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

Characterization of the highly variable region surrounding the blaCTX-M-9 gene in non-related Escherichia coli from Barcelona

OBJECTIVES

The dispersion of a clone, a plasmid or a mobile element carrying the bla(CTX-M-9) gene was evaluated in 30 Escherichia coli strains isolated in Barcelona between 1996 and 1999. The presence of the previously described orf513-bearing class 1 integron, In60, carrying the bla(CTX-M-9) gene, was also studied.

METHODS

The clonality was analysed by pulsed-field gel electrophoresis. Plasmid analysis was performed by S1 digestion and hybridization with the CTX-M-9 probe. PCR mapping using specific designed primers was used to study the presence of In60 and In60-like structures.

RESULTS

The clonality between the 30 strains was minor. The size of bla(CTX-M-9) carrying plasmids ranged between approximately 80 and 430 kb. One strain produced only a chromosome-encoded CTX-M-9 beta-lactamase. Thirty-six per cent of the strains showed differences with respect to the In60 structure due to an insertion or deletion events.

CONCLUSIONS

These findings suggest that the bla(CTX-M-9) gene may be carried by a mobile element that disperses it between plasmids. The fast dispersion of the CTX-M-9 enzyme could therefore be due to both diffusion of plasmids and mobile elements.

Transcriptional analysis of the bla(CTX-M-2) gene in Salmonella enterica serovar Infantis

Transcriptional organization of bla(CTX-M-2) present in a multiresistance plasmid of Salmonella enterica serovar Infantis suggests the presence of more than one promoter involved in the expression of the beta-lactamase gene. At least two bla(CTX-M-2)-specific mRNAs (near to 1 kb and 5 kb) were evidenced. Two +1 signals were detected at -22 bp and -59 bp of bla(CTX-M-2) defining two putative promoters.

The genomic island SGI1, containing the multiple antibiotic resistance region of Salmonella enterica serovar Typhimurium DT104 or variants of it, is widely distributed in other S. enterica serovars

The global dissemination of the multiply-antibiotic-resistant Salmonella enterica serovar Typhimurium DT104 clone with the resistance genes located in a class 1 integron, here designated In104, within genomic island SGI1 is a significant public health issue. Here, we have shown that SGI1 and variants of it carrying different combinations of resistance genes are found in several Salmonella enterica serovars. These are serovars Cerro, Derby, Dusseldorf, Infantis, Kiambu, and Paratyphi B dT(+) isolated from human infections and serovar Emek from sewage effluent. Two new variants, SGI1-I and SGI1-J, both of which include the dfrA1-orfC cassette array, were identified.

Emergence of plasmid-mediated resistance to quinolones in Enterobacteriaceae

Although quinolone resistance results mostly from chromosomal mutations in Enterobacteriaceae, it may also be mediated by plasmid-encoded Qnr determinants. Qnr proteins protect DNA from quinolone binding and compromise the efficacy of quinolones such as nalidixic acid. Qnr proteins (QnrA-like, QnrB and QnrS) have been identified worldwide with a quite high prevalence among Asian isolates with a frequent association with clavulanic acid inhibited expanded-spectrum beta-lactamases and plasmid-mediated cephalosporinases. The qnrA genes are embedded in complex sul1-type integrons. A very recent identification of the origin of QnrA determinants in the water-borne species Shewanella algae underlines the role of the environment as a reservoir for this emerging threat. It may help to determine the location of in vivo transfer of qnrA genes. Further analysis of the role (if any) of quinolones for enhancing this gene transfer may be conducted. This could prevent the spread, if still possible, of this novel antibiotic resistance mechanism.

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.

The 120 592 bp IncF plasmid pRSB107 isolated from a sewage-treatment plant encodes nine different antibiotic-resistance determinants, two iron-acquisition systems and other putative virulence-associated functions

