23 results on '"Bonnin, Rémy A"'
Search Results
2. Antimicrobial Resistance in Enterobacterales Recovered from Urinary Tract Infections in France.
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Farfour, Eric, Dortet, Laurent, Guillard, Thomas, Chatelain, Nicolas, Poisson, Agathe, Mizrahi, Assaf, Fournier, Damien, Bonnin, Rémy A., Degand, Nicolas, Morand, Philippe, Janvier, Frédéric, Fihman, Vincent, Corvec, Stéphane, Broutin, Lauranne, Le Brun, Cécile, Yin, Nicolas, Héry-Arnaud, Geneviève, Grillon, Antoine, Bille, Emmanuelle, and Jean-Pierre, Hélène
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DRUG resistance in microorganisms ,URINARY tract infections ,ESCHERICHIA coli ,URINARY organs ,ENTEROBACTER cloacae ,DRUG resistance in bacteria ,PATHOLOGICAL laboratories ,LONG-term care facilities - Abstract
In the context of increasing antimicrobial resistance in Enterobacterales, the management of these UTIs has become challenging. We retrospectively assess the prevalence of antimicrobial resistance in Enterobacterales isolates recovered from urinary tract samples in France, between 1 September 2017, to 31 August 2018. Twenty-six French clinical laboratories provided the susceptibility of 134,162 Enterobacterales isolates to 17 antimicrobials. The most frequent species were E. coli (72.0%), Klebsiella pneumoniae (9.7%), Proteus mirabilis (5.8%), and Enterobacter cloacae complex (2.9%). The overall rate of ESBL-producing Enterobacterales was 6.7%, and ranged from 1.0% in P. mirabilis to 19.5% in K. pneumoniae, and from 3.1% in outpatients to 13.6% in long-term care facilities. Overall, 4.1%, 9.3% and 10.5% of the isolates were resistant to cefoxitin, temocillin and pivmecillinam. Cotrimoxazole was the less active compound with 23.4% resistance. Conversely, 4.4%, 12.9%, and 14.3% of the strains were resistant to fosfomycin, nitrofurantoin, and ciprofloxacin. However, less than 1% of E. coli was resistant to fosfomycin and nitrofurantoin. We identified several trends in antibiotics resistances among Enterobacterales isolates recovered from the urinary tract samples in France. Carbapenem-sparing drugs, such as temocillin, mecillinam, fosfomycin, cefoxitin, and nitrofurantoin, remained highly active, including towards ESBL-E. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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3. Undetectable Production of the VIM-1 Carbapenemase in an Atlantibacter hermannii Clinical Isolate.
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Girlich, Delphine, Bonnin, Rémy A., Proust, Alexis, Naas, Thierry, and Dortet, Laurent
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IMIPENEM ,CARBAPENEMASE ,CARBAPENEMS ,ENTEROBACTER cloacae ,CHROMOSOME duplication ,ESCHERICHIA coli ,HOSPITAL patients - Abstract
The differential expression of VIM-1 in Atlantibacter hermannii WEB-2 and Enterobacter hormaechei ssp. hoffmannii WEB-1 clinical isolates from a rectal swab of a hospitalized patient in France was investigated. A. hermannii WEB-2 was resistant to all β-lactams except carbapenems. It produced ESBL SHV-12, but the Carba NP test failed to detect any carbapenemase activity despite the production of VIM-1. Conversely, E. hormaechei WEB-1, previously recovered from the same patient, was positive for the detection of carbapenemase activity. The bla
VIM–1 gene was located on a plasmid and embedded within class 1 integron. Both plasmids were of the same IncA incompatibility group and conferred the same resistance pattern when electroporated in Escherichia coli TOP10 or Enterobacter cloacae CIP7933. Quantitative RT-PCR experiments indicated a weaker replication of pWEB-2 in A. hermannii as compared to E. hormaechei. An isogenic mutant of A. hermannii WEB-2 selected after sequential passages with increased concentrations of imipenem possessed higher MICs for carbapenems and cephalosporins including cefiderocol, higher levels of the blaVIM–1 gene transcripts, and detectable carbapenemase activity using the Carba NP test. Assessment of read coverage demonstrated that a duplication of the region surrounding blaVIM–1 gene occurred in the A. hermannii mutant with detectable carbapenemase activity. The lack of detection of the VIM-1 carbapenemase activity in A. hermannii WEB-2 isolate was likely due to a weak replication of the IncA plasmid harboring the blaVIM–1 gene. Imipenem as selective pressure led to a duplication of this gene on the plasmid and to the restoration of a significant carbapenem-hydrolyzing phenotype. [ABSTRACT FROM AUTHOR]- Published
- 2021
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4. Emergence and Polyclonal Dissemination of OXA-244-Producing Escherichia coli, France.
