Benoît Doublet - Academia.edu (original) (raw)

Papers by Benoît Doublet

Frontiers in microbiology, 2017

Proteae, and especially Proteus mirabilis, are often the cause of urinary tract infections (UTIs)... more Proteae, and especially Proteus mirabilis, are often the cause of urinary tract infections (UTIs) in humans. They were reported as carriers of extended-spectrum β-lactamase (ESBL) genes, and recently of carbapenemases, mostly carried by the Salmonella genomic island 1 (SGI1) and Proteus genomic island 1 (PGI1). Proteae have also lately become an increasing cause of UTIs in companion animals, but antimicrobial susceptibility data in animals are still scarce. Here, we report the characterization of 468 clinical epidemiologically unrelated Proteae strains from animals collected between 2013 and 2015 in France. Seventeen P. mirabilis strains (3.6%) were positive for SGI1/PGI1 and 18 Proteae (3.8%) were resistant to extended-spectrum cephalosporins (ESC). The 28 isolates carrying SGI1/PGI1 and/or ESC-resistance genes were isolated from cats, dogs, and horses. ESBL genes were detected in six genetically related P. mirabilis harboring blaV EB-6 on the SGI1-V variant, but also independently...

Journal of Medical Microbiology, 2010

This study was designed to determine the genetic basis of florfenicol and ceftiofur resistance in... more This study was designed to determine the genetic basis of florfenicol and ceftiofur resistance in Escherichia coli isolates recovered from French cattle. In these isolates, ceftiofur resistance was conferred by bla CMY-2 located on three distinct conjugative plasmids on a specific DNA fragment, ISEcp1-bla CMY-2-blc-sugE. Two of the plasmids also carried the floR gene conferring resistance to florfenicol. The floR gene was shown to be associated with the insertion sequence ISCR2. Mobile elements appear to contribute to the mobilization of floR and bla CMY-2 genes in E. coli. The presence of bla CMY-2 and floR on the same plasmid highlights the potential risk for a co-selection of the bla CMY-2 gene through the use of florfenicol in food animal production.

To understand the evolutionary dynamics of extended-spectrum b-lactamase (ESBL)-encoding genes in... more To understand the evolutionary dynamics of extended-spectrum b-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBLencoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic ...

Journal of Management, 2005

Each year at this time, it has been my tradition to provide a brief summary of our progress and t... more Each year at this time, it has been my tradition to provide a brief summary of our progress and to thank those of you who have reviewed manuscripts during the year for your service to mSphere, the American Society for Microbiology, and the scientific enterprise overall. The COVID-19 pandemic has caused us to operate differently with respect to logistics, but fortunately our reviewers have been willing and able to help our authors by providing fair, thoughtful reviews. For doing this while dealing with all the stresses that the pandemic has rained upon us, this year you have my extra special gratitude and that of our senior editors and editors. Despite the pandemic, our submission numbers have greatly increased (.1,200 as of Thanksgiving). Our team interprets this as meaning that you, our authors, have trust in our process and the quality that the name mSphere carries with it. I therefore thank all of you who have submitted manuscripts in 2020 for that vote of confidence. At the begi...

Actuellement, un des problemes majeurs de sante publique est l’emergence de souches bacteriennes ... more Actuellement, un des problemes majeurs de sante publique est l’emergence de souches bacteriennes pathogenes multiresistantes aux antibiotiques. Les transferts horizontaux de genes de resistances aux antibiotiques sont largement favorises lorsqu’ils sont presents sur des elements genetiques mobiles. Salmonella Genomic Island 1 (SGI1) est un element integratif mobilisable multiresistant aux antibiotiques identifie chez Salmonella mais egalement present chez plusieurs autres enterobacteries. Pour son transfert, SGI1 est specifiquement mobilise en trans par les plasmides conjugatif de la famille IncA/C. Recemment, un phenomene d’incompatibilite a ete demontre entre SGI1 et les plasmides IncA/C qui serait contrebalance par un systeme Toxine-Antitoxine (TA) encode par SGI1 (sgiAT). En presence de plasmide IncA/C, ce systeme TA joue un role important sur la maintenance de SGI1 dans la population bacterienne. Le but de mon projet de these est de dechiffrer les mecanismes de mobilisation con...

