Composite integron array generated by insertion of an ORF341-type integron within a Tn21-like element

dfrA trimethoprim resistance genes found in Gram-negative bacteria: compilation and unambiguous numbering

To track the spread of antibiotic resistance genes, accurate identification of individual genes is essential. Acquired trimethoprim resistance genes encoding trimethoprim-insensitive homologues of the sensitive dihydrofolate reductases encoded by the folA genes of bacteria are increasingly found in genome sequences. However, naming and numbering in publicly available records (journal publications or entries in the GenBank non-redundant DNA database) has not always been unambiguous. In addition, the nomenclature has evolved over time. Here, the changes in nomenclature and the most commonly encountered problems and pitfalls affecting dfrA gene identification arising from historically incorrect or inaccurate numbering are explained. The complete set of dfrA genes/DfrA proteins found in Gram-negative bacteria for which readily searchable sequence information is currently available has been compiled using less than 98% identity for both the gene and the derived protein sequence as the criteria for assignment of a new number. In most cases, trimethoprim resistance has been demonstrated. The gene context, predominantly in a gene cassette or near the ori end of CR1 or CR2, is also covered. The RefSeq database that underpins the programs used to automatically identify resistance genes in genome data sets has been curated to assign all sequences listed to the correct number. This led to the assignment of corrected or new gene numbers to several mis-assigned sequences. The unique numbers assigned for the dfrA/DfrA set are now listed in the RefSeq database, which we propose provides a way forward that should end future duplication of numbers and the confusion that causes.

Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim

Trimethoprim is a synthetic antibacterial agent that targets folate biosynthesis by competitively binding to the di-hydrofolate reductase enzyme (DHFR). Trimethoprim is often administered synergistically with sulfonamide, another chemotherapeutic agent targeting the di-hydropteroate synthase (DHPS) enzyme in the same pathway. Clinical resistance to both drugs is widespread and mediated by enzyme variants capable of performing their biological function without binding to these drugs. These mutant enzymes were assumed to have arisen after the discovery of these synthetic drugs, but recent work has shown that genes conferring resistance to sulfonamide were present in the bacterial pangenome millions of years ago. Here, we apply phylogenetics and comparative genomics methods to study the largest family of mobile trimethoprim-resistance genes (dfrA). We show that most of the dfrA genes identified to date map to two large clades that likely arose from independent mobilization events. In contrast to sulfonamide resistance (sul) genes, we find evidence of recurrent mobilization in dfrA genes. Phylogenetic evidence allows us to identify novel dfrA genes in the emerging pathogen Acinetobacter baumannii, and we confirm their resistance phenotype in vitro. We also identify a cluster of dfrA homologues in cryptic plasmid and phage genomes, but we show that these enzymes do not confer resistance to trimethoprim. Our methods also allow us to pinpoint the chromosomal origin of previously reported dfrA genes, and we show that many of these ancient chromosomal genes also confer resistance to trimethoprim. Our work reveals that trimethoprim resistance predated the clinical use of this chemotherapeutic agent, but that novel mutations have likely also arisen and become mobilized following its widespread use within and outside the clinic. Hence, this work confirms that resistance to novel drugs may already be present in the bacterial pangenome, and stresses the importance of rapid mobilization as a fundamental element in the emergence and global spread of resistance determinants.

Characterization of Novel Integrons, In1085 and In1086, and the Surrounding Genes in Plasmids from Enterobacteriaceae, and the Role for attCaadA16 Structural Features during attI1 × attC Integration