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Emeraud, Cecile, Girlich, Delphine, Bonnin, Rémy A., Jousset, Agnès B., Naas, Thierry, and Dortet, Laurent
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ESCHERICHIA coli - Abstract
Since 2016, OXA-244-producing Escherichia coli has been increasingly isolated in France. We sequenced 97 OXA-244-producing E. coli isolates and found a wide diversity of sequence types and a high prevalence of sequence type 38. Long-read sequencing demonstrated the chromosomal location of blaOXA-244 inside the entire or truncated Tn51098. [ABSTRACT FROM AUTHOR]
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- 2021
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5. Characterization of VIM-1-, NDM-1- and OXA-48-producing Citrobacter freundii in France.
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Biez, Laura, Bonnin, Rémy A., Naas, Thierry, and Dortet, Laurent
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BACTERIAL proteins , *CITROBACTER , *ENTEROBACTERIACEAE diseases , *HYDROLASES , *MICROBIAL sensitivity tests , *ANTIBIOTICS , *PHARMACODYNAMICS - Published
- 2022
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6. Screening of OXA-244 producers, a difficult-to-detect and emerging OXA-48 variant?
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Emeraud, Cecile, Biez, Laura, Girlich, Delphine, Jousset, Agnès B, Naas, Thierry, Bonnin, Rémy A, and Dortet, Laurent
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IMIPENEM ,ESCHERICHIA coli ,AMINO acids ,CARBAPENEMS ,BETA lactamases ,ANTI-infective agents ,BACTERIAL proteins ,IN vitro studies ,SEQUENCE analysis ,BACTERIOLOGY technique ,HYDROLASES - Abstract
Background: OXA-244, a single amino acid variant of OXA-48, demonstrates weaker hydrolytic activity towards carbapenems and temocillin compared with OXA-48. Of note, these antimicrobials are present in high concentrations in several carbapenemase-producing Enterobacterales (CPE) screening media. As a result, some screening media fail to grow OXA-244-producing isolates, while the prevalence of OXA-244 producers is constantly increasing in France.Methods: Here, we evaluate the performance of three commercially available CPE screening media [ChromID® CARBA SMART (bioMérieux), Brilliance™ CRE (Thermo Fisher) and mSuperCARBA™ (MAST Diagnostic)] for their ability to detect OXA-244 producers (n = 101). As OXA-244 producers may also express an ESBL, two additional ESBL screening media were tested (Brilliance™ ESBL and ChromID® BLSE). MICs of temocillin and imipenem were determined by broth microdilution. The clonality of OXA-244-producing Escherichia coli isolates (n = 97) was assessed by MLST.Results: Overall, the sensitivity of the ChromID® CARBA SMART, Brilliance™ CRE and mSuperCARBA™ media were 14% (95% CI = 8.1%-22.5%), 54% (95% CI = 43.3%-63.4%) and 99% (95% CI = 93.8%-100%), respectively, for the detection of OXA-244 producers. Among the 101 OXA-244-producing isolates, 96% were E. coli and 77%-78% grew on ESBL screening media. MLST analysis identified five main STs among OXA-244-producing E. coli isolates: ST38 (n = 37), ST361 (n = 17), ST69 (n = 12), ST167 (n = 11) and ST10 (n = 8).Conclusions: Our results demonstrated that the mSuperCARBA™ medium is very efficient in the detection of OXA-244 producers, unlike the ChromID® CARBA SMART medium. The high prevalence of ESBLs among OXA-244 producers allowed detection of 77%-78% of them using ESBL-specific screening media. [ABSTRACT FROM AUTHOR]- Published
- 2020
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7. Emergence of New Non-Clonal Group 258 High-Risk Clones among Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Isolates, France.