Microbiology Spectrum

Poultry production is a main contributor of the global trend of antimicrobial resistance arising ... more Poultry production is a main contributor of the global trend of antimicrobial resistance arising from food-producing animals worldwide. In Lebanon, inappropriate use of antibiotics is frequent in chickens for prophylactic reasons and to improve productivity, resulting in an alarming prevalence of extended-spectrum β-lactamase (ESBL)/AmpC-producing Escherichia coli , also resistant to other medically important antibiotics (i.e., colistin and ciprofloxacin).

Frontiers in Microbiology

Editorial on the Research Topic Genetics of Acquired Antimicrobial Resistance in Animal and Zoono... more Editorial on the Research Topic Genetics of Acquired Antimicrobial Resistance in Animal and Zoonotic Pathogens Antimicrobial resistance has become a global public health concern due to multidrug-resistant (MDR) bacteria and to the lack of novel antibiotics. Resistant bacteria, including zoonotic pathogens, can be exchanged between animals and humans through direct contact, the food chain, or contamination of the shared environment. Resistance to medically-important antibiotics such as extended spectrum beta-lactams, carbapenems, fluoroquinolones, or aminoglycosides, is of increasing magnitude among zoonotic pathogens. Acquired antimicrobial resistance is the result of an evolutionary process by which microorganisms adapt to antibiotics through several mechanisms including alteration of drug target by mutations and horizontal transfer of novel/foreign genes, referred to as resistance genes. Acquired resistance genes coding for any of the three major resistance mechanisms, i.e., enzymatic inactivation, reduced intracellular accumulation, or modification of the cellular target sites are associated with mobile genetic elements including plasmids, transposons, gene cassettes, integrative, and conjugative elements or other mobile elements (Schwarz et al., 2017). This Research Topic is focused on acquired antimicrobial resistance mechanisms in animal and zoonotic pathogens isolated from food-producing animals, food products, companion animals, humans, and the environment. Different sets of articles document the most important aspects of the genetics of acquired antimicrobial resistance extending from medically-important resistance genes such as those conferring resistance to extended spectrum cephalosporins and more recently those conferring resistance to colistin, emerging epidemic clones, primary mobile genetic elements such as class 1 integrons, culture-independent approach of resistomes, dissemination between animals and humans, to the "One Health" concept. First, in an elegant review article, Imperial and Ibana addressed the global problem of the spread of emerging antibiotic-resistant bacteria in the "One Health" perspective. They summarized the processes that govern the spread of antibiotic resistance in relation to resistance genes, their horizontal transfer through mobile genetic elements, the microbial ecology of resistant bacteria in the human gut microbiota, and their dissemination by international travel of humans, animals, or food. Finally, they discussed the probiotic use in both human and veterinary applications to tackle the antibiotic resistance threat and concluded on the "double-edged sword" with potential risk in propagating antibiotic resistance by probiotics. Salmonella enterica spp. are important zoonotic pathogens related to foodborne diseases worldwide. In the present Research Topic, Zhao et al. and Zhao et al. contributed with two research articles dealing with antimicrobial resistance of S. enterica serotypes isolated from food-producing animals (chickens, ducks, and pigs) in farms and slaughterhouses in the Shandong province, China.

International Journal of Antimicrobial Agents

The objective was to identify the genetic determinants and supports of expanded-spectrum cephalos... more The objective was to identify the genetic determinants and supports 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 ESBL/AmpC resistance genes were identified using 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, and plasmid MLST. The ESC-resistant E. coli isolates were typed by XbaI macrorestriction analysis. Sixteen stables out of 41 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 suggesting that 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-resistance 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-resistance IncHI1 plasmids carrying ESBL gene possibly mediated by the use of scFOS as prebiotic in horses.

Microbial Genomics

We undertook a comprehensive comparative analysis of a collection of 30 small (<25 kb) non-con... more We undertook a comprehensive comparative analysis of a collection of 30 small (<25 kb) non-conjugative Escherichia coli plasmids previously classified by the gene sharing approach into 10 families, as well as plasmids found in the National Center for Biotechnology Information (NCBI) nucleotide database sharing similar genomic sequences. In total, 302 mobilizable (belonging to 2 MOBrep and 5 MOBRNA families) and 106 non-transferable/relaxase-negative (belonging to three ReLRNA families) plasmids were explored. The most striking feature was the specialization of the plasmid family types that was not related to their transmission mode and replication system. We observed a range of host strain specificity, from narrow E. coli host specificity to broad host range specificity, including a wide spectrum of Enterobacteriaceae . We found a wide variety of toxin/antitoxin systems and colicin operons in the plasmids, whose numbers and types varied according to the plasmid family type. The plasmids carried genes conferring resistance spanning almost all of the antibiotic classes, from those to which resistance developed early, such as sulphonamides, to those for which resistance has only developed recently, such as colistin. However, the prevalence of the resistance genes varied greatly according to the family type, ranging from 0 to 100 %. The evolutionary history of the plasmids based on the family type core genes showed variability within family nucleotide divergences in the range of E. coli chromosomal housekeeping genes, indicating long-term co-evolution between plasmids and host strains. In rare cases, a low evolutionary divergence suggested the massive spread of an epidemic plasmid. Overall, the importance of these small non-conjugative plasmids in bacterial adaptation varied greatly according to the type of family they belonged to, with each plasmid family having specific hosts and genetic traits.

