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Carbapenemase-producing Escherichia coli (CP-Ec) represents a major public health threat with a risk of dissemination in the community as has occurred for lineages producing extended-spectrum β-lactamases. To characterize the extent of CP-Ec spread in France, isolates from screening and infection samples received at the French National Reference Center (F-NRC) laboratory for carbapenemase-producing Enterobacterales were investigated. A total of 691 CP-Ec isolates collected between 2012 and 2015 and 22 isolates collected before 2012 were fully sequenced. Analysis of their genome sequences revealed some disseminating multidrug-resistant (MDR) lineages frequently acquiring diverse carbapenemase genes mainly belonging to clonal complex 23 (CC23) (sequence type 410 [ST410]) and CC10 (ST10 and ST167) and sporadic isolates, including rare ST131 isolates (n = 17). However, the most represented sequence type (ST) was ST38 (n = 92) with four disseminated lineages carrying blaOXA-48-like genes inserted in the chromosome. Globally, the most frequent carbapenemase gene (n = 457) was blaOXA-48. It was also less frequently associated with MDR isolates being the only resistance gene in 119 isolates. Thus, outside the ST38 clades, its acquisition was frequently sporadic with no sign of dissemination, reflecting the circulation of the IncL plasmid pOXA-48 in France and its high frequency of conjugation. In contrast, blaOXA-181 and blaNDM genes were often associated with the evolution of MDR E. coli lineages characterized by mutations in ftsI and ompC. IMPORTANCE Carbapenemase-producing Escherichia coli (CP-Ec) might be difficult to detect, as MICs can be very low. However, their absolute number and their proportion among carbapenem-resistant Enterobacterales have been increasing, as reported by WHO and national surveillance programs. This suggests a still largely uncharacterized community spread of these isolates. Here, we have characterized the diversity and evolution of CP-Ec isolated in France before 2016. We show that carbapenemase genes are associated with a wide variety of E. coli genomic backgrounds and a small number of dominant phylogenetic lineages. In a significant proportion of CP-Ec, the most frequent carbapenemase gene blaOXA-48, was detected in isolates lacking any other resistance gene, reflecting the dissemination of pOXA-48 plasmids, likely in the absence of any antibiotic pressure. In contrast, carbapenemase gene transfer may also occur in multidrug-resistant E. coli, ultimately giving rise to at-risk lineages encoding carbapenemases with a high potential of dissemination.

Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain 'live' (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines' implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.

Background: To investigate the potential correlation between the rates of antimicrobial drug consumption and the prevalence of antimicrobial resistance among clinical Acinetobacter baumannii recovered in a tertiary care hospital in Tunisia. Methods: The microbiological and epidemiological profiles of A. baumannii infections at the Hospital Sahloul, Sousse, were investigated between 2001 to 2004 and 2012 to 2015 along with the consumption record of broad-spectrum antibiotics. Results: Our data showed that extensively drug-resistant A. baumannii (XDRAb) isolates increased from 11.2% to 30.5% between 2012 and 2015 and disseminated endemically for a long time. Furthermore, we evidenced a drastic increase of carbapenem-resistant A. baumannii isolates from 29.5% in 2001 up to 88.6% in 2015 (612/691). This rise could be paralleled with a significant increase in antibiotic consumption over the last 15 years, especially with the sharp increase in the annual consumption of imipenem (r = 0.816 and p 3). A noteworthy correlation between carbapenem use and resistance rate (r = 0.778, p Conclusion: Feedback of these data to clinicians and decision-makers in the local setting was crucial to promote the rational use of antimicrobials and to raise awareness to strictly implement hygiene measures to limit the spread of these XDRAb isolates, to prevent colonization and subsequent infection.

Over the last two decades, antimicrobial resistance has become a global health problem. In Gram-negative bacteria, metallo-β-lactamases (MBLs), which inactivate virtually all β-lactams, increasingly contribute to this phenomenon. The aim of this study is to characterize VIM-52, a His224Arg variant of VIM-1, identified in a clinical isolate. VIM-52 conferred lower MICs to cefepime and ceftazidime as compared to VIM-1. These results were confirmed by steady state kinetic measurements, where VIM-52 yielded a lower activity towards ceftazidime and cefepime but not against carbapenems. Residue 224 is part of the L10 loop (residues 221-241), which borders the active site. As Arg 224 and Ser 228 are both playing an important and interrelated role in enzymatic activity, stability and substrate specificity for the MBLs, targeted mutagenesis at both positions were performed and further confirmed their crucial role for substrate specificity.