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Bonnin, Rémy A., Jousset, Agnès B., Chiarelli, Adriana, Emeraud, Cécile, Glaser, Philippe, Naas, Thierry, and Dortet, Laurent
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KLEBSIELLA pneumoniae , *DRUG resistance in microorganisms , *SEQUENCE analysis , *KLEBSIELLA , *BACTERIAL proteins , *RESEARCH , *RESEARCH methodology , *MEDICAL cooperation , *EVALUATION research , *KLEBSIELLA infections , *HYDROLASES , *COMPARATIVE studies , *CELLS , *ANTIBIOTICS , *PHARMACODYNAMICS ,WESTERN countries - Abstract
The worldwide spread of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) isolates was reported to be caused by dissemination of 1 clonal complex (i.e., clonal group [CG] 258, which includes sequence types [STs] 258 and 512). We conducted whole-genome sequencing and epidemiologic analysis of all KPC-Kp isolates in France in 2018 and found that new successful high-risk clones of ST147, ST307, ST231, and ST383 are now the main drivers of blaKPC genes. The blaKPC genes were mostly carried by Tn4401a and Tn4401d structures and a new non-Tn4401 element. Our epidemiologic investigations showed that the emergence of these non-CG258 KPC-Kp isolates in France was linked to dissemination of these clones from Portugal. Thus, KPC-Kp epidemiology has changed in Europe, at least in several non-KPC-endemic countries of western Europe, such as France and Portugal, where CG258 is not the most prevalent clone. [ABSTRACT FROM AUTHOR]
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- 2020
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8. Long-lasting successful dissemination of resistance to oxazolidinones in MDR Staphylococcus epidermidis clinical isolates in a tertiary care hospital in France.
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Dortet, Laurent, Glaser, Philippe, Kassis-Chikhani, Najiby, Girlich, Delphine, Ichai, Philippe, Boudon, Marc, Samuel, Didier, Creton, Elodie, Imanci, Dilek, Bonnin, Rémy, Fortineau, Nicolas, and Naas, Thierry
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STAPHYLOCOCCUS epidermidis ,OXAZOLIDINONES ,MULTIDRUG resistance in bacteria ,TERTIARY care ,LINEZOLID ,GENETIC mutation ,PUBLIC health ,THERAPEUTICS - Abstract
Objectives: Patient- and procedure-related changes in modern medicine have turned CoNS into one of the major nosocomial pathogens. Treatments of CoNS infections are challenging owing to the large proportion of MDR strains and oxazolidinones often remain the last active antimicrobial molecules. Here, we have investigated a long-lasting outbreak (2010-13) due to methicillin- and linezolid-resistant (LR) CoNS (n = 168), involving 72 carriers and 49 infected patients.Methods: Antimicrobial susceptibilities were tested by the disc diffusion method and MICs were determined by broth microdilution or Etest. The clonal relationship of LR Staphylococcus epidermidis (LRSE) was first determined using a semi-automated repetitive element palindromic PCR (rep-PCR) method. Then, WGS was performed on all cfr-positive LRSE (n = 30) and LRSE isolates representative of each rep-PCR-defined clone (n = 17). Self-transferability of cfr-carrying plasmids was analysed by filter-mating experiments.Results: This outbreak was caused by the dissemination of three clones (ST2, ST5 and ST22) of LRSE. In these clones, linezolid resistance was caused by (i) mutations in the chromosome-located genes encoding the 23S RNA and L3 and L4 ribosomal proteins, but also by (ii) the dissemination of two different self-conjugative plasmids carrying the cfr gene encoding a 23S RNA methylase. By monitoring linezolid prescriptions in two neighbouring hospitals, we highlighted that the spread of LR-CoNS was strongly associated with linezolid use.Conclusions: Physicians should be aware that plasmid-encoded linezolid resistance has started to disseminate among CoNS and that rational use of oxazolidinones is critical to preserve these molecules as efficient treatment options for MDR Gram-positive pathogens. [ABSTRACT FROM AUTHOR]- Published
- 2018
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9. Carbapenemase-producing Acinetobacter spp. in Cattle, France.
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Poirel, Laurent, Berçot, Béatrice, Millemann, Yves, Bonnin, Rémy A., Pannaux, Glenn, and Nordmann, Patrice
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DRUG resistance in microorganisms ,GRAM-negative bacteria ,DAIRY cattle ,ACINETOBACTER ,PENICILLIN ,BETA lactam antibiotics ,CARBAPENEMS ,TETRACYCLINES ,KANAMYCIN ,FOSFOMYCIN - Abstract
The article focuses on a study which examined the possible occurrence of carbapenemase-producing gram-negative bacteria in dairy cattle in France. Rectal swabs were collected from a number of cows at a dairy farm in August 2010. Isolates belonging to the Acinetobacter genomospecies were detected via molecular techniques based on sequencing of the gyrA, gyrB and rpoB genes. Results of the study showed that all isolates except one were resistant to penicillins, combinations of penicillins and Β-lactamase inhibitors and carbapenems. It also found resistance to tetracycline, kanamycin and fosfomycin among the isolates.