Frontiers in Microbiology

The integrative mobilizable elements of SGI1-family considerably contribute to the spread of resi... more 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.

Salmonella enterica serotype Kentucky (S. Kentucky) can be a common causative agent of salmonello... more Salmonella enterica serotype Kentucky (S. Kentucky) can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S. Kentucky ST198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug resistant (MDR) S. Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island 1 (variant SGI1-K) conferring resistance ampicillin, streptomycin, gentamicin, sulfamethoxazole, and tetracycline. Phylogeographic analysis indicates this clone emerged in Egypt b...

Journal of Veterinary Internal Medicine

Funding information Institut national de recherche agro-alimentaire (INRA); l'Institut Francais d... more Funding information Institut national de recherche agro-alimentaire (INRA); l'Institut Francais du cheval et de l'équitation (IFCE); OIE Reference Laboratory for E. coli 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 β-lactamase (ESBL)-producing, and AmpC β-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/AmpCassociated 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 bla CTX-M-1. Virulence gene iutA was identified in 1 ESBL/AmpCproducing 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.

Scientific Reports

During infection, Salmonella senses and responds to harsh environments within the host. Persisten... more During infection, Salmonella senses and responds to harsh environments within the host. Persistence in a bile-rich environment is important for Salmonella to infect the small intestine or gallbladder and the multidrug efflux system AcrAB-TolC is required for bile resistance. The genes encoding this system are mainly regulated by the ramRA locus, which is composed of the divergently transcribed ramA and ramR genes. The acrAB and tolC genes are transcriptionally activated by RamA, whose encoding gene is itself transcriptionally repressed by RamR. RamR recognizes multiple drugs; however, the identity of the environmental signals to which it responds is unclear. Here, we describe the crystal structures of RamR in complexes with bile components, including cholic acid and chenodeoxycholic acid, determined at resolutions of 2.0 and 1.8 Å, respectively. Both cholic and chenodeoxycholic acids form four hydrogen bonds with Tyr59, Thr85, Ser137 and Asp152 of RamR, instead of π-π interactions with Phe155, a residue that is important for the recognition of multiple compounds including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6 G. Binding of these compounds to RamR reduces its DNA-binding affinity, resulting in the increased transcription of ramA and acrAB-tolC. Our results reveal that Salmonella senses bile acid components through RamR and then upregulates the expression of RamA, which can lead to induction of acrAB-tolC expression with resulting tolerance to bile-rich environments. Salmonella is a bacterial pathogen that causes a variety of foodborne illnesses in humans. During the course of its infection of the intestinal tract and gallbladder, Salmonella is exposed to bile acids. These are detergent-like biological substances that are synthesized in the liver from cholesterol and stored in the gallbladder. These bile acids possess strong antimicrobial activity, disrupt cell membranes, denature proteins and trigger DNA damage 1,2. Enteric bacteria such as Salmonella must tolerate the presence of bile acids in order to survive in the gastrointestinal transit and gallbladder 3,4. Enteric bacteria have developed an intrinsic resistance to the toxic effects of bile acids, due to the low permeability of their outer membranes to lipophilic solutes and the presence of active efflux mechanisms 5,6. Salmonella enterica serovar Typhimurium (S. Typhimurium) contains at least nine multidrug efflux systems 7. Among these, the AcrAB-TolC system, whose AcrB transporter belongs to the resistance-nodulation-cell division family, is particularly effective in generating bile acid resistance 7,8. Bile induces the expression of acrAB 8 , and this induction is mediated by the transcriptional regulators RamA and RamR 9,10. The global transcriptional activator RamA, which belongs to the AraC/XylS family of regulatory proteins, activates the expression of acrAB and tolC genes 9. The local transcriptional repressor RamR, which is located directly upstream of ramA, belongs to the TetR family of regulatory proteins and represses the expression of both ramA and ramR (Fig. 1a) 10,11. Additionally, it has recently been found that bile inhibits the binding of RamR to the ramA promoter region and activates ramA gene expression, resulting in the increased expression of acrAB and tolC 10. Our previous biochemical and structural studies found that RamR can recognize multiple compounds, including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6 G 12. Binding of these compounds to RamR results in the increased expression of ramA; all the compounds recognized by RamR are also known