Novel class 1 integrons In1085 and In1086, containing the class D β-lactamase -encoding gene bla_OXA, were identified in clinical enterobacterial strains. In this study, we aimed to characterize the genetic contexts of In1085 and In1086, with the goal of identifying putative mechanisms of integron mobilization. Four plasmids, approximately 5.3, 5.3, 5.7, and 6.6 kb, from 71 clinical Enterobacteriaceae strains were found to contain class 1 integrons (In37, In62, In1085, and In1086, respectively). Two of these plasmids, pEco336 and pNsa292, containing In1085 and In1086, respectively, were further characterized by antibiotic susceptibility testing, conjugation experiments, PCR, sequencing, and gene mapping. The OXA-type carbapenemase activities of the parental strains were also assessed. The results revealed that the novel integrons had different genetic environments, and therefore demonstrated diverse biochemical characteristics. Using evolutionary inferences based on the recombination of gene cassettes, we also identified a role for attC_aadA16 structural features during attI1 × attC insertion reactions. Our analysis showed that gene cassette insertions in the bottom strand of attC_aadA16 in the correct orientation lead to the expression the encoded genes from the Pc promoter. Our study suggests that the genetic features harbored within the integrons are inserted in a discernable pattern, involving the stepwise and parallel evolution of class 1 integron variations under antibiotic selection pressures in a clinical setting.

Differentiation of IncL and IncM Plasmids Associated with the Spread of Clinically Relevant Antimicrobial Resistance

Introduction

bla_OXA-48, bla_NDM-1 and bla_CTX-M-3 are clinically relevant resistance genes, frequently associated with the broad-host range plasmids of the IncL/M group. The L and M plasmids belong to two compatible groups, which were incorrectly classified together by molecular methods. In order to understand their evolution, we fully sequenced four IncL/M plasmids, including the reference plasmids R471 and R69, the recently described bla_OXA-48-carrying plasmid pKPN-El.Nr7 from a Klebsiella pneumoniae isolated in Bern (Switzerland), and the bla_SHV-5 carrying plasmid p202c from a Salmonella enterica from Tirana (Albania).

Methods

Sequencing was performed using 454 Junior Genome Sequencer (Roche). Annotation was performed using Sequin and Artemis software. Plasmid sequences were compared with 13 fully sequenced plasmids belonging to the IncL/M group available in GenBank.

Results

Comparative analysis of plasmid genomes revealed two distinct genetic lineages, each containing one of the R471 (IncL) and R69 (IncM) reference plasmids. Conjugation experiments demonstrated that plasmids representative of the IncL and IncM groups were compatible with each other. The IncL group is constituted by the bla_OXA-48-carrying plasmids and R471. The IncM group contains two sub-types of plasmids named IncM1 and IncM2 that are each incompatible.

Conclusion

This work re-defines the structure of the IncL and IncM families and ascribes a definitive designation to the fully sequenced IncL/M plasmids available in GenBank.

Molecular characterization of multidrug-resistant Escherichia coli isolates from Irish cattle farms

This study describes the genotypic characteristics of a collection of 100 multidrug-resistant (MDR) Escherichia coli strains recovered from cattle and the farm environment in Ireland in 2007. The most prevalent antimicrobial resistance identified was to streptomycin (100%), followed by tetracycline (99%), sulfonamides (98%), ampicillin (82%), and neomycin (62%). Resistance was mediated predominantly by strA-strB (92%), tetA (67%), sul2 (90%), bla(TEM) (79%), and aphA1 (63%) gene markers, respectively. Twenty-seven isolates harbored a class 1 integrase (intI1), while qacEΔ1 and sul1 markers were identified in 25 and 26 isolates, respectively. The variable regions of these integrons contained aminoglycoside, trimethoprim, and β-lactam resistance determinants (aadA12, aadB-aadA1, bla(OXA-30)-aadA1, dfrA1-aadA1, dfrA7). Class 2 integrons were identified less frequently (4%) and contained the gene cassette array dfrA1-sat1-aadA1. Resistance to ampicillin, neomycin, streptomycin, sulfonamide, and tetracycline was associated with transferable high-molecular-weight plasmids, as demonstrated by conjugation assays. A panel of virulence markers was screened for by PCR, and genes identified included vt1, K5 in 2 isolates, papC in 10 isolates, and PAI IV(536) in 37 isolates. MDR commensal E. coli isolates from Irish cattle displayed considerable diversity with respect to the genes identified. Our findings highlight the importance of the commensal microflora of food-producing animals as a reservoir of transferable MDR.