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- 2012
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10. Whole-genome sequencing of NDM-1-producing ST85 Acinetobacter baumannii isolates from Tunisia.
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Jaidane, Nadia, Naas, Thierry, Oueslati, Saoussen, Bernabeu, Sandrine, Boujaafar, Noureddine, Bouallegue, Olfa, and Bonnin, Rémy A.
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ACINETOBACTER baumannii , *BETA lactamases , *ELECTROPORATION , *ELECTRON-transfer catalysis , *ACINETOBACTER , *POLYMERASE chain reaction , *MOLECULAR cloning - Abstract
Highlights • Genomic analysis of NDM-producing Acinetobacter baumannii from Tunisia. • The clonal relationship revealed that these isolates were highly related. • This clone corresponds to a clone recovered from France 5 years ago. • Conjugation and electroporation experiments suggested that the bla NDM-1 gene is likely to be chromosomally located. ABSTRACT Background New Delhi metallo-β-lactamase (NDM)-producing Acinetobacter baumannii have been described in several countries worldwide, and studies have suggested that Acinetobacter spp. could play the role of intermediate progenitor of the bla NDM-1 gene between environmental progenitor and Enterobacteriaceae. Materials and methods In total, 246 carbapenem-resistant A. baumannii isolates from a teaching hospital in Sousse, Tunisia were investigated between 1st June 2013 and 31st December 2015 to detect metallo-ß-lactamase (MBL) production. Polymerase chain reaction (PCR), antibiotic susceptibility testing, and genetic and whole-genome sequencing tools were used to study the underlying carbapenem resistance mechanisms. Results PCR screening of the 246 carbapenem-resistant A. baumannii isolates revealed that 242 of 246 isolates harboured carbapenemase genes (seven of 246 positive for bla NDM-1 , four of 246 positive for bla NDM-1 and bla OXA-23 , 231 positive for bla OXA-23). Conjugation and electroporation experiments suggested that the bla NDM-1 gene is likely to be chromosomally located. All the NDM-1-producing A. baumannii isolates were clonally related, and belonged to ST85 according to the Pasteur Institute's multi-locus sequence typing scheme. Analysis of the immediate genetic environment of the bla NDM-1 gene revealed that the gene was located within a truncated isoform of Tn 125 transposon (ΔTn 125). The bla OXA-23 gene was located within transposon Tn 2008. Conclusion This study showed the dissemination of a single clone of NDM-1-producing A. baumannii in a Tunisian hospital. Countries in north Africa may constitute a significant reservoir for NDM-1-producing A. baumannii. The spread of the bla NDM-1 gene in A. baumannii was linked to clonal spread in this study. [ABSTRACT FROM AUTHOR]
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- 2018
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11. IMI-Type Carbapenemase-Producing Enterobacter cloacae Complex, France and Overseas Regions, 2012-2022.
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Emeraud C, Girlich D, Deschamps M, Rezzoug I, Jacquemin A, Jousset AB, Lecolant S, Locher L, Birer A, Naas T, Bonnin RA, and Dortet L
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- France epidemiology, Humans, History, 21st Century, Disease Outbreaks, beta-Lactamases genetics, beta-Lactamases metabolism, Enterobacter cloacae genetics, Enterobacter cloacae enzymology, Enterobacter cloacae isolation & purification, Enterobacter cloacae drug effects, Enterobacteriaceae Infections epidemiology, Enterobacteriaceae Infections microbiology, Bacterial Proteins genetics, Bacterial Proteins metabolism, Microbial Sensitivity Tests, Anti-Bacterial Agents pharmacology
- Abstract
We characterized a collection of IMI-like-producing Enterobacter spp. isolates (n = 112) in France. The main clone corresponded to IMI-1-producing sequence type 820 E. cloacae subspecies cloacae that was involved in an outbreak. Clinicians should be aware of potential antimicrobial resistance among these bacteria.
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- 2024
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12. Comparison of the French novel disc diffusion-based algorithm and the current EUCAST guidelines for the screening of carbapenemase-producing Enterobacterales.