mSphere

Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that... more Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that harbors a great diversity of antimicrobial resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis . A serious threat to public health was revealed in the recent description in P. mirabilis of a SGI1-derivative multidrug resistance island named PGI1 ( Proteus genomic island 1) carrying extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase resistance genes, bla VEB-6 and bla NDM-1 , respectively. Here, we report the first description of Salmonella genomic island 1 (SGI1) in a multidrug-resistant clinical Morganella morganii subsp. morganii strain isolated from a patient in France in 2013. Complete-genome sequencing of the strain revealed SGI1 variant SGI1-L carrying resistance genes dfrA15 , floR , tetA (G), bla PSE-1 (now referred to as bla CARB-2 ), and sul1 , conferring resistance to trimethoprim, phenicols, tetracyclines, amoxi...

Microbial genomics, 2018

To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in... more To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic...

Journal of Global Antimicrobial Resistance

mBio, Aug 23, 2016

For 100 years, it has been obvious that Salmonella enterica strains sharing the serotype with the... more For 100 years, it has been obvious that Salmonella enterica strains sharing the serotype with the formula 1,4,[5],12:b:1,2-now known as Paratyphi B-can cause diseases ranging from serious systemic infections to self-limiting gastroenteritis. Despite considerable predicted diversity between strains carrying the common Paratyphi B serotype, there remain few methods that subdivide the group into groups that are congruent with their disease phenotypes. Paratyphi B therefore represents one of the canonical examples in Salmonella where serotyping combined with classical microbiological tests fails to provide clinically informative information. Here, we use genomics to provide the first high-resolution view of this serotype, placing it into a wider genomic context of the Salmonella enterica species. These analyses reveal why it has been impossible to subdivide this serotype based upon phenotypic and limited molecular approaches. By examining the genomic data in detail, we are able to ident...

Environmental Microbiology Reports, 2016

Wastewater treatment plants (WWTP) receiving effluents from food-producing animals and humans may... more Wastewater treatment plants (WWTP) receiving effluents from food-producing animals and humans may contribute to the spread of extended-spectrum β-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.

The Journal of antimicrobial chemotherapy, Jan 11, 2015

To characterize MDR genomic islands related to Salmonella genomic island 1 (SGI1) and Proteus gen... more To characterize MDR genomic islands related to Salmonella genomic island 1 (SGI1) and Proteus genomic island 1 (PGI1) in Proteus mirabilis from human and animal sources in France in light of the previously reported cases. A total of 52 and 46 P. mirabilis clinical strains from human and animal sources, respectively, were studied for the period 2010-13. MDR was assessed by antimicrobial susceptibility testing, PCR detection of SGI1 and PGI1 and PCR mapping of the MDR regions. The diversity of the SGI1/PGI1-positive P. mirabilis strains was assessed by PFGE. Twelve P. mirabilis strains (5 humans and 7 dogs) were found to harbour an MDR island related to SGI1 or PGI1. Among them, several SGI1 variants were identified in diverse P. mirabilis genetic backgrounds. The variant SGI1-V, which harbours the ESBL blaVEB-6 gene, was found in closely genetically related human and dog P. mirabilis strains. The recently described PGI1 element was also identified in human and dog strains. Finally, o...

Front. Microbiol., 2013

A screening for non-target mutations affecting fluoroquinolone susceptibility was conducted in ep... more A screening for non-target mutations affecting fluoroquinolone susceptibility was conducted in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198. Among a panel of representative isolates (n = 27), covering the epidemic, only three showed distinct mutations in ramR resulting in enhanced expression of genes encoding the AcrAB-TolC efflux system and low increase in ciprofloxacin MIC. No mutations were detected in other regulatory regions of this efflux system. Ciprofloxacin resistance in serovar Kentucky ST198 is thus currently mainly due to multiple target gene mutations.

