Conjugative IncC Plasmid Entry Triggers the SOS Response and Promotes Effective Transfer of the Integrative Antibiotic Resistance Element SGI1.

The broad-host-range IncC plasmid family and the integrative mobilizable Salmonella genomic island 1 (SGI1) and its derivatives enable the spread of medically important antibiotic resistance genes among Gram-negative pathogens. Although several aspects of the complex functional interactions between IncC plasmids and SGI1 have been recently deciphered regarding their conjugative transfer and incompatibility, the biological signal resulting in the hijacking of the conjugative plasmid by the integrative mobilizable element remains unknown. Here, we demonstrate that the conjugative entry of IncC/IncA plasmids is detected at an early stage by SGI1 through the transient activation of the SOS response, which induces the expression of the SGI1 master activators SgaDC, shown to play a crucial role in the complex biology between SGI1 and IncC plasmids. Besides, we developed an original tripartite conjugation approach to directly monitor SGI1 mobilization in a time-dependent manner following conjugative entry of IncC plasmids. Finally, we propose an updated biological model of the conjugative mobilization of the chromosomal resistance element SGI1 by IncC plasmids. IMPORTANCE Antimicrobial resistance has become a major public health issue, particularly with the increase of multidrug resistance (MDR) in both animal and human pathogenic bacteria and with the emergence of resistance to medically important antibiotics. The spread between bacteria of successful mobile genetic elements, such as conjugative plasmids and integrative elements conferring multidrug resistance, is the main driving force in the dissemination of acquired antibiotic resistances among Gram-negative bacteria. Broad-host-range IncC plasmids and their integrative mobilizable SGI1 counterparts contribute to the spread of critically important resistance genes (e.g., extended-spectrum ß-lactamases [ESBLs] and carbapenemases). A better knowledge of the complex biology of these broad-host-range mobile elements will help us to understand the dissemination of antimicrobial resistance genes that occurred across Gammaproteobacteria borders.

Spread of multidrug-resistant IncHI1 plasmids carrying ESBL gene blaCTX-M-1 and metabolism operon of prebiotic oligosaccharides in commensal Escherichia coli from healthy horses, France.

The objective of the study was to identify the genetic determinants and characteristics of expanded-spectrum cephalosporin (ESC) resistance in commensal Escherichia coli from healthy horses in France in 2015. Faecal samples from 744 adult horses were screened for ESC-resistant E. coli isolates. The extended-spectrum beta-lactamase (ESBL)/AmpC resistance genes were identified using polymerase chain reaction (PCR) and sequencing. ESC phenotypes were horizontally transferred by conjugation or transformation. Plasmids carrying ESBL/AmpC genes were typed by PCR-based replicon typing, restriction fragment length polymorphism (RFLP), and plasmid multilocus sequence typing (pMLST). The ESC-resistant E. coli isolates were typed by XbaI macrorestriction analysis. Sixteen of 41 stables harboured at least one horse carrying ESC-resistant E. coli. The proportion of individually tested horses carrying ESC-resistant E. coli was 8.5% (28/328). Fifty non-redundant ESC-resistant E. coli isolates showing a great diversity of XbaI macrorestriction profiles belonged mainly to phylogroup B1, and were negative for major E. coli virulence genes, indicating they are commensal isolates. ESBL blaCTX-M genes were dominant (blaCTX-M-1, n=34; blaCTX-M-2, n=8; blaCTX-M-14, n=2) and located on conjugative plasmids belonging to various incompatibility groups (IncHI1, IncI1, IncN, IncY, or non-typeable). Among these, the multidrug-resistant IncHI1-pST9 plasmids were dominant and simultaneously harboured the blaCTX-M-1/2 genes and an operon enabling the metabolism of short-chain fructo-oligosaccharides (scFOS). In conclusion, commensal E. coli of French horses displayed a significant distribution of IncHI1-pST9 plasmids carrying both the blaCTX-M-1/2 gene and the fos metabolism operon. This finding highlights the risk of co-selection of multidrug-resistant IncHI1 plasmids carrying ESBL genes possibly mediated by the use of scFOS as prebiotic in horses.