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Duque M, Bonnin RA, and Dortet L
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- Humans, Enterobacteriaceae Infections microbiology, Carbapenem-Resistant Enterobacteriaceae drug effects, Carbapenem-Resistant Enterobacteriaceae isolation & purification, Disk Diffusion Antimicrobial Tests methods, Disk Diffusion Antimicrobial Tests standards, Enterobacteriaceae drug effects, Enterobacteriaceae enzymology, France, Microbial Sensitivity Tests standards, beta-Lactamases metabolism, Algorithms, Bacterial Proteins genetics, Anti-Bacterial Agents pharmacology
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- 2024
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13. Specificities and Commonalities of Carbapenemase-Producing Escherichia coli Isolated in France from 2012 to 2015.
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Patiño-Navarrete R, Rosinski-Chupin I, Cabanel N, Zongo PD, Héry M, Oueslati S, Girlich D, Dortet L, Bonnin RA, Naas T, and Glaser P
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- Humans, Escherichia coli, Phylogeny, France, Escherichia coli Infections epidemiology, Carbapenem-Resistant Enterobacteriaceae
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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 bla
OXA-48-like genes inserted in the chromosome. Globally, the most frequent carbapenemase gene ( n . 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-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 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- ftsI 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- ompC. IMPORTANCE , 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.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.- Published
- 2022
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14. Outbreak of OXA-48-producing Enterobacterales in a haematological ward associated with an uncommon environmental reservoir, France, 2016 to 2019.
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Jolivet S, Couturier J, Vuillemin X, Gouot C, Nesa D, Adam M, Brissot E, Mohty M, Bonnin RA, Dortet L, and Barbut F
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- Bacterial Proteins, Citrobacter freundii enzymology, Cronobacter sakazakii enzymology, Disease Reservoirs microbiology, Escherichia coli enzymology, France epidemiology, Hospitals, Humans, Infection Control, Water Microbiology, beta-Lactamases genetics, Cross Infection microbiology, Disease Outbreaks, Enterobacteriaceae Infections microbiology, Toilet Facilities
- Abstract
The hospital water environment, including the wastewater drainage system, is increasingly reported as a potential reservoir for carbapenemase-producing Enterobacterales (CPE). We investigated a persistent outbreak of OXA-48 CPE (primarily Citrobacter freundii ) in a haematological ward of a French teaching hospital by epidemiological, microbiological and environmental methods. Between January 2016 and June 2019, we detected 37 new OXA-48 CPE-colonised and/or ‑infected patients in the haematological ward. In October 2017, a unit dedicated to CPE-colonised and/or ‑infected patients was created. Eleven additional sporadic acquisitions were identified after this date without any obvious epidemiological link between patients, except in one case. Environmental investigations of the haematological ward (June-August 2018) identified seven of 74 toilets and one of 39 drains positive for OXA-48 CPE (seven C. freundii , one Enterobacter sakazakii , one Escherichia coli ). Whole genome comparisons identified a clonal dissemination of OXA-48-producing C. freundii from the hospital environment to patients. In addition to strict routine infection control measures, an intensive cleaning programme was performed (descaling and bleaching) and all toilet bowls and tanks were changed. These additional measures helped to contain the outbreak. This study highlights that toilets can be a possible source of transmission of OXA-48 CPE.
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- 2021
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15. Polyclonal Dissemination of NDM-1- and NDM-9-Producing Escherichia coli and Klebsiella pneumoniae in French Polynesia.
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Oueslati S, Emeraud C, Grosperrin V, Levy M, Cotellon G, Creton E, Gauthier L, Bonnin RA, Naas T, and Dortet L
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- Anti-Bacterial Agents pharmacology, Escherichia coli genetics, France, Humans, Plasmids genetics, Polynesia, beta-Lactamases genetics, Klebsiella Infections drug therapy, Klebsiella pneumoniae genetics
- Abstract
The whole-genome sequencing analysis revealed a polyclonal dissemination of NDM-1 and NDM-9 variants in Escherichia coli ( n = 20) and Klebsiella pneumoniae ( n = 2) in Tahiti since 2015 via interspecies transfer of three different bla -carrying plasmids (IncR, IncHI2, and IncF) and patient-to-patient cross-transmission. It highlights the potential risk of importation of NDM producers in France, where French Polynesia is not considered
NDM a foreign country from which repatriated patients have to be screened.stricto sensu a foreign country from which repatriated patients have to be screened., (Copyright © 2021 American Society for Microbiology.)- Published
- 2021
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16. Genomic analysis of VIM-2-producing Enterobacter hormaechei subsp. steigerwaltii.