Frontiers in microbiology, 2017

Proteae, and especially Proteus mirabilis, are often the cause of urinary tract infections (UTIs)... more Proteae, and especially Proteus mirabilis, are often the cause of urinary tract infections (UTIs) in humans. They were reported as carriers of extended-spectrum β-lactamase (ESBL) genes, and recently of carbapenemases, mostly carried by the Salmonella genomic island 1 (SGI1) and Proteus genomic island 1 (PGI1). Proteae have also lately become an increasing cause of UTIs in companion animals, but antimicrobial susceptibility data in animals are still scarce. Here, we report the characterization of 468 clinical epidemiologically unrelated Proteae strains from animals collected between 2013 and 2015 in France. Seventeen P. mirabilis strains (3.6%) were positive for SGI1/PGI1 and 18 Proteae (3.8%) were resistant to extended-spectrum cephalosporins (ESC). The 28 isolates carrying SGI1/PGI1 and/or ESC-resistance genes were isolated from cats, dogs, and horses. ESBL genes were detected in six genetically related P. mirabilis harboring blaV EB-6 on the SGI1-V variant, but also independently...

Journal of Medical Microbiology, 2010

This study was designed to determine the genetic basis of florfenicol and ceftiofur resistance in... more This study was designed to determine the genetic basis of florfenicol and ceftiofur resistance in Escherichia coli isolates recovered from French cattle. In these isolates, ceftiofur resistance was conferred by bla CMY-2 located on three distinct conjugative plasmids on a specific DNA fragment, ISEcp1-bla CMY-2-blc-sugE. Two of the plasmids also carried the floR gene conferring resistance to florfenicol. The floR gene was shown to be associated with the insertion sequence ISCR2. Mobile elements appear to contribute to the mobilization of floR and bla CMY-2 genes in E. coli. The presence of bla CMY-2 and floR on the same plasmid highlights the potential risk for a co-selection of the bla CMY-2 gene through the use of florfenicol in food animal production.

To understand the evolutionary dynamics of extended-spectrum b-lactamase (ESBL)-encoding genes in... more To understand the evolutionary dynamics of extended-spectrum b-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBLencoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic ...

Journal of Management, 2005

Each year at this time, it has been my tradition to provide a brief summary of our progress and t... more Each year at this time, it has been my tradition to provide a brief summary of our progress and to thank those of you who have reviewed manuscripts during the year for your service to mSphere, the American Society for Microbiology, and the scientific enterprise overall. The COVID-19 pandemic has caused us to operate differently with respect to logistics, but fortunately our reviewers have been willing and able to help our authors by providing fair, thoughtful reviews. For doing this while dealing with all the stresses that the pandemic has rained upon us, this year you have my extra special gratitude and that of our senior editors and editors. Despite the pandemic, our submission numbers have greatly increased (.1,200 as of Thanksgiving). Our team interprets this as meaning that you, our authors, have trust in our process and the quality that the name mSphere carries with it. I therefore thank all of you who have submitted manuscripts in 2020 for that vote of confidence. At the begi...

Actuellement, un des problemes majeurs de sante publique est l’emergence de souches bacteriennes ... more Actuellement, un des problemes majeurs de sante publique est l’emergence de souches bacteriennes pathogenes multiresistantes aux antibiotiques. Les transferts horizontaux de genes de resistances aux antibiotiques sont largement favorises lorsqu’ils sont presents sur des elements genetiques mobiles. Salmonella Genomic Island 1 (SGI1) est un element integratif mobilisable multiresistant aux antibiotiques identifie chez Salmonella mais egalement present chez plusieurs autres enterobacteries. Pour son transfert, SGI1 est specifiquement mobilise en trans par les plasmides conjugatif de la famille IncA/C. Recemment, un phenomene d’incompatibilite a ete demontre entre SGI1 et les plasmides IncA/C qui serait contrebalance par un systeme Toxine-Antitoxine (TA) encode par SGI1 (sgiAT). En presence de plasmide IncA/C, ce systeme TA joue un role important sur la maintenance de SGI1 dans la population bacterienne. Le but de mon projet de these est de dechiffrer les mecanismes de mobilisation con...

Microbiology Spectrum

Poultry production is a main contributor of the global trend of antimicrobial resistance arising ... more Poultry production is a main contributor of the global trend of antimicrobial resistance arising from food-producing animals worldwide. In Lebanon, inappropriate use of antibiotics is frequent in chickens for prophylactic reasons and to improve productivity, resulting in an alarming prevalence of extended-spectrum β-lactamase (ESBL)/AmpC-producing Escherichia coli , also resistant to other medically important antibiotics (i.e., colistin and ciprofloxacin).