Identification and Characterization of oriT and Two Mobilization Genes Required for Conjugative Transfer of Salmonella Genomic Island 1.

The integrative mobilizable elements of SGI1-family considerably contribute to the spread of resistance to critically important antibiotics among enteric bacteria. Even though many aspects of SGI1 mobilization by IncA and IncC plasmids have been explored, the basic transfer elements such as oriT and self-encoded mobilization proteins remain undiscovered. Here we describe the mobilization region of SGI1 that is well conserved throughout the family and carries the oriT SGI1 and two genes, mpsA and mpsB (originally annotated as S020 and S019, respectively) that are essential for the conjugative transfer of SGI1. OriT SGI1, which is located in the vicinity of the two mobilization genes proved to be a 125-bp GC-rich sequence with several important inverted repeat motifs. The mobilization proteins MpsA and MpsB are expressed from a bicistronic mRNA, although MpsB can be produced from its own mRNA as well. The protein structure predictions imply that MpsA belongs to the lambda tyrosine recombinase family, while MpsB resembles the N-terminal core DNA binding domains of these enzymes. The results suggest that MpsA may act as an atypical relaxase, which needs MpsB for SGI1 transfer. Although the helper plasmid-encoded relaxase proved not to be essential for SGI1 transfer, it appeared to be important to achieve the high transfer rate of the island observed with the IncA/IncC-SGI1 system.

Prevalence, risk factors, and characterization of multidrug resistant and extended spectrum ß-lactamase/AmpC ß-lactamase producing Escherichia coli in healthy horses in France in 2015.

BACKGROUND: Although antimicrobial resistance is increasingly common in equine medicine, molecular and epidemiological data remains scarce. OBJECTIVES: We estimated the prevalence of, and risk factors for, shedding of multidrug resistant (MDR), extended spectrum ß-lactamase (ESBL)-producing, and AmpC ß-lactamase-producing, or some combination of these in Escherichia coli in horses in France. We characterized ESBL/AmpC isolates for antimicrobial susceptibility and the presence of virulence and ESBL/AmpC-associated resistance genes. ANIMALS: Fecal samples from healthy adult horses at 41 premises were collected. A questionnaire was completed by each premises manager. A subset of these samples was tested to build 2 bacterial collections. METHODS: Indicator (without enrichment) and specific (enrichment with ceftriaxone) E. coli tested for antimicrobial susceptibility. Prevalence of isolates nonsusceptible to antimicrobials was estimated at the horse and the premises level. The ESBL/AmpC and virulence genes were identified by PCR. Multivariable logistic regression was used to investigate risk factors for MDR and ESBL/AmpC isolates at premises. RESULTS: Approximately 44% of horses shed MDR E. coli. Resistance most commonly was observed to ampicillin, streptomycin, and amoxicillin/clavulanic acid. Twenty-nine percent of premises housed horses shedding ESBL/AmpC-producing isolates. The ESBL/AmpC gene most commonly identified was blaCTX-M-1 . Virulence gene iutA was identified in 1 ESBL/AmpC-producing isolate. Medical treatment, staff numbers, and activity were identified as risk factors for housing horses shedding ESBL/AmpC-producing E. coli isolates. CONCLUSIONS AND CLINICAL IMPORTANCE: Prevalence of healthy horses harboring ESBL/AmpC genes and MDR isolates in their intestinal microbiota is substantial. Risk factors could be used to elaborate guidelines to prevent their dissemination.

Dominant plasmids carrying extended-spectrum ß-lactamases blaCTX-M genes in genetically diverse Escherichia coli from slaughterhouse and urban wastewaters.