Molecular characterisation of Vibrio cholerae O1 strains carrying an SXT/R391-like element from cholera outbreaks in Kenya: 1994-2007

BACKGROUND

Over the last decade, cholera outbreaks in parts of Kenya have become common. Although a number of recent studies describe the epidemiology of cholera in Kenya, there is paucity of information concerning the diversity and occurrence of mobile genetic elements in Vibrio cholerae strains implicated in these outbreaks. A total of 65 Vibrio cholerae O1 El Tor serotype Inaba isolated between 1994 and 2007 from various outbreaks in Kenya were investigated for mobile genetic elements including integrons, transposons, the integrating conjugative elements (ICEs), conjugative plasmids and for their genotypic relatedness.

RESULTS

All the strains were haemolytic on 5% sheep blood and positive for the Vibrio cholerae El Tor-specific haemolysin toxin gene (hylA) by PCR. They all contained strB, sulII, floR and the dfrA1 genes encoding resistance to streptomycin, sulfamethoxazole, chloramphenicol and trimethoprim respectively. These genes, together with an ICE belonging to the SXT/R391 family were transferable to the rifampicin-resistant E. coli C600 en bloc. All the strains were negative for integron class 1, 2 and 3 and for transposase gene of transposon Tn7 but were positive for integron class 4 and the trpM gene of transposon Tn21. No plasmids were isolated from any of the 65 strains. All the strains were also positive for all V. cholera El Tor pathogenic genes except the NAG- specific heat-stable toxin (st) gene. None of the strains were positive for virulence genes associated with the V. cholerae classical biotype. All the strains were positive for El Tor-specific CTXphi bacteriophage rstrR repressor gene (CTXETPhi) but negative for the Classical, Calcutta, and the Environmental repressor types. Pulse Field Gel Electrophoresis (PFGE) showed that regardless of the year of isolation, all the strains bearing the SXT element were clonally related.

CONCLUSIONS

This study demonstrates that the V. cholerae O1 strains carrying an SXT/R391-like element implicated in recent cholera outbreaks in Kenya has not changed significantly between 1994 and 2007 and are clonally related.

Antimicrobial resistance in nontyphoidal Salmonella from food sources in Colombia: evidence for an unusual plasmid-localized class 1 integron in serotypes Typhimurium and Anatum

Seventy-two isolates representing 18 serotypes recovered from various food samples collected in Colombia were tested for antimicrobial susceptibilities. The collection was further characterized for extended-spectrum cephalosporin, aminoglycoside, and tetracycline resistance markers. Multidrug resistant (MDR) isolates were further investigated for class 1 integrons and were evaluated for the presence of conjugative plasmids along with a determination of the incompatibility group by polymerase chain reaction (PCR). Antibiogram analysis showed that the incidence rate of ceftiofur resistance was moderately high (15%). A similar level of resistance to neomycin and oxytetracycline (11% and 10%, respectively) was also observed. There was a high prevalence of gene cassettes as part of one or more class 1 integrons (61%), many of which contained determinants that contributed to the resistance profile. Class 1 integrons identified in MDR Salmonella enterica serotypes Typhimurium and Anatum isolates were characterized. Sequencing identified several incomplete open reading frames (ORFs) as part of a gene cassette (bla-( imp-13 ), dfr7, blr1088, and aac8) along with a complete gene cassette (bla-(oxa2)) in each case. A mosaic of gene cassettes was identical in the two Salmonella serotypes. These integrons were located to a conjugative replicon. Plasmid profiling and incompatibility typing identified three plasmids belonging to Inc groups A/C, P, and W. Our study highlights the role of integrons, contributing to a MDR phenotype that is capable of dissemination to other bacteria.

Genetic environment of quinolone resistance gene qnrB2 in a complex sul1-type integron in the newly described Salmonella enterica serovar Keurmassar

A qnrB2 determinant was described for a new complex sul1-type integron from Salmonella enterica serovar Keurmassar. The genetic structure contained two class 1 integrons surrounding two common regions (CRs) separated by a partial 3' conserved segment. The qnrB2 gene is adjacent to the first CR.