Frontiers in Microbiology

Editorial on the Research Topic Genetics of Acquired Antimicrobial Resistance in Animal and Zoono... more Editorial on the Research Topic Genetics of Acquired Antimicrobial Resistance in Animal and Zoonotic Pathogens Antimicrobial resistance has become a global public health concern due to multidrug-resistant (MDR) bacteria and to the lack of novel antibiotics. Resistant bacteria, including zoonotic pathogens, can be exchanged between animals and humans through direct contact, the food chain, or contamination of the shared environment. Resistance to medically-important antibiotics such as extended spectrum beta-lactams, carbapenems, fluoroquinolones, or aminoglycosides, is of increasing magnitude among zoonotic pathogens. Acquired antimicrobial resistance is the result of an evolutionary process by which microorganisms adapt to antibiotics through several mechanisms including alteration of drug target by mutations and horizontal transfer of novel/foreign genes, referred to as resistance genes. Acquired resistance genes coding for any of the three major resistance mechanisms, i.e., enzymatic inactivation, reduced intracellular accumulation, or modification of the cellular target sites are associated with mobile genetic elements including plasmids, transposons, gene cassettes, integrative, and conjugative elements or other mobile elements (Schwarz et al., 2017). This Research Topic is focused on acquired antimicrobial resistance mechanisms in animal and zoonotic pathogens isolated from food-producing animals, food products, companion animals, humans, and the environment. Different sets of articles document the most important aspects of the genetics of acquired antimicrobial resistance extending from medically-important resistance genes such as those conferring resistance to extended spectrum cephalosporins and more recently those conferring resistance to colistin, emerging epidemic clones, primary mobile genetic elements such as class 1 integrons, culture-independent approach of resistomes, dissemination between animals and humans, to the "One Health" concept. First, in an elegant review article, Imperial and Ibana addressed the global problem of the spread of emerging antibiotic-resistant bacteria in the "One Health" perspective. They summarized the processes that govern the spread of antibiotic resistance in relation to resistance genes, their horizontal transfer through mobile genetic elements, the microbial ecology of resistant bacteria in the human gut microbiota, and their dissemination by international travel of humans, animals, or food. Finally, they discussed the probiotic use in both human and veterinary applications to tackle the antibiotic resistance threat and concluded on the "double-edged sword" with potential risk in propagating antibiotic resistance by probiotics. Salmonella enterica spp. are important zoonotic pathogens related to foodborne diseases worldwide. In the present Research Topic, Zhao et al. and Zhao et al. contributed with two research articles dealing with antimicrobial resistance of S. enterica serotypes isolated from food-producing animals (chickens, ducks, and pigs) in farms and slaughterhouses in the Shandong province, China.

International Journal of Antimicrobial Agents

The objective was to identify the genetic determinants and supports of expanded-spectrum cephalos... more The objective was to identify the genetic determinants and supports 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 ESBL/AmpC resistance genes were identified using 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, and plasmid MLST. The ESC-resistant E. coli isolates were typed by XbaI macrorestriction analysis. Sixteen stables out of 41 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 suggesting that 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-resistance 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-resistance IncHI1 plasmids carrying ESBL gene possibly mediated by the use of scFOS as prebiotic in horses.

Microbial Genomics

We undertook a comprehensive comparative analysis of a collection of 30 small (<25 kb) non-con... more We undertook a comprehensive comparative analysis of a collection of 30 small (<25 kb) non-conjugative Escherichia coli plasmids previously classified by the gene sharing approach into 10 families, as well as plasmids found in the National Center for Biotechnology Information (NCBI) nucleotide database sharing similar genomic sequences. In total, 302 mobilizable (belonging to 2 MOBrep and 5 MOBRNA families) and 106 non-transferable/relaxase-negative (belonging to three ReLRNA families) plasmids were explored. The most striking feature was the specialization of the plasmid family types that was not related to their transmission mode and replication system. We observed a range of host strain specificity, from narrow E. coli host specificity to broad host range specificity, including a wide spectrum of Enterobacteriaceae . We found a wide variety of toxin/antitoxin systems and colicin operons in the plasmids, whose numbers and types varied according to the plasmid family type. The plasmids carried genes conferring resistance spanning almost all of the antibiotic classes, from those to which resistance developed early, such as sulphonamides, to those for which resistance has only developed recently, such as colistin. However, the prevalence of the resistance genes varied greatly according to the family type, ranging from 0 to 100 %. The evolutionary history of the plasmids based on the family type core genes showed variability within family nucleotide divergences in the range of E. coli chromosomal housekeeping genes, indicating long-term co-evolution between plasmids and host strains. In rare cases, a low evolutionary divergence suggested the massive spread of an epidemic plasmid. Overall, the importance of these small non-conjugative plasmids in bacterial adaptation varied greatly according to the type of family they belonged to, with each plasmid family having specific hosts and genetic traits.