The antibiotic-multiresistance IncF plasmid pRSB107 was isolated by a transformation-based approach from activated-sludge bacteria of a wastewater-treatment plant. It confers resistance to ampicillin, penicillin G, chloramphenicol, erythromycin, kanamycin, neomycin, streptomycin, sulfonamides, tetracycline and trimethoprim and against mercuric ions. Complete sequencing of this plasmid revealed that it is 120 592 bp in size and has a G+C content of 53.1 mol%. The plasmid backbone is composed of three replicons, RepFIA, RepFIB and RepFII, which are almost identical to corresponding regions located on the F-plasmid and on R100. The three replicons encode replication initiation (rep) and replication control, multimer resolution (mrs), post-segregational killing of plasmid-free cells (psk) and active plasmid partitioning (sopABC locus). Part of the F-leading region and remnants of the F-homologous DNA-transfer (tra) module complete the pRSB107 backbone. Plasmid pRSB107 contains a complex, highly mosaic 35 991 bp antibiotic-resistance region consisting of a Tn21- and a Tn10-derivative and a chloramphenicol-resistance module. The Tn21 derivative is composed of a mercury-resistance region (mer), a Tn4352B-like kanamycin/neomycin-resistance transposon, a streptomycin/sulfonamide-resistance module, remnants of the beta-lactam-resistance transposon Tn1, a macrolide-resistance module flanked by copies of IS26 and IS6100, remnants of Tn402 integrating a class 1 integron and the Tn21-specific transposition module. A truncated version of the tetracycline-resistance transposon Tn10 and the chloramphenicol acetyltransferase gene catA complete the pRSB107 resistance region. In addition to antibiotic resistance, pRSB107 encodes the following putative virulence-associated functions: (i) an aerobactin iron-acquisition siderophore system (iuc/iut); (ii) a putative high-affinity Fe(2+) uptake system which was previously identified on a pathogenicity island of Yersinia pestis and in the genome of the phytopathogen Erwinia carotovora subsp. atroseptica SCRI1043; (iii) an sn-glycerol-3-phosphate transport system (ugp); and (iv) the virulence-associated genes vagCD having a possible function in stable plasmid inheritance. All the accessory modules are framed by insertion sequences, indicating that pRSB107 was gradually assembled by integration of different horizontally acquired DNA segments via transposition or homologous recombination.

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.

Complex multiple antibiotic and mercury resistance region derived from the r-det of NR1 (R100)

The sequence of the 45.2-kb multidrug and mercury resistance region of pRMH760, a large plasmid from a clinical isolate of Klebsiella pneumoniae collected in 1997 in Australia, was completed. Most of the modules found in the resistance determinant (r-det), or Tn2670, region of NR1 (also known as R100), isolated from a Shigella flexneri strain in Japan in the late 1950s, were present in pRMH760 but in a different configuration. The location was also different, with the Tn2670-derived region flanked by the transposition module of Tn1696 and a mercury resistance module almost identical to one found in the plasmid pDU1358. This arrangement is consistent with a three-step process. First, the r-det was circularized via homologous recombination between the IS1 elements and reincorporated at a new location, possibly in a different plasmid, via homologous recombination between the 5'-conserved (5'-CS) or 3'-CS of the In34 integron in the r-det and the same region of a second class 1 integron in a Tn1696 relative. Subsequently, resolvase-mediated recombination between the res sites in the r-det and a second mercury resistance transposon removed one end of the Tn1696-like transposon and part of the second transposon. Other events occurring within the r-det-derived portion have also contributed to the formation of the pRMH760 resistance region. Tn2 or a close relative that includes the bla(TEM-1b) gene had moved into the Tn21 mercury resistance module with subsequent deletion of the adjacent sequence, and all four 38-bp inverted repeats corresponding to Tn21 family transposon termini have been interrupted by an IS4321-like element.

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.

Functional and structural characterization of the genetic environment of an extended-spectrum beta-lactamase blaVEB gene from a Pseudomonas aeruginosa isolate obtained in India

A Pseudomonas aeruginosa clinical strain isolated from a patient hospitalized in a New Delhi, India, hospital was resistant to expanded-spectrum cephalosporins, imipenem, and aztreonam. A bla(VEB-1)-like gene named bla(VEB-1a), which codes for the extended-spectrum beta-lactamase VEB-1a, was identified. The genetic environment of bla(VEB-1a) was peculiar: (i) no 5' conserved sequence (5'-CS) region was present upstream of the beta-lactamase gene, whereas bla(VEB-1)-like genes are usually associated with class 1 integrons; (ii) bla(VEB-1a) was inserted between two truncated 3'-CS regions in a direct repeat; and (iii) four 135-bp repeated DNA sequences (repeated elements) were located on each side of the bla(VEB-1a) gene. Expression of the bla(VEB-1a) gene was driven by a strong promoter located in one of these repeated sequences. In addition, cloning of the beta-lactamase content of this P. aeruginosa isolate followed by expression in Escherichia coli identified the naturally occurring AmpC beta-lactamase and a gene encoding an OXA-2-like beta-lactamase located in a class 1 integron, In78, in which an insertion sequence, ISpa7, was inserted within its 5'-CS region.

Molecular analysis of metallo-beta-lactamase gene bla(SPM-1)-surrounding sequences from disseminated Pseudomonas aeruginosa isolates in Recife, Brazil

The spread of clonally related carbapenem-resistant Pseudomonas aeruginosa producing the metallo-beta-lactamase SPM-1 was found in Recife, Brazil. Upstream of bla(SPM-1), a novel common region (CR4) was identified, comprising an open reading frame, orf495, whose product shares significant identity with putative recombinases, such as Orf513. CR4 may be responsible for mobilization and expression of bla(SPM-1).