Class 1 integrons and their conjugal transfer with and without virulence-associated genes in extra-intestinal and intestinal Escherichia coli of poultry

Multiple-drug resistance in enteric bacteria is frequently associated with integrons. To determine whether integrons may play a role in avian pathogenic Escherichia coli, isolates of extra-intestinal (n = 27) and intestinal (n = 40) E. coli from dead chicks and turkey poults were analysed for the presence of class 1 integrons and of the virulence-associated genes iss, tsh and colV. Eleven extra-intestinal strains possessed a 1.0 kb class 1 integron with a variable region of aadA1 and were resistant to tetracycline. These traits were indicative of the presence of the Tn21 transposon, which was confirmed by polymerase chain reaction. All extra-intestinal strains had the colV, iss and tsh genes, but none of these genes were cotransferred with the 1.0 kb integron when conjugal transferability was tested. The integron content of the intestinal strains showed considerable variability: one or two of four different class 1 integrons, which varied from 1.0 to 2.4 kb in size, were detected in the 11 strains. The aadA7 gene of the 1.0 kb integron, the dfrA1-aadA1 genes of the 1.6 kb integron and the folA-catB3-aadA5 genes of the 2.4 kb integron were identical to those described by other workers. However, the orfIN682-dhfrV-orfD gene cassette arrangement of the 1.5 kb integron of an intestinal strain of serogroup O5 had no similarity to any previously reported integrons. Conjugal transfer of the 1.6 and 2.4 kb integrons was successful, and in a serogroup O33 intestinal E. coli strain the iss gene was apparently cotransferred with a 1.6 kb integron. The 1.0 and 1.5 kb integrons were not transferable. Our data suggest that intestinal E. coli strains of poultry may be a reservoir for emerging multiresistant strains of avian pathogenic E. coli.

Dissemination and persistence of blaCTX-M-9 are linked to class 1 integrons containing CR1 associated with defective transposon derivatives from Tn402 located in early antibiotic resistance plasmids of IncHI2, IncP1-alpha, and IncFI groups

This study analyzes the diversity of In60, a class 1 integron bearing CR1 and containing bla(CTX-M-9), and its association with Tn402, Tn21, and classical conjugative plasmids among 45 CTX-M-9-producing clinical strains (41 Escherichia coli strains, 2 Klebsiella pneumoniae strains, 1 Salmonella enterica strain, and 1 Enterobacter cloacae strain). Forty-five patients in a Spanish tertiary care hospital were studied (1996 to 2003). The diversity of In60 and association of In60 with Tn402 or mercury resistance transposons were investigated by overlapping PCR assays and/or hybridization. Plasmid characterization included comparison of restriction fragment length polymorphism patterns and determination of incompatibility group by PCR-based replicon typing, sequencing, and hybridization. CTX-M-9 plasmids belonged to IncHI2 (n = 26), IncP-1alpha (n = 10), IncFI (n = 4), and IncI (n = 1) groups. Genetic platforms containing bla(CTX-M-9) were classified in six types in relation to the In60 backbone and in eight subtypes in relation to Tn402 derivatives. They were associated with Tn21 sequences when located in IncP-1alpha or IncHI2 plasmids. Our study identified bla(CTX-M-9) in a high diversity of CR1-bearing class 1 integrons linked to different Tn402 derivatives, often to Tn21, highlighting the role of recombination events in the evolution of antibiotic resistance plasmids. The presence of bla(CTX-M-9) on broad-host-range IncP-1alpha plasmids might contribute to its dissemination to hosts that were not members of the family Enterobacteriaceae.

ISCR elements: novel gene-capturing systems of the 21st century?

