic A. baumannii strains, and no significant correlation between the presence of plasmids and antibiotic resistance. Hence, it is likely that integrons play an important role in antibiotic resistance and thereby in the epidemic behavior of A. baumannii. Because the integrase gene PCR identified almost three-quarters of the epidemic A. baumannii isolates (17 of 23), this seems to be a rapid and simple technique for the routine screening and identification of clinical A. baumannii isolates with epidemic potential.

Acinetobacter↗
PubMed2004

Italian metallo-beta-lactamases: a national problem? Report from the SENTRY Antimicrobial Surveillance Programme.

OBJECTIVES: As part of the SENTRY Antimicrobial Surveillance Programme, 383 non-replicative randomly collected Pseudomonas aeruginosa isolates were collected during 1999-2002. These strains originated from three geographically distinct hospitals within Italy: Genoa (Northern Italy); Rome and Catania (Sicily), and were further studied to identify the prevalence of metallo-beta-lactamase (MbetaL) alleles across Italy and to determine their genetic details. METHODS: Multidrug-resistant (MDR) strains were identified by MIC analysis followed by genotyping and PCR-based strategies. RESULTS: Initial MIC analysis identified 31 MDR isolates that displayed an Etest MbetaL-positive phenotype. Of these, 25 produced either the MbetaL VIM-1 or IMP-13 as detected by PCR and sequencing. VIM-1-producing isolates were found at all sites, whereas IMP-13-producing isolates were only found in Rome. MbetaL-producing isolates were found at all Italian SENTRY sites and together amounted to 6.5% of all P. aeruginosa isolates. Genetic analysis indicated that many strains contained multiple integrons and identified two novel MbetaL integrons, one from the site in Genoa and one from Sicily. Integrons identical in structure and sequence to In70, the first identified and characterized bla(VIM)-containing integron from Verona, were found in isolates with distinct ribotypes at the Roman and Sicilian sites indicating that this integron has recently disseminated across Italy. All 25 MbetaL-producing isolates were genetically linked in that all isolates contained Tn5051 sequences and all harboured the insertion sequence IsPa7 which may be involved in the mobilization of these resistance alleles. CONCLUSIONS: Taken together, these results indicate that Italy has a nationwide problem of MDR P. aeruginosa produced by mobile MbetaL genes.

Anti-Bacterial Agents↗
PubMed2006

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

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.

Anti-Infective Agents↗
PubMed2006

SGI1-K, a variant of the SGI1 genomic island carrying a mercury resistance region, in Salmonella enterica serovar Kentucky.

A multiple-antibiotic-resistant Salmonella enterica serovar Kentucky strain was found to contain SGI1-K, a variant form of the Salmonella genomic island 1 (SGI1) with an In4-type class 1 integron that contains only one cassette array, aacCA5-aadA7, and an adjacent mercury resistance module. Part of the 3'-conserved segment (3'-CS) of the integron, together with the inverted short segment from the right-hand end of the integron transposition module normally found between the 3'-CS and IS6100 in In4 family integrons, has been removed by an IS6100-mediated deletion. IRt, the right-hand inverted repeat found at the outer end of the integron, abuts a mercury resistance region instead of the usual SGI1 backbone segment. The mer module is a hybrid of those found in Tn501 and Tn21. This mer region and a further uncharacterized segment of at least 10 kb appear to have been incorporated between IRt and the SGI1 backbone. These findings demonstrate that the multidrug resistance region in SGI1 can incorporate new DNA segments in the same way as multiple antibiotic resistance regions in plasmids.

Base Sequence↗
PubMed2006

Emergence of DHA-1-producing Klebsiella spp. in the Parisian region: genetic organization of the ampC and ampR genes originating from Morganella morganii.

Eleven Klebsiella pneumoniae clinical isolates and one Klebsiella oxytoca clinical isolate showing various pulsed-field gel electrophoresis types and producing an inducible DHA-1 class C beta-lactamase were isolated in the Parisian region between 1998 and 2003. The aim of this study was to compare the genetic organization of the bla(DHA-1) genes in this collection of clinical isolates. In four isolates, the Morganella morganii-derived genomic region containing bla(DHA-1) was inserted in an entire complex sul1-type integron, including a region common to In6-In7 (CR1), as previously described in a bla(DHA-1)-producing Salmonella enterica serovar Enteritidis KF92 isolate from Saudi Arabia in 1992. Different gene cassette arrays were characterized in each of these integrons. In two of them, an additional 10-kb fragment was inserted between the CR1 and the M. morganii-derived region and was similar to the sap (ABC transporter family) and psp (phage shock protein) operons originated from Salmonella enterica serovar Typhimurium. The length of the M. morganii region was variable, suggesting that several independent recombination events have occurred and that open reading frame orf513 encodes a recombinase involved in the mobilization of the resistance genes. The genetic organization of bla(DHA-1) was identical in the eight other isolates. This structure is likely derived from a complex integron following the insertion of IS26, leading to the deletion of the first part of integron. The horizontal transfer of one plasmid carrying that truncated integron was shown for seven of these isolates.