Additional file 3: Table S3. Oligonucleotides used in this work. Table S4. Mutations detected in MG1655 strains derivatives mutated in ftsI. Table S5. Genomic features of the E. coli ST410 isolate Ec-MAD. Table S6. Antibiotics susceptibility testing of the ST410 isolate Ec-MAD. Table S7. Distribution and effect of point mutations in the OXA-181 E. coli ST410 subclade MRCA. Table S8. Mutations predicted with a functional effect using the SIFT algorithm. Table S10. Antibiotic resistance gene content of ST410 isolates analysed in Fig. 7.

International audience; Colistin has become a last-resort antibiotic for the treatment of infections caused by highly drug-resistant Gram-negative bacteria. Moreover, it has been widely used in the livestock sector. As a consequence, colistin resistance is emerging worldwide. Among the colistin resistance mechanisms, the spread of the plasmid-encoded colistin resistance gene mcr-1 (mostly in Escherichia coli) is of particular concern due to its increased transferability compared to that of chromosome-encoded resistance. The early detection of MCR-1-producing bacteria is essential to prevent further spread and provide appropriate antimicrobial therapy. Lateral flow immunoassays (LFIAs) were manufactured with selected monoclonal antibodies. A collection of 177 human and 121 animal enterobacterial isolates was tested in a multicentric study. One bacterial colony grown on agar plates was suspended in extraction buffer and dispensed on the cassette. Migration was allowed for 15 min, and the results were monitored by the appearance of a specific band. The positive results showed a pink line resulting in an unambiguous interpretation. All MCR-1-producing isolates were found to be positive by the LFIA, and no false-negative results were observed. Three out of four MCR-2-producing isolates were also found to be positive. Our test does not detect MCR-3-, MCR-4-, or MCR-5-producing isolates. LFIA allows the detection of MCR-1 with 100% sensitivity and 98% specificity. This test is fast, sensitive, specific, easy to use, and cost-effective and can therefore be implemented in any microbiology laboratory worldwide. LFIA is a major tool for the rapid detection and monitoring of MCR-1 producers in humans and animals.

Ocular herpes simplex keratitis (HSK) is a consequence of viral reactivations from trigeminal ganglia (TG) and occurs almost exclusively in the same eye in humans. In our murine oro-ocular (OO) model, HSV-1 inoculation in one side of the lip propagates virus to infect the ipsilateral TG. Replication here allows infection of the brainstem, and infection of the contralateral TG. Interestingly, HSK is observed in our OO model only from the eye ipsilateral to site of lip infection. Thus, unilateral restriction of HSV-1 may be due to differential kinetics of virus arrival in the ipsilateral versus contralateral TG. We inoculated mice with HSV-1 reporter viruses, and then superinfected them to monitor changes in acute and latent phase gene expression in TG after superinfection, compared to control (single inoculation). Delaying superinfection by 4 days after initial right lip inoculation elicited failed superinfecting-virus gene expression, and eliminated clinical signs of disease. Initial inoculation with a thymidine kinase-deficient HSV-1 (TKdel) completely abolished reactivation of WT superinfecting virus from TG during latent stage. In light of these seemingly failed infections, viral genome was detected in both TGs. Our data demonstrate that inoculation of HSV-1 in the lip propagates virus to both TG, but with delay in reaching the TG contralateral to the side of lip infection. This delay is responsible for restricting viral replication to the ipsilateral TG, which abrogates ocular disease and viral reactivations from the contralateral side. These observations may help to understand why HSK is observed unilaterally in humans, and provides insight into vaccine strategies to protect against HSK.IMPORTANCEHerpetic keratitis (HK) is the leading cause of blindness by an infectious agent in the developed world. This disease can occur after reactivation of Herpes simplex virus 1 in the trigeminal ganglia leading to dissemination of virus to, and infection of, the cornea. A clinical paradox is evidenced by the bilateral presence of latent viral genomes in both trigeminal ganglia, while for any given patient the disease is unilateral with recurrences in a single eye. Our study links the kinetics of early infection to unilateral disease phenomenon, and demonstrates protection against viral reactivation when kinetics are exploited. Our results have direct implications in the understanding of human disease pathogenesis, and immunotherapeutic strategies for the treatment of HK and viral reactivations.