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Bonnin RA, Girlich D, Jousset AB, Emeraud C, Creton E, Gauthier L, Jové T, Dortet L, and Naas T
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- Bacterial Proteins genetics, Bacterial Proteins metabolism, Carbapenems pharmacology, DNA, Bacterial genetics, Drug Resistance, Bacterial, Enterobacteriaceae Infections epidemiology, France epidemiology, Humans, Integrons, Microbial Sensitivity Tests, Mutation, Phenotype, Phylogeny, Plasmids genetics, Polymorphism, Single Nucleotide, Anti-Bacterial Agents pharmacology, DNA Transposable Elements, Enterobacter drug effects, Enterobacter genetics, Enterobacteriaceae Infections microbiology, beta-Lactamases genetics
- Abstract
Carbapenemase-producing Enterobacterales (CPE) is a major public-health concern. Here we describe the occurrence of bla
VIM-2 in three isolates of Enterobacter hormaechei subsp. steigerwaltii. The blaVIM-2 gene was part of a class II transposon Tn1332 and was embedded in a remnant of a class 1 integron. Tn1332 was carried by a large, conjugative, non-typeable plasmid. The three isolates belonged to sequence type 90 (ST90). Two isolates (90H2 and 90H3) were highly related [<10 single nucleotide polymorphisms (SNPs)], whereas isolate 104D2 exhibited more than 50 SNPs and Tn1332 was inserted in a different place in the plasmid. Another IncHI-type plasmid carrying the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-15 was identified in 90H2 and 90H3. Among the three isolates, isolate 104D2 was negative for detection of carbapenemase activity using the biochemical Carba NP test, despite the presence of Tn1332 on the same plasmid. Mutants of 104D2 with higher minimum inhibitory concentrations (MICs) for carbapenems were obtained and one mutant (m104D2) was analysed. In contrast to 104D2, mutant m104D2 gave a positive Carba NP test. The mutant possessed two copies of Tn1332 per cell and a nonsense mutation in WecA, an enzyme involved in enterobacterial common antigen and peptidoglycan intermediate biosynthesis. This study describes the first occurrence of Tn1332 in Enterobacterales and the phenotypic diversity of VIM-2-producing E. hormaechei., (Copyright © 2021 Elsevier Ltd and International Society of Antimicrobial Chemotherapy. All rights reserved.)- Published
- 2021
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17. Carbapenemase-producing Enterobacterales outbreak: Another dark side of COVID-19.
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Farfour E, Lecuru M, Dortet L, Le Guen M, Cerf C, Karnycheff F, Bonnin RA, Vasse M, and Lesprit P
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- Adult, Aged, COVID-19 transmission, Coinfection microbiology, Coinfection transmission, Cross Infection microbiology, Cross Infection transmission, Disease Outbreaks, Enterobacteriaceae Infections microbiology, Enterobacteriaceae Infections transmission, Female, France epidemiology, Humans, Intensive Care Units, Male, Middle Aged, COVID-19 microbiology, Carbapenem-Resistant Enterobacteriaceae, Coinfection epidemiology, Cross Infection epidemiology, Enterobacteriaceae Infections epidemiology, SARS-CoV-2
- Abstract
In the hospital department dedicated to COVID-19-patient, infection prevention and control measures were upgraded. Therefore, the cross-transmission of other micro-organisms was thought unlikely to occur. However, we report an outbreak of NDM-5-producing Escherichia. coli in a 12-beds ICU dedicated to COVID-19 patients. This outbreak involved 6 patients of which 5 were asymptomatic carriers and 1 was infected. Several findings might have contributed to cross-transmission including the multiple-bedroom configuration of the department, uncomplete compliance for standard and contact precautions, overwork due to the burden of the disease, lack of training of staff for the care of ICU-patients, and misuse of gloves. Furthermore, as infection prevention and control measures were thought to be applied, contact patients were not screened for eXDR carriage. Applying rigorously standard and contact precautions and performing screening in contact patients when indicated must be the rules in COVID-19 wards., (Copyright © 2020 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
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18. A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales.