Frontiers in Microbiology

The integrative mobilizable elements of SGI1-family considerably contribute to the spread of resi... more 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.

Salmonella enterica serotype Kentucky (S. Kentucky) can be a common causative agent of salmonello... more Salmonella enterica serotype Kentucky (S. Kentucky) can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S. Kentucky ST198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug resistant (MDR) S. Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island 1 (variant SGI1-K) conferring resistance ampicillin, streptomycin, gentamicin, sulfamethoxazole, and tetracycline. Phylogeographic analysis indicates this clone emerged in Egypt b...

Journal of Veterinary Internal Medicine

Funding information Institut national de recherche agro-alimentaire (INRA); l'Institut Francais d... more Funding information Institut national de recherche agro-alimentaire (INRA); l'Institut Francais du cheval et de l'équitation (IFCE); OIE Reference Laboratory for E. coli 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 β-lactamase (ESBL)-producing, and AmpC β-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/AmpCassociated 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 bla CTX-M-1. Virulence gene iutA was identified in 1 ESBL/AmpCproducing 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.

Scientific Reports

During infection, Salmonella senses and responds to harsh environments within the host. Persisten... more During infection, Salmonella senses and responds to harsh environments within the host. Persistence in a bile-rich environment is important for Salmonella to infect the small intestine or gallbladder and the multidrug efflux system AcrAB-TolC is required for bile resistance. The genes encoding this system are mainly regulated by the ramRA locus, which is composed of the divergently transcribed ramA and ramR genes. The acrAB and tolC genes are transcriptionally activated by RamA, whose encoding gene is itself transcriptionally repressed by RamR. RamR recognizes multiple drugs; however, the identity of the environmental signals to which it responds is unclear. Here, we describe the crystal structures of RamR in complexes with bile components, including cholic acid and chenodeoxycholic acid, determined at resolutions of 2.0 and 1.8 Å, respectively. Both cholic and chenodeoxycholic acids form four hydrogen bonds with Tyr59, Thr85, Ser137 and Asp152 of RamR, instead of π-π interactions with Phe155, a residue that is important for the recognition of multiple compounds including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6 G. Binding of these compounds to RamR reduces its DNA-binding affinity, resulting in the increased transcription of ramA and acrAB-tolC. Our results reveal that Salmonella senses bile acid components through RamR and then upregulates the expression of RamA, which can lead to induction of acrAB-tolC expression with resulting tolerance to bile-rich environments. Salmonella is a bacterial pathogen that causes a variety of foodborne illnesses in humans. During the course of its infection of the intestinal tract and gallbladder, Salmonella is exposed to bile acids. These are detergent-like biological substances that are synthesized in the liver from cholesterol and stored in the gallbladder. These bile acids possess strong antimicrobial activity, disrupt cell membranes, denature proteins and trigger DNA damage 1,2. Enteric bacteria such as Salmonella must tolerate the presence of bile acids in order to survive in the gastrointestinal transit and gallbladder 3,4. Enteric bacteria have developed an intrinsic resistance to the toxic effects of bile acids, due to the low permeability of their outer membranes to lipophilic solutes and the presence of active efflux mechanisms 5,6. Salmonella enterica serovar Typhimurium (S. Typhimurium) contains at least nine multidrug efflux systems 7. Among these, the AcrAB-TolC system, whose AcrB transporter belongs to the resistance-nodulation-cell division family, is particularly effective in generating bile acid resistance 7,8. Bile induces the expression of acrAB 8 , and this induction is mediated by the transcriptional regulators RamA and RamR 9,10. The global transcriptional activator RamA, which belongs to the AraC/XylS family of regulatory proteins, activates the expression of acrAB and tolC genes 9. The local transcriptional repressor RamR, which is located directly upstream of ramA, belongs to the TetR family of regulatory proteins and represses the expression of both ramA and ramR (Fig. 1a) 10,11. Additionally, it has recently been found that bile inhibits the binding of RamR to the ramA promoter region and activates ramA gene expression, resulting in the increased expression of acrAB and tolC 10. Our previous biochemical and structural studies found that RamR can recognize multiple compounds, including berberine, crystal violet, dequalinium, ethidium bromide and rhodamine 6 G 12. Binding of these compounds to RamR results in the increased expression of ramA; all the compounds recognized by RamR are also known