We compared extended-spectrum β-lactamase-producing Escherichia coli isolates from meat and fish, gut-colonized women, and infected patients in Cambodia. Nearly half of isolates from women were phylogenetically related to food-origin isolates; a subset had identical multilocus sequence types, extended-spectrum β-lactamase types, and antimicrobial resistance patterns. Eating sun-dried poultry may be an exposure route. ispartof: EMERGING INFECTIOUS DISEASES vol:25 issue:1 pages:126-131 ispartof: location:United States status: published

Background Polymyxins are currently considered a last-resort treatment for infections caused by MDR Gram-negative bacteria. Recently, the emergence of carbapenemase-producing Enterobacteriaceae has accelerated the use of polymyxins in the clinic, resulting in an increase in polymyxin-resistant bacteria. Polymyxin resistance arises through modification of lipid A, such as the addition of phosphoethanolamine (pETN). The underlying mechanisms involve numerous chromosome-encoded genes or, more worryingly, a plasmid-encoded pETN transferase named MCR. Currently, detection of polymyxin resistance is difficult and time consuming. Objectives To develop a rapid diagnostic test that can identify polymyxin resistance and at the same time differentiate between chromosome- and plasmid-encoded resistances. Methods We developed a MALDI-TOF MS-based method, named the MALDIxin test, which allows the detection of polymyxin resistance-related modifications to lipid A (i.e. pETN addition), on intact bacteria, in Results Using a characterized collection of polymyxin-susceptible and -resistant Escherichia coli, we demonstrated that our method is able to identify polymyxin-resistant isolates in 15 min whilst simultaneously discriminating between chromosome- and plasmid-encoded resistance. We validated the MALDIxin test on different media, using fresh and aged colonies and show that it successfully detects all MCR-1 producers in a blindly analysed set of carbapenemase-producing E. coli strains. Conclusions The MALDIxin test is an accurate, rapid, cost-effective and scalable method that represents a major advance in the diagnosis of polymyxin resistance by directly assessing lipid A modifications in intact bacteria.

Carbapenemase-producing have increasingly been reported worldwide, with an ever-increasing heterogeneity of carbapenem resistance mechanisms depending on the bacterial species and its geographical location. OXA-198 is a plasmid-encoded class D β-lactamase involved in carbapenem-resistance in one isolate from Belgium. In the setting of a multicentre survey of carbapenem-resistance in in Belgian hospitals in 2013, three additional OXA-198 producing originating from patients hospitalized at one hospital were detected. To reveal the molecular mechanism underlying the reduced susceptibility to carbapenems, MICs, whole genome sequencing (WGS) and PCR reactions to confirm the genetic organization were performed. The plasmid harboring gene was characterized alongside with the genetic relatedness of the four isolates. The gene was harbored on a class 1 integron carried itself by a ca. 49-kb IncP-type plasmid proposed as IncP11. The same plasmid was present in all four isolates. MLST typing revealed that they all belonged to ST-446 and SNP analysis revealed only a few differences between these isolates. This report describes the structure of a 49-kb plasmid harbouring the gene and the first description of OXA-198 producing isolates associated with a hospital-associated cluster episode.

International audience; The global spread of carbapenemase-producing Enterobacteriaceae (CPE) that are often resistant to most, if not all, classes of antibiotics is a major public health concern. The NDM-1 carbapenemase is among the most worrisome carbapenemases given its rapid worldwide spread. We have developed and evaluated a lateral flow immunoassay (LFIA) (called the NDM LFIA) for the rapid and reliable detection of NDM-like carbapenemase-producing Enterobacteriaceae from culture colonies. We evaluated the NDM LFIA using 175 reference enterobacterial isolates with characterized β-lactamase gene content and 74 nonduplicate consecutive carbapenem-resistant clinical isolates referred for expertise to the French National Reference Center (NRC) for Antibiotic Resistance during a 1-week period (in June 2016). The reference collection included 55 non-carbapenemase producers and 120 carbapenemase producers, including 27 NDM producers. All 27 NDM-like carbapenemase producers of the reference collection were correctly detected in less than 15 min by the NDM LFIA, including 22 strains producing NDM-1, 2 producing NDM-4, 1 producing NDM-5, 1 producing NDM-7, and 1 producing NDM-9. All non-NDM-1 producers gave a negative result with the NDM LFIA. No cross-reaction was observed with carbapenemases (VIM, IMP, NDM, KPC, and OXA-48-like), extended-spectrum β-lactamases (ESBLs) (TEM, SHV, and CTX-M), AmpCs (CMY-2, DHA-2, and ACC-1), and oxacillinases (OXA-1, -2, -9, and -10). Similarly, among the 74 referred nonduplicate consecutive clinical isolates, all 7 NDM-like producers were identified. Overall, the sensitivity and specificity of the assay were 100% for NDM-like carbapenemase detection with strains cultured on agar. The NDM LFIA was efficient, rapid, and easy to implement in the routine workflow of a clinical microbiology laboratory for the confirmation of NDM-like carbapenemase-producing Enterobacteriaceae.