Wastewater treatment plants (WWTP) receiving effluents from food-producing animals and humans may contribute to the spread of extended-spectrum ß-lactamases (ESBL)-carrying plasmids. This study was designed to investigate extended-spectrum cephalosporin resistant Escherichia coli strains, CTX-M distributions and the genetic lineage of blaCTX-M -carrying plasmids from urban and slaughterhouse wastewaters. The level of extended-spectrum cephalosporin-resistant E. coli in slaughterhouse wastewater entering the WWTP was negligible compared with that of urban wastewater. The blaCTX-M-1 gene was predominant in slaughterhouse wastewater whereas diverse blaCTX-M genes were encountered in urban wastewater and WWTP outlet. Characterization of the main CTX-M-producing E. coli isolates by antibiotic resistance phenotyping, genotyping and typing of plasmids carrying blaCTX-M genes revealed that blaCTX-M-1 and blaCTX-M-15 genes were harboured by the predominant blaCTX-M-1 IncI1/ST3 and blaCTX-M-15 F31:A4:B1 plasmids, which were recovered from unrelated E. coli genotypes in both slaughterhouse and urban wastewaters. This study highlighted the spread of predominant blaCTX-M-1 and blaCTX-M-15 plasmid lineages in diverse E. coli genotypes from humans and food-producing animals, their mixing in WWTP and final release into the aquatic environment. This could have a serious negative impact on public health and requires further evaluation.

Extended-spectrum ß-lactamase- and AmpC ß-lactamase-producing D-tartrate-positive Salmonella enterica serovar Paratyphi B from broilers and human patients in Belgium, 2008-10.

OBJECTIVES: To characterize the genetic determinants responsible for extended-spectrum cephalosporin (ESC) resistance of d-tartrate-positive Salmonella enterica subsp. enterica serovar Paratyphi B (serovar Paratyphi B dT+) strains that have emerged in poultry and humans in Belgium during 2008-10. METHODS: The ESC resistance genes among non-redundant serovar Paratyphi B dT+ strains were determined using PCR and sequencing. ESC phenotypes were horizontally transferred by conjugation. Extended-spectrum ß-lactamase (ESBL)- or AmpC-carrying plasmids were typed by PCR-based replicon typing, plasmid multilocus sequence typing and restriction fragment length polymorphism. The genetic relationship of ESC-resistant strains was assessed by XbaI PFGE and multilocus sequence typing. RESULTS: Since 2008, the proportion of serovar Paratyphi B dT+ strains from broiler origin has increased significantly to reach 36.5% in 2010. Among 95 non-duplicate serovar Paratyphi B dT+ strains, 35% were resistant to ESCs. At the same time, a few ESC-resistant serovar Paratyphi B dT+ strains from humans were also detected in Belgium. The most prevalent ESBL gene, blaCTX-M-1, and the AmpC cephalosporinase gene blaCMY-2 were identified on various conjugative IncI1 plasmids of different sequence types and with different additional non-ß-lactam phenotypes. Interestingly, the blaCTX-M-2 gene was located on large multireplicon IncHI2/P plasmids. In addition, highly ESC-resistant strains contained both the ESBL CTX-M-2 and the AmpC CMY-2 encoded by the IncHI2/P and IncI1 plasmids, respectively. All ESC-resistant serovar Paratyphi B dT+ strains belonged to sequence type 28 and showed the common PFGE pattern X8, as well as the chromosomal class 2 integron cassette array dfrA1-sat2-aadA1 previously described in the European poultry-associated serovar Paratyphi B dT+ clonal population. CONCLUSIONS: This study showed that the clonal population of multidrug-resistant serovar Paratyphi B dT+, persisting in broilers in Belgium for the last decade, recently acquired various plasmid-borne ESC resistance determinants, constituting a major concern for public health. Further surveillance programmes and research are an absolute necessity to understand their epidemiology and to propose interventions to limit the spread of ESC- and multidrug-resistant Salmonella spp.

Complete nucleotide sequence of the multidrug resistance IncA/C plasmid pR55 from Klebsiella pneumoniae isolated in 1969.