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Bonnin RA, Girlich D, Jousset AB, Gauthier L, Cuzon G, Bogaerts P, Haenni M, Madec JY, Couvé-Deacon E, Barraud O, Fortineau N, Glaser P, Glupczynski Y, Dortet L, and Naas T
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- Animals, Bacterial Proteins classification, Bacterial Proteins genetics, Belgium, Chromosomes, Bacterial genetics, DNA Transposable Elements genetics, DNA, Bacterial genetics, France, Genes, Bacterial genetics, Humans, Plasmids genetics, Proteus mirabilis isolation & purification, beta-Lactamases classification, beta-Lactamases genetics, Bacterial Proteins biosynthesis, Proteus mirabilis enzymology, Proteus mirabilis genetics, beta-Lactamases biosynthesis
- Abstract
In Enterobacterales, the most common carbapenemases are Ambler's class A (KPC-like), class B (NDM-, VIM- or IMP-like) or class D (OXA-48-like) enzymes. This study describes the characterization of twenty-four OXA-23 or OXA-58 producing-Proteus mirabilis isolates recovered from human and veterinary samples from France and Belgium. Twenty-two P. mirabilis isolates producing either OXA-23 (n = 21) or OXA-58 (n = 1), collected between 2013 and 2018, as well as 2 reference strains isolated in 1996 and 2015 were fully sequenced. Phylogenetic analysis revealed that 22 of the 24 isolates, including the isolate from 1996, belonged to a single lineage that has disseminated in humans and animals over a long period of time. The bla
OXA-23 gene was located on the chromosome and was part of a composite transposon, Tn6703, bracketed by two copies of IS15∆II. Sequencing using Pacbio long read technology of OXA-23-producing P. mirabilis VAC allowed the assembly of a 55.5-kb structure encompassing the blaOXA-23 gene in that isolate. By contrast to the blaOXA-23 genes, the blaOXA-58 gene of P. mirabilis CNR20130297 was identified on a 6-kb plasmid. The acquisition of the blaOXA-58 gene on this plasmid involved XerC-XerD recombinases. Our results suggest that a major clone of OXA-23-producing P. mirabilis is circulating in France and Belgium since 1996.- Published
- 2020
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19. Diversity of Carbapenemase-Producing Escherichia coli Isolates in France in 2012-2013.
- Author
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Gauthier L, Dortet L, Cotellon G, Creton E, Cuzon G, Ponties V, Bonnin RA, and Naas T
- Subjects
- Africa, Northern epidemiology, Bacterial Proteins metabolism, Carbapenems pharmacology, Colistin pharmacology, Epidemiological Monitoring, Escherichia coli classification, Escherichia coli drug effects, Escherichia coli isolation & purification, Escherichia coli Infections drug therapy, Escherichia coli Infections microbiology, Fosfomycin pharmacology, France epidemiology, Gene Expression, Humans, Incidence, Multilocus Sequence Typing, Nitrofurantoin pharmacology, Phylogeny, Turkey epidemiology, Urinary Tract Infections drug therapy, Urinary Tract Infections microbiology, beta-Lactamases metabolism, Anti-Bacterial Agents pharmacology, Bacterial Proteins genetics, Escherichia coli genetics, Escherichia coli Infections epidemiology, Genetic Variation, Urinary Tract Infections epidemiology, beta-Lactamases genetics
- Abstract
With the dissemination of carbapenemase-producing Enterobacteriaceae (CPE) strains worldwide, carbapenem-hydrolyzing enzymes are increasingly reported among isolates of Escherichia coli , the first hospital and community-acquired opportunistic pathogen. Here, we have performed an epidemiological survey of carbapenemase-producing E. coli (CP- Ec ) isolates received at the French National Reference Centre (F-NRC) in 2012 and 2013. Antimicrobial susceptibilities for last-resort antibiotics and antimicrobial compounds commonly used to treat urinary tract infections were determined by broth microdilution. Clonal relationship was assessed using repetitive sequence-based PCR (rep-PCR) and multilocus sequence typing (MLST). From this collection of 140 carbapenemase-producing E. coli isolates, 74% produced an OXA-48-like carbapenemase and 21% produced an NDM carbapenemase. A link with a foreign country was suspected for 37% of infected/colonized patients. Most of the isolates were from screening (56%) and from urine samples (26%). Colistin, fosfomycin, and nitrofurantoin possessed the most consistent activity, with 100%, 95%, and 96% isolates susceptible, respectively. A wide diversity of carbapenemase-producing E. coli isolates has been found (50 different sequence types [STs]). The most prevalent clones were (i) E. coli sequence type 38 (ST38) producing OXA-48 ( n = 21), a clone linked to Turkey and North African countries, (ii) E. coli ST-90 producing OXA-204 ( n = 9), which was responsible for an outbreak related to a contaminated duodenoscope, and (iii) E. coli ST-410 producing OXA-181 ( n = 5), which was recovered from patients of different geographical origins. These specific clones might be considered high-risk clones for the dissemination of carbapenemases in E. coli The wide diversity of STs, combined with the increasing number of CP- Ec isolates received by the F-NRC, suggests a likely dissemination of CP- Ec isolates in the community., (Copyright © 2018 American Society for Microbiology.)