Bacterial Proteins↗
PubMed2005

Towards more virulent and antibiotic-resistant Salmonella?

Salmonella are well-known pathogens. Virulence determinants can be present on the chromosome, usually encoded on pathogenicity islands, or on plasmids and bacteriophages. Antibiotic resistance determinants usually are encoded on plasmids, but can also be present on the multidrug resistance region of Salmonella Genomic Island 1 (SGI1). Virulence plasmids show a remarkable diversity in the combination of virulence factors they encode, which appears to adapt them to specific hosts and the ability to cause gastroenteritidis or systemic disease. The appearance of plasmids with two replicons may help to extend the host range of these plasmids and thereby increase the virulence of previously non- or low pathogenic serovars. Antibiotic resistance among Salmonella is also increasing. This increase is not only in the percentage isolates resistant to a particular antibiotic, but also the development of resistance against newer antibiotics. The increased occurrence of integrons is particularly worrying. Integrons can harbour a varying set of antibiotic resistance encoding gene cassettes. Gene cassettes can be exchanged between integrons. Although the gene cassettes currently present in Salmonella integrons encode for older antibiotics (however, some still frequently used) gene cassettes encoding resistance against the newest antibiotics has been documented in Enterobacteriaceae. Furthermore, beta-lactamases with activity against broad-spectrum cephalosporins, which are often used in empiric therapy, have been found associated with integrons. So, empiric treatment of Salmonella infections becomes increasingly more difficult. The most worrisome finding is that virulence and resistance plasmids form cointegrates. These newly formed plasmids can be selected by antibiotic pressure and thereby for virulence factors. Taken together these trends may lead to more virulent and antibiotic-resistant Salmonella.

Drug Resistance, Bacterial↗
PubMed2005

DNA sequence analysis of the genetic environment of various blaCTX-M genes.

OBJECTIVES: Over a 3 year period (2000-2003) 21 Escherichia coli, 5 Klebsiella pneumoniae, 1 Serratia marcescens and 1 Proteus mirabilis producing CTX-M-type beta-lactamase were collected from five different hospitals in Paris, France. This study was conducted to analyse the genetic environment of these 28 bla(CTX-M) genes. METHODS: Antimicrobial susceptibility testing was performed by the disc diffusion method and MICs of various beta-lactams were determined by an agar dilution method. PCR was used to detect and sequence alleles encoding CTX-M, TEM, SHV and CMY enzymes. The genetic environment was analysed by amplification and direct sequencing using various set of PCR primers or cloning in pBK-CMV. RESULTS: Sequence analysis revealed that these isolates contained seven different bla(CTX-M) genes: bla(CTX-M-1) (4 strains), bla(CTX-M-2) (2 strains), bla(CTX-M-3) (4 strains), bla(CTX-M-9) (1 strain), bla(CTX-M-14) (5 strains), bla(CTX-M-15) (11 strains), bla(CTX-M-24) (1 strain). TEM-1 was associated with CTX-M-type enzymes in 15 isolates. Two strains produced both CTX-M-15 and SHV-2 or CTX-M-14 and CMY-2. In 25 strains the insertion sequence ISEcp1 was located upstream of the 5' end of the bla(CTX-M) gene. Among these strains, in five isolates, ISEcp1 was disrupted by insertion sequences such as IS26 (in three of them) or IS1 or IS10. Insertion sequence IS903 was found downstream of bla(CTX-M-14) or bla(CTX-M-24). Examination of the other three bla(CTX-M) genes (two bla(CTX-M-2) and one bla(CTX-M-9)) by cloning, sequencing and PCR analysis revealed the presence of complex Class 1 integrons, In35, an integron similar to In60 and a novel integron. CONCLUSIONS: This work further confirmed the predominant role of ISEcp1 in the mobilization of bla(CTX-M) genes of the CTX-M-1 cluster and the presence of In35, of an integron similar to In60 and a novel complex Class 1 integron.