The global spread of carbapenemase-producing Enterobacteriaceae (CPE) that are often resistant to most, if not all, classes of antibiotics is a major public health concern. The NDM-1 carbapenemase is among the most worrisome carbapenemases given its rapid worldwide spread. We have developed and evaluated a lateral flow immunoassay (LFIA) (called the NDM LFIA) for the rapid and reliable detection of NDM-like carbapenemase-producing Enterobacteriaceae from culture colonies. We evaluated the NDM LFIA using 175 reference enterobacterial isolates with characterized β-lactamase gene content and 74 nonduplicate consecutive carbapenem-resistant clinical isolates referred for expertise to the French National Reference Center (NRC) for Antibiotic Resistance during a 1-week period (in June 2016). The reference collection included 55 non-carbapenemase producers and 120 carbapenemase producers, including 27 NDM producers. All 27 NDM-like carbapenemase producers of the reference collection were correctly detected in less than 15 min by the NDM LFIA, including 22 strains producing NDM-1, 2 producing NDM-4, 1 producing NDM-5, 1 producing NDM-7, and 1 producing NDM-9. All non-NDM-1 producers gave a negative result with the NDM LFIA. No cross-reaction was observed with carbapenemases (VIM, IMP, NDM, KPC, and OXA-48-like), extended-spectrum β-lactamases (ESBLs) (TEM, SHV, and CTX-M), AmpCs (CMY-2, DHA-2, and ACC-1), and oxacillinases (OXA-1, -2, -9, and -10). Similarly, among the 74 referred nonduplicate consecutive clinical isolates, all 7 NDM-like producers were identified. Overall, the sensitivity and specificity of the assay were 100% for NDM-like carbapenemase detection with strains cultured on agar. The NDM LFIA was efficient, rapid, and easy to implement in the routine workflow of a clinical microbiology laboratory for the confirmation of NDM-like carbapenemase-producing Enterobacteriaceae.

Objectives The objective of this study was the evaluation of the performance of two commercially available biochemical tests for the rapid detection of carbapenemase-producing Enterobacteriaceae compared with a home-made technique. Methods A collection of 150 enterobacterial isolates, including 132 isolates with decreased susceptibility to at least one carbapenem molecule, were tested for carbapenemase activity using the RAPIDEC® CARBA NP (bioMérieux), the Rapid CARB Screen® (Rosco Diagnostica) and the home-made Carba NP test. This strain collection included 55 non-carbapenemase producers, 21 KPC producers, 21 NDM producers, 17 VIM producers, 11 IMP producers, 16 OXA-48 producers and 9 OXA-48-like producers (OXA-162, OXA-181, OXA-204, OXA-232 and OXA-244). Results The RAPIDEC® CARBA NP detected all carbapenemase producers except a single OXA-244 producer. Using the Rapid CARB Screen®, one KPC-2, two NDM-1, one OXA-48 and five OXA-48 variant producers gave equivocal results and one OXA-244 producer was not detected. Using the Carba NP test, the same OXA-244 producer was not detected and one OXA-181 producer and one OXA-244 producer gave equivocal results. Sensitivity and specificity were 99% (95% CI 94.3%-99.8%) and 100% (95% CI 93.5%-100%), respectively, for the RAPIDEC® CARBA NP test, 89.5% (95% CI 81.7%-94.2%) and 70.9% (95% CI 57.9%-81.2%) for the Rapid CARB Screen® and 96.8% (95% CI 91.1%-98.9%) and 100% (95% CI 93.5%-100%) for the Carba NP test. The impact of the use of an adequate bacterial inoculum for obtaining the optimal performance with the RAPIDEC® CARBA NP was noted. Conclusions The RAPIDEC® CARBA NP possesses the best performance for rapid and efficient detection of carbapenemase-producing Enterobacteriaceae