OBJECTIVES: To determine the complete nucleotide sequence of the multidrug resistance IncA/C plasmid pR55 from a clinical Klebsiella pneumoniae strain that was isolated from a urinary tract infection in 1969 in a French hospital and compare it with those of contemporary emerging IncA/C plasmids. METHODS: The plasmid was purified and sequenced using a 454 sequencing approach. After draft assembly, additional PCRs and walking reads were performed for gap closure. Sequence comparisons and multiple alignments with other IncA/C plasmids were done using the BLAST algorithm and CLUSTAL W, respectively. RESULTS: Plasmid pR55 (170 810 bp) revealed a shared plasmid backbone (>99% nucleotide identity) with current members of the IncA/C(2) multidrug resistance plasmid family that are widely disseminating antibiotic resistance genes. Nevertheless, two specific multidrug resistance gene arrays probably acquired from other genetic elements were identified inserted at conserved hotspot insertion sites in the IncA/C backbone. A novel transposon named Tn6187 showed an atypical mixed transposon configuration composed of two mercury resistance operons and two transposition modules that are related to Tn21 and Tn1696, respectively, and an In0-type integron. CONCLUSIONS: IncA/C(2) multidrug resistance plasmids have a broad host range and have been implicated in the dissemination of antibiotic resistance among Enterobacteriaceae from humans and animals. This typical IncA/C(2) genetic scaffold appears to carry various multidrug resistance gene arrays and is now also a successful vehicle for spreading AmpC-like cephalosporinase and metallo-ß-lactamase genes, such as bla(CMY) and bla(NDM), respectively.

Early strains of multidrug-resistant Salmonella enterica serovar Kentucky sequence type 198 from Southeast Asia harbor Salmonella genomic island 1-J variants with a novel insertion sequence.

Salmonella genomic island 1 (SGI1) is a 43-kb integrative mobilizable element that harbors a great diversity of multidrug resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. The majority of SGI1 variants contain an In104-derivative complex class 1 integron inserted between resolvase gene res and open reading frame (ORF) S044 in SGI1. Recently, the international spread of ciprofloxacin-resistant S. enterica serovar Kentucky sequence type 198 (ST198) containing SGI1-K variants has been reported. A retrospective study was undertaken to characterize ST198 S. Kentucky strains isolated before the spread of the epidemic ST198-SGI1-K population in Africa and the Middle East. Here, we characterized 12 ST198 S. Kentucky strains isolated between 1969 and 1999, mainly from humans returning from Southeast Asia (n = 10 strains) or Israel (n = 1 strain) or from meat in Egypt (n = 1 strain). All these ST198 S. Kentucky strains did not belong to the XbaI pulsotype X1 associated with the African epidemic clone but to pulsotype X2. SGI1-J subgroup variants containing different complex integrons with a partial transposition module and inserted within ORF S023 of SGI1 were detected in six strains. The SGI1-J4 variant containing a partially deleted class 1 integron and thus showing a narrow resistance phenotype to sulfonamides was identified in two epidemiologically unrelated strains from Indonesia. The four remaining strains harbored a novel SGI1-J variant, named SGI1-J6, which contained aadA2, floR2, tetR(G)-tetA(G), and sul1 resistance genes within its complex integron. Moreover, in all these S. Kentucky isolates, a novel insertion sequence related to the IS630 family and named ISSen5 was found inserted upstream of the SGI1 complex integron in ORF S023. Thus, two subpopulations of S. Kentucky ST198 independently and exclusively acquired the SGI1 during the 1980s and 1990s. Unlike the ST198-X1 African epidemic subpopulation, the ST198-X2 subpopulation mainly from Asia harbors variants of the SGI1-J subgroup that are encountered mainly in the Far East, as previously described for S. enterica serovars Emek and Virchow.

The Salmonella genomic island 1 is specifically mobilized in trans by the IncA/C multidrug resistance plasmid family.