"Common regions" (CRs), such as Orf513, are being increasingly linked to mega-antibiotic-resistant regions. While their overall nucleotide sequences show little identity to other mobile elements, amino acid alignments indicate that they possess the key motifs of IS91-like elements, which have been linked to the mobility ent plasmids in pathogenic Escherichia coli. Further inspection reveals that they possess an IS91-like origin of replication and termination sites (terIS), and therefore CRs probably transpose via a rolling-circle replication mechanism. Accordingly, in this review we have renamed CRs as ISCRs to give a more accurate reflection of their functional properties. The genetic context surrounding ISCRs indicates that they can procure 5' sequences via misreading of the cognate terIS, i.e., "unchecked transposition." Clinically, the most worrying aspect of ISCRs is that they are increasingly being linked with more potent examples of resistance, i.e., metallo-beta-lactamases in Pseudomonas aeruginosa and co-trimoxazole resistance in Stenotrophomonas maltophilia. Furthermore, if ISCR elements do move via "unchecked RC transposition," as has been speculated for ISCR1, then this mechanism provides antibiotic resistance genes with a highly mobile genetic vehicle that could greatly exceed the effects of previously reported mobile genetic mechanisms. It has been hypothesized that bacteria will surprise us by extending their "genetic construction kit" to procure and evince additional DNA and, therefore, antibiotic resistance genes. It appears that ISCR elements have now firmly established themselves within that regimen.

Antimicrobial resistance islands: resistance gene clusters in Salmonella chromosome and plasmids

Genes conferring simultaneous resistance to different classes of antimicrobials, confer a selective advantage to the host, particularly when those corresponding antibiotics are administered. Multiple resistance genes clustered within the same genetic locus (resistance island) can be transferred en bloc to other organisms. In this chapter we review novel multidrug resistance islands recently described in Salmonella.

Integrons and transposons on the Salmonella enterica serovar typhimurium virulence plasmid

A virulence plasmid was identified in a multidrug-resistant Salmonella enterica serotype Typhimurium strain carrying the spvC, rck, and pefA virulence genes and two class 1 integrons linked to the Tn21 and Tn1696 transposons. A novel trimethoprim resistance gene, designated dfrA23, was also identified within the integron region. The association of multidrug resistance and virulence determinants represents an interesting example of virulence plasmid evolution.

Dissemination of transferable AmpC-type beta-lactamase (CMY-10) in a Korean hospital

To determine dissemination and genotype of AmpC beta-lactamases and an extended-spectrum beta-lactamase among clinical isolates of Enterobacteriaceae, we performed antibiotic susceptibility testing, pI determination, induction test, plasmid profiles, transconjugation test, enterobacterial repetitive consensus (ERIC)-PCR, and DNA sequencing. Among the 51 clinical isolates collected from a university hospital in Korea, six isolates were resistant to cephamycins. All six isolates produced a plasmid-encoded AmpC-type beta-lactamase, CMY-10. Five strains also produced one or more other beta-lactamases: SHV-12, an extended-spectrum beta-lactamase (five isolates); TEM-1, a class A beta-lactamase (two isolates); and a chromosomal AmpC beta-lactamase (one isolate, a strain of Enterobacter aerogenes, which produced all four of the beta-lactamases that were identified). One of six isolates produced only CMY-10. ERIC-PCR analysis revealed that dissemination of CMY-10 and SHV-12 was due to a clonal outbreak of a resistant strain and to the interspecies spread of resistance to cephamycins and broad-spectrum beta-lactams in Korea. CMY-10 beta-lactamase genes that are responsible for the resistance to cephamycins (cefoxitin and cefotetan), amoxicillin, cephalothin, and amoxicillin-clavulanic acid were cloned and characterized from six clinical isolates. A sequence identical to the common regions in In6, In7, and a novel integron from pSAL-1 was found upstream from blaCMY-10 gene at nucleotides 1-71. A total of 15 nucleotides (I-15) or 18 nucleotides (I-18) between position 71 and 72 were inserted into the blaCMY-10 gene. The blaCMY-10 gene might be inserted into a sul1-type complex integron by I-15 or I-18.