A Klebsiella pneumoniae clinical isolate resistant to imipenem was recovered from blood culture of a 4 years old child with the diagnosis of acute precursor B cell lymphoblastic leukemia. PCR assays of Klebsiella pneumoniae isolate were positive with blaCTX-M and blaVIM genes. Sequence analysis of the 160 bp amplicon matched with blaVIM 1. Patient was discharged on the 15th day of ciprofloxacin theraphy with remission. We report here the first VIM-1 positive Klebsiella pneumoniae isolate case from Akdeniz University Hospital. Urgent and rapid precautions must be preferred including antibiotic policy and infection control practices when the first case with different resistance patern is detected. Key words: K. Pneumoniae; Metallo-Β-Lactamases; VIM 1., Akut Prekürsör B Hücreli Lenfoblastik Lösemi tanısıyla izlenen 4 yaşındaki bir çocuğun kan kültürü örneğinden imipenem dirençli Klebsiella pneumoniae izole edildi. İzolatın PCR analizi sonuçları VIM ve CTX- M enzimleri açısından pozitif olarak saptandı. Yapılan DNA sekans analizi sonucunda 160bp'lik bölge blaVIM-1 ile uyumlu olarak bulundu. Hasta siprofloksasin tedavisinin 15. gününde remisyonla taburcu edildi. Bu olguda Akdeniz Üniversitesi Hastanesi'nde ilk kez saptanan VIM 1 pozitif Klebsiella pneumoniae izolatı sunulmuştur. Farklı direnç paternine sahip bir vaka görüldüğünde, hızlı bir şekilde antibiyotik politikalarını da içeren infeksiyon kontrol önlemleri alınmalıdır. Anahtar kelimeler: K. Pneumoniae; Metallo-Β-Laktamaz; VIM 1.

International audience

VEB-1 extended-spectrum beta-lactamase-producing Acinetobacter baumannii was responsible for an outbreak in hospitals in France. A national alert was triggered in September 2003 when 4 hospitals reported clusters of A. baumannii infection with similar susceptibility profiles. Case definitions and laboratory guidelines were disseminated, and prospective surveillance was implemented; strains were sent to a single laboratory for characterization and typing. From April 2003 through June 2004, 53 hospitals reported 290 cases of A. baumannii infection or colonization; 275 isolates were bla(VEB-1)-positive and clonally related. Cases were first reported in 5 districts of northern France, then in 10 other districts in 4 regions. Within a region, interhospital spread was associated with patient transfer. In northern France, investigation and control measures led to a reduction of reported cases after January 2004. The national alert enabled early control of new clusters, demonstrating the usefulness of early warning about antimicrobial drug resist.

International audience; Four isolates (KP1–4) were recovered sequentially from an infected patient. Whilst KP1–3 were resistant to all β-lactams except carbapenems, KP4 recovered after 24 days of imipenem-containing treatment showed additional resistance to carbapenems. No carbapenem hydrolysis could be identified in KP4. Molecular characterisation revealed that KP1–4 were indistinguishable by pulsed-field gel electrophoresis, contained a 95-kb self-transferable plasmid harbouring and genes and a 65-kb plasmid that was not transferred by conjugation into , and harboured the plasmid-mediated AmpC β-lactamase gene. In addition, KP4 failed to express OmpK36 owing to a point mutation leading to a premature stop of the protein. This study demonstrates development of carbapenem resistance related to loss of OmpK36 expression in a isolate harbouring extended-spectrum β-lactamse and plasmid-mediated cephalosporinase genes following prolonged imipenem exposure.

During a PCR-based surveillance study of beta-lactam resistance, 125 multidrug-resistant (MDR) Acinetobacter baumannii isolates were obtained from 18 hospitals in Belgium from January 2008 to December 2009. Nine GES-positive A. baumannii isolates were detected at 6 Belgian hospitals. DNA sequencing of the blaGES genes identified GES-11, GES-12 and a novel variant GES-14 which differs from GES-11 by a single amino acid substitution (Gly170Ser). All index isolates were travel-associated and originated from patients transferred from Turkey (n=2), Egypt (n=2) and Palestinian territories (Gaza) (n=2). A nosocomial outbreak involving three additional patients occurred in a burn unit at a single hospital. No clonal relatedness could be established between the 6 index isolates by PFGE analysis. Three different alleles (the plasmid-located blaGES-11 and blaGES-12 and a likely chromosomal-located novel variant blaGES-14) were detected as part of a class 1 integron also including aac6'Ib and dfrA7 genes. Restriction analysis of plasmids suggests a common origin for the plasmids bearing blaGES-11 and blaGES-12. Cloning of the blaGES genes in E. coli identified GES-14 as hydrolyzing imipenem while GES-12 showed the highest specific activity against ceftazidime. This report highlights the emergence of various blaGES-like genes, especially those conferring carbapenem-resistance in A. baumannii and its importation in Western Europe from Middle Eastern countries.