mSphere

Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that... more Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that harbors a great diversity of antimicrobial resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis . A serious threat to public health was revealed in the recent description in P. mirabilis of a SGI1-derivative multidrug resistance island named PGI1 ( Proteus genomic island 1) carrying extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase resistance genes, bla VEB-6 and bla NDM-1 , respectively. Here, we report the first description of Salmonella genomic island 1 (SGI1) in a multidrug-resistant clinical Morganella morganii subsp. morganii strain isolated from a patient in France in 2013. Complete-genome sequencing of the strain revealed SGI1 variant SGI1-L carrying resistance genes dfrA15 , floR , tetA (G), bla PSE-1 (now referred to as bla CARB-2 ), and sul1 , conferring resistance to trimethoprim, phenicols, tetracyclines, amoxi...

Microbial genomics, 2018

To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in... more To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic...

Journal of Global Antimicrobial Resistance

mBio, Aug 23, 2016

For 100 years, it has been obvious that Salmonella enterica strains sharing the serotype with the... more For 100 years, it has been obvious that Salmonella enterica strains sharing the serotype with the formula 1,4,[5],12:b:1,2-now known as Paratyphi B-can cause diseases ranging from serious systemic infections to self-limiting gastroenteritis. Despite considerable predicted diversity between strains carrying the common Paratyphi B serotype, there remain few methods that subdivide the group into groups that are congruent with their disease phenotypes. Paratyphi B therefore represents one of the canonical examples in Salmonella where serotyping combined with classical microbiological tests fails to provide clinically informative information. Here, we use genomics to provide the first high-resolution view of this serotype, placing it into a wider genomic context of the Salmonella enterica species. These analyses reveal why it has been impossible to subdivide this serotype based upon phenotypic and limited molecular approaches. By examining the genomic data in detail, we are able to ident...

Environmental Microbiology Reports, 2016

Wastewater treatment plants (WWTP) receiving effluents from food-producing animals and humans may... more Wastewater treatment plants (WWTP) receiving effluents from food-producing animals and humans may contribute to the spread of extended-spectrum β-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.

The Journal of antimicrobial chemotherapy, Jan 11, 2015

To characterize MDR genomic islands related to Salmonella genomic island 1 (SGI1) and Proteus gen... more To characterize MDR genomic islands related to Salmonella genomic island 1 (SGI1) and Proteus genomic island 1 (PGI1) in Proteus mirabilis from human and animal sources in France in light of the previously reported cases. A total of 52 and 46 P. mirabilis clinical strains from human and animal sources, respectively, were studied for the period 2010-13. MDR was assessed by antimicrobial susceptibility testing, PCR detection of SGI1 and PGI1 and PCR mapping of the MDR regions. The diversity of the SGI1/PGI1-positive P. mirabilis strains was assessed by PFGE. Twelve P. mirabilis strains (5 humans and 7 dogs) were found to harbour an MDR island related to SGI1 or PGI1. Among them, several SGI1 variants were identified in diverse P. mirabilis genetic backgrounds. The variant SGI1-V, which harbours the ESBL blaVEB-6 gene, was found in closely genetically related human and dog P. mirabilis strains. The recently described PGI1 element was also identified in human and dog strains. Finally, o...

Front. Microbiol., 2013

A screening for non-target mutations affecting fluoroquinolone susceptibility was conducted in ep... more A screening for non-target mutations affecting fluoroquinolone susceptibility was conducted in epidemic multidrug-resistant Salmonella enterica serovar Kentucky ST198. Among a panel of representative isolates (n = 27), covering the epidemic, only three showed distinct mutations in ramR resulting in enhanced expression of genes encoding the AcrAB-TolC efflux system and low increase in ciprofloxacin MIC. No mutations were detected in other regulatory regions of this efflux system. Ciprofloxacin resistance in serovar Kentucky ST198 is thus currently mainly due to multiple target gene mutations.