Salmonella genomic island 1 multidrug resistance gene clusters in Salmonella enterica serovar Agona isolated in Belgium in 1992 to 2002

Salmonella genomic island 1 (SGI1) harbors a multidrug resistance (MDR) gene cluster which is a complex class 1 integron. Variant SGI1 MDR gene clusters conferring different MDR profiles have also been identified in several Salmonella enterica serovars and classified as SGI1-A to -F. A retrospective study was undertaken to characterize MDR regions from serovar Agona strains harboring SGI1 isolated from poultry in Belgium between 1992 and 2002. A total of 171 serovar Agona strains, displaying resistance to at least one antibiotic, were studied for the presence of SGI1. SGI1 was detected in 94 serovar Agona strains. The most prevalent variant was SGI1-A (85%), which harbors within the SGI1 complex class 1 integron a common region (CR1) containing orf513, a putative transposase gene, adjacent to the dfrA10 trimethoprim resistance gene. A new variant SGI1 named SGI1-G was identified in two strains. It consisted of the pse-1 gene cassette, as in SGI1-B, but with additional insertion of the orf513/dfrA10 region structure. Seven strains displaying the typical SGI1 MDR profile (Ap Cm Ff Sm Sp Su Tc) showed genetic variation at the 3' end of SGI1. These strains harbored the insertion of the CR1 containing orf513 as in SGI1-A, -D, and -G. However, downstream the right end of CR1, they presented different 7.4- to 8.5-kb deletions of the SGI1 3' end that extended to the chromosomal genes yieE and yieF. These results suggest a possible role of CR1 in deletion formation, as has been reported for some insertion sequences. Pulsed-field gel electrophoresis analysis showed that all the serovar Agona SGI1-carrying strains belonged to a single clone. Thus, SGI1 is largely encountered in serovar Agona strains isolated from poultry in Belgium, the most prevalent variant being SGI1-A. SGI1 MDR region undergoes recombinational events resulting in a diversity of MDR gene clusters.

Resistance integrons and super-integrons

Integrons are genetic elements composed of a gene encoding an integrase, gene cassettes and an integration site for the gene cassettes (att). The integrase excises and integrates the gene cassettes from and into the integron, but integrons themselves are not mobile. Two groups of integrons are known: resistance integrons and super-integrons. Nearly all known gene cassettes from resistance integrons encode resistance to antibiotics or disinfectants. These integrons are found on transposons, plasmids and the bacterial chromosome. Gene cassettes in super-integrons encode a variety of different functions. Super-integrons are located on the bacterial chromosome. More than 100 gene cassettes may be present, in contrast to resistance integrons where less than ten cassettes are present. Many species harbour super-integrons, which are species-specific, whereas particular resistance integrons can be found in a variety of species. The gene cassettes in resistance integrons probably originated from super-integrons. In the last few years, a variety of new gene cassettes have been described. Many of these encode resistance against newer antibiotics such as cephalosporins and carbapenems. Resistance integrons have been found in isolates from a wide variety of sources, including food.

Characterization and Localization of Drug Resistance Determinants in Multidrug-Resistant, Integron-CarryingSalmonella entericaSerotype Typhimurium Strains

The genetic background of the antimicrobial resistance of 10 selected multiresistant Salmonella serotype Typhimurium (S. Typhimurium) strains (including the emerging monophasic variant [4,5,12:i:- ]) was investigated. All strains shared class 1 integrons (with seven types of variable regions) and belonged to different lineages (L1-L6) according to their phage types, DNA polymorphisms by XbaI-pulsed-field gel electrophoresis (PFGE), integrons, and/or resistance patterns. The strains were screened for the presence and localization (chromosomal or plasmid) of 32 DNA sequences representing integron-, Tn21-like transposon-, resistance-, and virulence-plasmid genes. Strains belonging to lineage L1 (definitive phage type DT104) carried the 90-kb Salmonella virulence plasmid together with the complete or partial chromosomally located Salmonella Genomic Island 1 (SGI1). All strains belonging to the other five lineages carried their resistance determinants on various resistance plasmids. Two of these strains showed complex plasmid profiles, which included a 95 kb virulence plasmid together with two or four resistance plasmids. Two strains carried a resistance plasmid that lacked the virulence-plasmid-encoding sequences. The remaining two strains carried two different hybrid virulence-resistance plasmids. Twenty-three of the DNA sequences could be assigned to distinct XbaI genomic restriction patterns (PFGE profiles). In this way, the influence of the resistance and virulence plasmids on the PFGE profiles was determined, and several groups of resistance genes could be identified. The data obtained represent a useful epidemiological tool for tracing the emergence and distribution of multiresistant S. Typhimurium worldwide.