Base Sequence↗
PubMed2002

Characterization of variant Salmonella genomic island 1 multidrug resistance regions from serovars Typhimurium DT104 and Agona.

Strains of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (DT104) and S. enterica serovar Agona (Agona) have been found to harbor Salmonella genomic island 1 (SGI1), a 43-kb genomic region that contains many of the drug resistance genes. Such strains are resistant to ampicillin (pse-1), chloramphenicol/florfenicol (floR), streptomycin/spectinomycin (aadA2), sulfonamides (sul1), and tetracycline [tet(G)] (commonly called the ACSSuT phenotype). All five resistance genes are found in a 13-kb multidrug resistance (MDR) region consisting of an unusual class I integron structure related to In4. We examined DT104 and Agona strains that exhibited other resistance phenotypes to determine if the resistance genes were associated with variant SGI1 MDR regions. All strains were found to harbor variant SGI1-like elements by using a combination of Southern hybridization, PCR mapping, and sequencing. Variant SGI1-like elements were found with MDR regions consisting of (i) an integron consisting of the SGI1 MDR region with the addition of a region containing a putative transposase gene (orf513) and dfrA10 located between duplicated qacEDelta1/sulI genes (SGI1-A; ACSSuTTm); (ii) an integron with either an aadA2 (SSu) or a pse-1 (ASu) cassette (SGI1-C and SGI1-B, respectively); (iii) an integron consisting of the SGI1-C MDR region plus an orf513/dfrA10 region as in SGI1-A (SGI1-D; ASSuTm; ampicillin resistance due to a TEM beta-lactamase); and (iv) an integron related to that in SGI1 but which contains a 10-kb inversion between two copies of IS6100, one which is inserted in floR (SGI1-E; ASSuT). We hypothesize that the MDR of SGI1 is subject to recombinational events that lead to the various resistance phenotypes in the Salmonella strains in which it is found.

Amino Acid Sequence↗
PubMed2005

Emergence of plasmid-mediated quinolone resistance in Escherichia coli in Europe.

Although quinolone resistance results mostly from chromosomal mutations, it may also be mediated by a plasmid-encoded qnr gene in members of the family Enterobacteriaceae. Thus, 297 nalidixic-acid resistant strains of 2,700 Escherichia coli strains that had been isolated at the Bicetre Hospital (Le Kremlin-Bicetre, France) in 2003 were screened for qnr by PCR. A single E. coli isolate that carried a ca. 180-kb conjugative plasmid encoding a qnr determinant was identified. It conferred low-level resistance to quinolones and was associated with a chromosomal mutation in subunit A of the topoisomerase II gene. The qnr gene was located on a sul1-type class 1 integron just downstream of a conserved region (CR) element (CR1) comprising the Orf513 recombinase. Promoter sequences for qnr expression overlapped the extremity of CR1, indicating the role of CR1 in the expression of antibiotic resistance genes. This integron was different from other qnr-positive sul1-type integrons identified in American and Chinese enterobacterial isolates. In addition, plasmid pQR1 carried another class 1 integron that was identical to In53 from E. coli. The latter integron possessed a series of gene cassettes, including those coding for the extended-spectrum beta-lactamase VEB-1, the rifampin ADP ribosyltransferase ARR-2, and several aminoglycoside resistance markers. This is the first report of plasmid-mediated quinolone resistance in Europe associated with an unknown level of plasmid-mediated multidrug resistance in Enterobacteriaceae.

Anti-Infective Agents↗
PubMed2003

Analysis of gene cassettes of streptomycin-spectinomycin resistance of Hungarian Salmonella enterica serotype Typhimurium strains.

By PCR using the ant(3")-Ia primer pair the aadA gene was detected in 34 streptomycin- and spectinomycin-resistant Salmonella enterica serotype Typhimurium strains. Out of them 12 belonged to DT104 and 22 to non-DT104 phage type. Using different primer combinations it was demonstrated that this gene was integron-associated in all cases: in the DT104 strains it was generally contained by a 1 kb integron while in the majority of the non-DT104 strains by a 2.05 kb (less often by a 1.9 or 1 kb) integron. In the case of integrons carrying multiple cassettes the cassette containing the aadA gene was located closer to the 3' end of the integron. The aadA genes of DT104 and non-DT104 strains were different: in the former group the aadA2 gene, while in the latter group (constituted by strains of five different phages types as well as unclassifiable and untypable strains) the aadA1 gene could be identified. The RH50/RH51 primer pair described by Collis and Hall (1992) proved to be suitable for rapid discrimination between the aadA1 and aadA2 genes on the basis that the RH51 primer bound exclusively to the aadA2 gene.