BACKGROUND: The Salmonella genomic island 1 (SGI1) is a Salmonella enterica-derived integrative mobilizable element (IME) containing various complex multiple resistance integrons identified in several S. enterica serovars and in Proteus mirabilis. Previous studies have shown that SGI1 transfers horizontally by in trans mobilization in the presence of the IncA/C conjugative helper plasmid pR55. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report the ability of different prevalent multidrug resistance (MDR) plasmids including extended-spectrum ß-lactamase (ESBL) gene-carrying plasmids to mobilize the multidrug resistance genomic island SGI1. Through conjugation experiments, none of the 24 conjugative plasmids tested of the IncFI, FII, HI2, I1, L/M, N, P incompatibility groups were able to mobilize SGI1 at a detectable level (transfer frequency <10(-9)). In our collection, ESBL gene-carrying plasmids were mainly from the IncHI2 and I1 groups and thus were unable to mobilize SGI1. However, the horizontal transfer of SGI1 was shown to be specifically mediated by conjugative helper plasmids of the broad-host-range IncA/C incompatibility group. Several conjugative IncA/C MDR plasmids as well as the sequenced IncA/C reference plasmid pRA1 of 143,963 bp were shown to mobilize in trans SGI1 from a S. enterica donor to the Escherichia coli recipient strain. Depending on the IncA/C plasmid used, the conjugative transfer of SGI1 occurred at frequencies ranging from 10(-3) to 10(-6) transconjugants per donor. Of particular concern, some large IncA/C MDR plasmids carrying the extended-spectrum cephalosporinase bla(CMY-2) gene were shown to mobilize in trans SGI1. CONCLUSIONS/SIGNIFICANCE: The ability of the IncA/C MDR plasmid family to mobilize SGI1 could contribute to its spread by horizontal transfer among enteric pathogens. Moreover, the increasing prevalence of IncA/C plasmids in MDR S. enterica isolates worldwide has potential implications for the epidemic success of the antibiotic resistance genomic island SGI1 and its close derivatives.

IncI1 plasmid carrying extended-spectrum-beta-lactamase gene blaCTX-M-1 in Salmonella enterica isolates from poultry and humans in France, 2003 to 2008.

We report the dissemination of a conjugative IncI1 plasmid carrying bla(CTX-M-1), conferring resistance to extended-spectrum cephalosporins, in Salmonella enterica isolates from poultry and humans in France from 2003 to 2008. By IncI1 plasmid subtyping, this plasmid was shown to be genetically related to that found in Escherichia coli isolates from healthy poultry in France.

Association of IS26-composite transposons and complex In4-type integrons generates novel multidrug resistance loci in Salmonella genomic island 1.

OBJECTIVES: Clinical isolates of Salmonella enterica serovar Haifa and Newport, which displayed extended multidrug resistance phenotypes, were investigated for the presence of Salmonella genomic island 1 (SGI1) and the genetic organization of its antibiotic resistance gene clusters. METHODS: The S. enterica strains were isolated from humans in France in 2003 and 2004. Antibiotic susceptibility tests and various molecular techniques were used for detection and characterization of SGI1. RESULTS: We identified SGI1 integrated in the 3' end of the chromosomal thdF gene in six multidrug-resistant serovar Haifa and Newport strains. Two strains, of serovar Haifa and Newport, harboured the previously described SGI1-H variant. A new variant of the novel SGI1-Ks group, named SGI1-K6, revealed IS26-mediated rearrangements of the antibiotic resistance gene cluster in two serovar Newport strains. Two other serovar Newport strains harboured the SGI1-L complex class 1 integron containing the dfrA15 and bla(PSE-1) resistance gene cassettes. In addition, these variants of SGI1 also contained large IS26-composite transposons inserted by a transposition event in the SGI1 backbone. These IS26-composite transposons showed a similar genetic structure to the SGI1-K variants containing an In4-type integron, a mercury resistance operon and parts of Tn1721 and Tn5393. These extended resistance gene clusters containing up to 10 antibiotic resistance genes were named SGI1-L1 and -L2. CONCLUSIONS: The serovar Haifa represents the 16th S. enterica serovar in which SGI1 has been identified. The genomic island SGI1 appears to be a hotspot of acquisition of antibiotic resistance genes by the transposition of In4-type integrons and large IS26-composite transposons.