The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons

IS5075 and IS4321 are closely related (93.1% identical) members of the IS1111 family that target a specific position in the 38-bp terminal inverted repeats of Tn21 family transposons and that are inserted in only one orientation. They are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (TAATGAG) or 6 bp (AATGAG) to the left of the left inverted repeats and 3 bp (AGA) or 4 bp (AGAT) to the right of the right inverted repeat. Circular forms of IS5075 and IS4321 in which the inverted repeats are separated by abutting terminal sequences (AGATAATGAG) were detected. A similar circular product was found for the related ISPa11. Transposition of IS4321 into the 38-bp target site was detected, but a flanking duplication was not generated. The precisely reconstituted target site was also identified. Over 50 members of the IS1111 family were identified. They encode related transposases, have related inverted repeats, and include related bases that lie outside these inverted repeats. In some, the flanking bases number 5 or 6 on the left and 4 or 3 on the right. Specific target sites were found for several of these insertion sequence (IS) elements. IS1111 family members therefore differ from the majority of IS elements, which are characterized by terminal inverted repeats and a target site duplication, and from members of the related IS110 family, which do not have obvious inverted repeats near their termini.

Multi-resistant Gram-negative bacilli: from epidemics to endemics

PURPOSE OF REVIEW

Infections due to multi-drug resistant Gram-negative bacilli represent a worrying situation for the management of hospitalized patients. In addition, these bacteria are increasingly involved in epidemics throughout the world. This review focuses on recent data that may help to understand the emergence and dissemination of multi-drug resistant bacilli and the current trend from epidemic to endemic situations.

RECENT FINDINGS

Well-established clones enhance their resistance phenotype by the acquisition of new resistant genes, via gene capture genetic units (plasmids, transposons or integrons), thus facilitating the co-selective process under different antimicrobial selective pressures and therefore the long-term persistence of organisms in selective environments. Not only resistant bacterial clones are selected, but also their genetic structures carrying resistance genes. Therefore, current epidemiology of multi-drug resistant bacilli is not only focused on bacterial clones but also on any kind of resistance gene capture units. In this scenario a multiclonal population structure of bacterial organisms corresponds to a collection of different strains sharing resistance genes carried by horizontally transferred genetic structures. As different strains tend to prefer different environments, this concept helps understand why the epidemiology of multi-drug resistant Gram-negative bacilli is moving from epidemics to endemics.

SUMMARY

The emergence and spread of multi-drug resistant bacilli in the nosocomial setting should be understood in terms of a complex interplay of bacterial clonality, resistance genes and genetic structures promoting rapid dissemination of antimicrobial resistance. Intervention strategies in the forthcoming scenario should identify existing epidemic and/or endemic situations involving clonal organisms or resistance genes carried by epidemic gene capture units.

Plasmid-mediated quinolone resistance in clinical isolates of Escherichia coli from Shanghai, China

Although quinolone resistance usually results from chromosomal mutations, recent studies indicate that quinolone resistance can also be plasmid mediated. The gene responsible, qnr, is distinct from the known quinolone resistance genes and in previous studies seemed to be restricted to Klebsiella pneumoniae and Escherichia coli isolates from the University of Alabama in Birmingham, where this resistance was discovered. In Shanghai, the frequency of ciprofloxacin resistance in E. coli has exceeded 50% since 1993. Seventy-eight unique ciprofloxacin-resistant clinical isolates of E. coli from Shanghai hospitals were screened for the qnr gene by colony blotting and Southern hybridization of plasmid DNA. Conjugation experiments were done with azide-resistant E. coli J53 as a recipient with selection for plasmid-encoded antimicrobial resistance (chloramphenicol, gentamicin, or tetracycline) and azide counterselection. qnr genes were sequenced, and the structure of the plasmid DNA adjacent to qnr was analyzed by primer walking with a sequential series of outward-facing sequencing primers with plasmid DNA templates purified from transconjugants. Six (7.7%) of 78 strains gave a reproducible hybridization signal with a qnr gene probe on colony blots and yielded strong signals on plasmid DNA preparations. Quinolone resistance was transferred from all six probe-positive strains. Transconjugants had 16- to 250-fold increases in the MICs of ciprofloxacin relative to that of the recipient. All six strains contained qnr with a nucleotide sequence identical to that originally reported, except for a single nucleotide change (CTA-->CTG at position 537) encoding the same amino acid. qnr was located in complex In4 family class 1 integrons. Two completely sequenced integrons were designated In36 and In37. Transferable plasmid-mediated quinolone resistance associated with qnr is thus prevalent in quinolone-resistant clinical strains of E. coli from Shanghai and may contribute to the rapid increase in bacterial resistance to quinolones in China.