Proteus mirabilis NEL-1 was isolated from a urine sample of a patient hospitalized in a long-term care facility. Strain NEL-1 produced a beta-lactamase with a pI of 5.2 conferring resistance to amoxicillin and amoxicillin-clavulanic acid. Sequencing of a PCR amplicon by using TEM-specific primers revealed a novel bla(TEM) gene, bla(TEM-67). TEM-67 was an IRT-1-like TEM derivative related to TEM-65 (Lys39, Cys244) with an additional Leu21Ile amino acid substitution in the leader peptide. The biochemical properties of TEM-67 were equivalent to those described for TEM-65. Analysis of sequences surrounding bla(TEM-67) revealed that it was located on a transposon, Tn1, which itself was located on a 48-kb non-self-transferable plasmid, pANG-1. Electroporation of plasmid pANG-1 into Escherichia coli DH10B resulted in the integration of bla(TEM-67) into the chromosome, whereas it remained episomal in the P. mirabilis CIP103181 reference strain. Further characterization of pANG-1 revealed the presence of two identical sequences on both sides of Tn1 that contained an IS26 insertion sequence followed by a novel colicin gene, colZ, which had 20% amino acid identity with other colicin genes. The characterization of this novel TEM derivative provides further evidence for the large diversity of plasmid-encoded beta-lactamases produced in P. mirabilis and for their spread to other enterobacterial species through transposable-element-mediated events.

Despite public health implications, factors contributing to the emergence and the dissemination of carbapenemase-producing E. coli lineages have not been explored. In this article, by using an in-depth evolutionary and functional analysis of E. coli Sequence Tyoe (ST)410 and by extending it to the whole E. coli species, we show that acquisition of carbapenemase genes followed different evolutionary trajectories. In most STs it occurred preferentially in specific disseminated lineages mutated in ftsI encoding penicillin-binding protein 3 (PBP3) and/or in the ompC and ompF porin genes. We also show that these mutations lead to a reduced susceptibility to some beta-lactams including ertapenem. In phylogroup D and in particular in ST38, a specific ompC allele might explain the high prevalence of CP-Ec isolates within this lineage. On the other hand, we did not identify mutations in ftsI and ompC among ST131 isolates. These new data on evolution of CP-Ec allow us to propose a model for their selection and dissemination.

Additional file 4: Figure S1. Number of antibiotic resistance genes (ARG) according to the phylogenetic group among E. coli ST410 isolates. Figure S2. Recombination events in isolates of the E. coli ST410 FQR clade. Figure S3. Phylogenetic distribution of E. coli isolates mutated in ftsI. Figure S4. Recombination events at the dcw and ompC loci. Figure S5. Phylogeny and mutations in non-redundant E. coli ST131 CP-Ec isolates. Figure S6. Phylogeny and mutations in non-redundant CP-Ec isolates of ST48, ST206, ST224, ST359, ST361, ST448 and ST617. Figure S7. Phylogeny and mutations in non-redundant E. coli isolates of phylogroup D. Figure S8. Phylogeny and mutations of ST10, ST226, and ST746 non-redundant E. coli isolates. Figure S9. Estimated fitness of E. coli ST410 strains in rich and minimal media.

Additional file 4: Figure S1. Number of antibiotic resistance genes (ARG) according to the phylogenetic group among E. coli ST410 isolates. Figure S2. Recombination events in isolates of the E. coli ST410 FQR clade. Figure S3. Phylogenetic distribution of E. coli isolates mutated in ftsI. Figure S4. Recombination events at the dcw and ompC loci. Figure S5. Phylogeny and mutations in non-redundant E. coli ST131 CP-Ec isolates. Figure S6. Phylogeny and mutations in non-redundant CP-Ec isolates of ST48, ST206, ST224, ST359, ST361, ST448 and ST617. Figure S7. Phylogeny and mutations in non-redundant E. coli isolates of phylogroup D. Figure S8. Phylogeny and mutations of ST10, ST226, and ST746 non-redundant E. coli isolates. Figure S9. Estimated fitness of E. coli ST410 strains in rich and minimal media.