Anti-Bacterial Agents↗
PubMed2004

Evaluation of genetic determinants involved in beta-lactam- and multiresistance in a surgical ICU.

Antibiotic resistance is a major and well-known problem in intensive care units (ICUs) world-wide and previously susceptible isolates become resistant through the acquisition of resistance determinants from other bacteria or the development of mutations, as is the case in beta-lactam resistance. We evaluated the presence of resistance determinants involved in beta-lactam resistance and multi-resistance in order to establish the contribution of horizontal gene transfer to the spread of resistance in a surgical ICU during an antibiotic rotation study. Pseudomonas aeruginosa and Enterobacteriaceae isolates were selected and iso-electric focusing (IEF), DNA-typing methods such as specific beta-lactamase and specific integron PCRs were performed to determine the presence of beta-lactamases. The PCRs specific for IMP-1, OXA-1, and VIM-type beta-lactamases performed on the selected P. aeruginosa and Enterobacteriaceae isolates with MICs for cephalosporins >1 mg/l did not demonstrate any of these beta-lactamases. IEF for 14 pseudomonads, representing 7 genotypes from 9 patients, showed a beta-lactamase with a pI larger than 8.5 in 13 of the isolates. The integrase PCR was positive for only five isolates from three patients and conserved segment PCR showed integrons of variable sizes (700, 900, 1,400 and 1,500 bp). Each patient had its own integron types. It can be concluded that integrons and associated resistance determinants played only a minor role in the surgical ICU and beta-lactam resistance among P. aeruginosa isolates was most likely due to the derepression of its AmpC gene.

Anti-Bacterial Agents↗
PubMed2003

The gene cassette metagenome is a basic resource for bacterial genome evolution.

Lateral gene transfer has been proposed as a fundamental process underlying bacterial diversity. Transposons, plasmids and phage are widespread and have been shown to significantly contribute to lateral gene transfer. However, the processes by which disparate genes are assembled and integrated into the host regulatory network to yield new phenotypes are poorly known. Recent discoveries about the integron/gene cassette system indicate it has the potential to play a role in this process. Gene cassettes are small mobile elements typically consisting of a promoterless orf and a recombination site. Integrons are capable of acquisition and re-arrangement of gene cassettes and of the expression of their associated genes. The potential of the integron/gene cassette system is thus largely determined by the diversity contained within the cassette pool and the rate at which integrons sample this pool. We show here using a polymerase chain reaction (PCR) approach by which the environmental gene cassette (EGC) metagenome can be directly sampled that this metagenome contains both protein-coding and non-protein coding genes. Environmental gene cassette-associated recombination sites showed greater diversity than previously seen in integron arrays. Class 1 integrons were shown to be capable of accessing this gene pool through tests of recombinational activity with a representative range of EGCs. We propose that gene cassettes represent a vast, prepackaged genetic resource that could be thought of as a metagenomic template for bacterial evolution.

Base Sequence↗
PubMed2006

The role of horizontal gene transfer in the spread of trimethoprim-sulfamethoxazole resistance among uropathogenic Escherichia coli in Europe and Canada.

OBJECTIVES: To describe the distribution of trimethoprim-sulfamethoxazole resistance genes and the role of horizontal gene transfer and clonal expansion in recent increases of antibiotic resistance rates among uropathogenic Escherichia coli in Europe and Canada. METHODS: We identified antibiotic resistance alleles sul1, sul2, sul3 and dfr along with type 1 and type 2 integrons among 350 uropathogenic E. coli isolates from a cross-sectional study of acute, uncomplicated, community-acquired urinary tract infections in 16 western European countries and Canada (ECOSENS). RESULTS: Trimethoprim resistance gene distributions showed no regional dependency (P = 0.84). The most common trimethoprim resistance gene was dfrA1, which occurred in 37.9% of dfr containing isolates. Similarly, the sulfamethoxazole resistance gene distributions did not vary significantly by region (P = 0.20). sul2, the most common sulfamethoxazole resistance gene, was found in 77.9% of sulfamethoxazole-resistant isolates. The distribution of type 1 and type 2 integrons varied slightly by region (P = 0.04) with type 1 integrons being the more common (85.9%). We observed 34 combinations of the sul genes, dfr genes and integron types; the most common combinations were broadly disseminated across every region examined. CONCLUSIONS: Horizontal gene transfer plays a larger role than clonal expansion in the increase of trimethoprim-sulfamethoxazole resistance levels in Europe and Canada.

Anti-Bacterial Agents↗