Tetracycline and streptomycin resistance genes, transposons, and plasmids in Salmonella enterica isolates from animals in Italy

Fifty-eight multidrug-resistant Salmonella enterica strains of 20 serotypes, isolated from animal sources in Italy, were analyzed for tet(A) and strA-strB, conferring tetracycline and streptomycin resistance, respectively. The strA and strB genes were highly prevalent in Salmonella strains of our collection, being detected in 84% of the streptomycin-resistant strains. In many strains, the strA and strB genes were linked to a particular Tn5393-derivative transposon characterized by the presence of the insertion sequence IS1133, previously identified only in the plant pathogen Erwinia amylovora. Sixty-eight percent of the tetracycline-resistant strains were tet(A) positive, indicating that this gene is widely diffused in Salmonella strains circulating in animals in Italy. Most of the tet(A) genes were localized within a deleted Tn1721 transposon variant. Two prevalent repN and repI1 resistance plasmids were identified in Salmonella isolates of our collection.

Multiple drug-resistant Mycobacterium tuberculosis: evidence for changing fitness following passage through human hosts

Recent studies have shown a difference in the genotype of resistant bacteria following passage in animals compared to those passaged in vitro. This suggests that organisms rapidly adapt to their environment of growth. We sought to investigate whether this phenomenon occurred in human infection and whether changes could be detected in the fitness (growth velocity) of isolates transmitted between human hosts. Isogenic strains of Mycobacterium tuberculosis were obtained from a well-documented hospital outbreak. The subjects included those who were HIV seropositive and immunocompromised. The relative fitness of each sample was measured using growth competition in vitro. The results confirmed that our method of measuring fitness was not influenced by the storage conditions of the isolates, and demonstrated that the fitness of genetically similar isolates obtained from different patients in the outbreak differed significantly, as reflected in the growth velocity of the strains. This study provides the first evidence that multiple drug resistant M. tuberculosis strains adapt to the environment of their human host.

In34, a complex In5 family class 1 integron containing orf513 and dfrA10

A complex class 1 integron, In34, found in a conjugative plasmid from a multidrug-resistant Klebsiella pneumoniae strain isolated in 1997 at a hospital in Sydney, Australia, was shown to have a backbone related to that of In2, which belongs to the In5 family. In In34, the aadB gene cassette replaces the aadA1a cassette in In2, and two additional resistance genes, dfrA10 and aphA1, that are not part of a gene cassette are present. The aphA1 gene is in a Tn4352-like transposon that is located in the tniA gene. The dfrA10 gene lies adjacent to a 2,154-bp DNA segment, known as the common region, that contains an open reading frame predicting a product of 513 amino acids (Orf513). Orf513 is 66 and 55% identical to the products of two further open reading frames that, like the common region, are found adjacent to antibiotic resistance genes. A 27-bp conserved sequence was found at one end of each type of common region. The loss of dfrA10 due to homologous recombination between flanking direct repeats and incorporation of the excised circle by homologous recombination were demonstrated. Part of In34 is identical to the sequenced portion of In7, which is from a multidrug-resistant Escherichia coli strain that had been isolated 19 years earlier in the same hospital. In34 and In7 are in plasmids that contain the same six resistance genes conferring resistance to ampicillin, chloramphenicol, gentamicin, kanamycin, neomycin, tobramycin, trimethoprim, and sulfonamides, but the plasmid backbones appear to be unrelated, suggesting that translocation of a multiple-drug-resistance-determining region as well as horizontal transfer may have occurred.