Novel insertion sequence- and transposon-mediated genetic rearrangements in genomic island SGI1 of Salmonella enterica serovar Kentucky.

Salmonella genomic island 1 (SGI1) is an integrative mobilizable element that harbors a multidrug resistance (MDR) gene cluster. Since its identification in epidemic Salmonella enterica serovar Typhimurium DT104 strains, variant SGI1 MDR gene clusters conferring different MDR phenotypes have been identified in several S. enterica serovars and classified as SGI1-A to -O. A study was undertaken to characterize SGI1 from serovar Kentucky strains isolated from travelers returning from Africa. Several strains tested were found to contain the partially characterized variant SGI1-K, recently described in a serovar Kentucky strain isolated in Australia. This variant contained only one cassette array, aac(3)-Id-aadA7, and an adjacent mercury resistance module. Here, the uncharacterized part of SGI1-K was sequenced. Downstream of the mer module similar to that found in Tn21, a mosaic genetic structure was found, comprising (i) part of Tn1721 containing the tetracycline resistance genes tetR and tet(A); (ii) part of Tn5393 containing the streptomycin resistance genes strAB, IS1133, and a truncated tnpR gene; and (iii) a Tn3-like region containing the tnpR gene and the beta-lactamase bla(TEM-1) gene flanked by two IS26 elements in opposite orientations. The rightmost IS26 element was shown to be inserted into the S044 open reading frame of the SGI1 backbone. This variant MDR region was named SGI1-K1 according to the previously described variant SGI1-K. Other SGI1-K MDR regions due to different IS26 locations, inversion, and partial deletions were characterized and named SGI1-K2 to -K5. Two new SGI1 variants named SGI1-P1 and -P2 contained only the Tn3-like region comprising the beta-lactamase bla(TEM-1) gene flanked by the two IS26 elements inserted into the SGI1 backbone. Three other new variants harbored only one IS26 element inserted in place of the MDR region of SGI1 and were named SGI1-Q1 to -Q3. Thus, in serovar Kentucky, the SGI1 MDR region undergoes recombinational and insertional events of transposon and insertion sequences, resulting in a higher diversity of MDR gene clusters than previously reported and consequently a higher diversity of MDR phenotypes.

Comparative analysis of IncHI2 plasmids carrying blaCTX-M-2 or blaCTX-M-9 from Escherichia coli and Salmonella enterica strains isolated from poultry and humans.

Salmonella enterica bla(CTX-M-2) and bla(CTX-M-9) plasmid backbones from isolates from Belgium and France were analyzed. The bla(CTX-M-2-)plasmids from both human and poultry isolates were related to the IncHI2 pAPEC-O1-R plasmid, previously identified in the United States in avian Escherichia coli strains; the bla(CTX-M-9) plasmids were closely related to the IncHI2 R478 plasmid.

Dissemination of an extended-spectrum-beta-lactamase blaTEM-52 gene-carrying IncI1 plasmid in various Salmonella enterica serovars isolated from poultry and humans in Belgium and France between 2001 and 2005.

We report here the dissemination of a conjugative IncI1 plasmid carrying bla(TEM-52) on a Tn3 transposon conferring resistance to extended-spectrum cephalosporins in Salmonella enterica serovar Agona, Derby, Infantis, Paratyphi B dT(+), and Typhimurium isolates from poultry and humans in Belgium and France from 2001 to 2005. The most prevalent serovar spreading this resistance was serovar Infantis.

Variant Salmonella genomic island 1-L antibiotic resistance gene cluster in Salmonella enterica serovar Newport.

We report a new Salmonella genomic island 1 variant antibiotic resistance gene cluster called SGI1-L in a Salmonella enterica serovar Newport isolate containing a dfrA15 gene cassette conferring resistance to trimethoprim. The isolate carried another class 1 integron containing the aacC5 and aadA7 gene cassettes conferring resistance to gentamicin and streptomycin/spectinomycin, respectively.