- Published
- 2018
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20. Detection of GES-5 Carbapenemase in Klebsiella pneumoniae, a Newcomer in France.
- Author
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Bonnin RA, Jousset AB, Urvoy N, Gauthier L, Tlili L, Creton E, Cotellon G, Arthur F, Dortet L, and Naas T
- Subjects
- Anti-Bacterial Agents metabolism, Anti-Bacterial Agents pharmacology, Bacterial Proteins metabolism, Carbapenems metabolism, Carbapenems pharmacology, Chromosome Mapping, France, Gene Expression, Humans, Integrons, Klebsiella Infections drug therapy, Klebsiella Infections microbiology, Klebsiella Infections pathology, Klebsiella pneumoniae classification, Klebsiella pneumoniae drug effects, Klebsiella pneumoniae isolation & purification, Male, Microbial Sensitivity Tests, Middle Aged, Multilocus Sequence Typing, Plasmids metabolism, Thailand, beta-Lactamases metabolism, Bacterial Proteins genetics, Genome, Bacterial, Klebsiella pneumoniae genetics, Plasmids chemistry, beta-Lactamases genetics
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- 2017
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21. Emergence of OXA-72-producing Acinetobacter pittii clinical isolates.
- Author
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Bonnin RA, Docobo-Pérez F, Poirel L, Villegas MV, and Nordmann P
- Subjects
- Acinetobacter classification, Acinetobacter genetics, Aged, 80 and over, Cluster Analysis, DNA, Bacterial genetics, France, Genotype, Humans, Middle Aged, Molecular Typing, Plasmids, Acinetobacter enzymology, Acinetobacter isolation & purification, Acinetobacter Infections microbiology, beta-Lactamases genetics
- Published
- 2014
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22. Multidrug-resistant Acinetobacter baumannii clone, France.
- Author
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Bonnin RA, Cuzon G, Poirel L, and Nordmann P
- Subjects
- Acinetobacter Infections drug therapy, Acinetobacter Infections ethnology, Acinetobacter baumannii drug effects, Acinetobacter baumannii enzymology, Acinetobacter baumannii isolation & purification, Algeria ethnology, Clone Cells, Cross Infection drug therapy, Cross Infection ethnology, Egypt ethnology, France epidemiology, Humans, Tunisia ethnology, beta-Lactam Resistance drug effects, beta-Lactamases genetics, beta-Lactamases metabolism, Acinetobacter Infections microbiology, Acinetobacter baumannii genetics, Anti-Bacterial Agents pharmacology, Carbapenems pharmacology, Cross Infection microbiology, beta-Lactam Resistance genetics
- Published
- 2013
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23. First identification of novel NDM carbapenemase, NDM-7, in Escherichia coli in France.
- Author
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Cuzon G, Bonnin RA, and Nordmann P
- Subjects
- Amino Acid Sequence, Bacterial Proteins chemistry, Escherichia coli drug effects, France, Genes, Bacterial genetics, Microbial Sensitivity Tests, Molecular Sequence Data, Mutant Proteins chemistry, Mutant Proteins metabolism, Sequence Alignment, beta-Lactamases chemistry, beta-Lactamases pharmacology, Bacterial Proteins metabolism, Escherichia coli enzymology, beta-Lactamases metabolism
- Abstract
Background: The NDM-1 carbapenemase has been identified in 2008 in Enterobacteriaceae. Since then, several reports have emphasized its rapid dissemination throughout the world. The spread of NDM carbapenemases involve several bla NDM gene variants associated with various plasmids among several Gram negative species., Methodology: A multidrug-resistant E. coli isolate recovered from urine of a patient who had travelled to Burma has been characterized genetically and biochemically., Principal Findings: E. coli COU was resistant to all antibiotics tested except amikacin, tigecycline, fosfomycin, and chloramphenicol. Analysis of the antibiotic resistance traits identified a metallo-ß-lactamase, a novel NDM variant, NDM-7. It differs from NDM-4 by a single amino acid substitution sharing an identical extended spectrum profile towards carbapenems. The bla NDM-7 gene was located on an untypeable conjugative plasmid and associated with a close genetic background similar to those described among the bla NDM-1 genes. The isolate also harbours bla CTXM-15 and bla OXA-1 genes and belonged to ST167., Significance: This study highlights that spread of NDM producers correspond to spread of multiple bla NDM genes and clones and therefore will be difficult to control.
- Published
- 2013
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