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1. Oxacillinase-484--Producing Enterobacterales, France, 2018-2023

Author

Emeraud, Cecile, Bernabeu, Sandrine, Girlich, Delphine, Rezzoug, Ines, Jousset, Agnes B., Birer, Aurelien, Naas, Thierry, Bonnin, Remy A., and Dortet, Laurent

Subjects
Enterobacteriaceae -- Physiological aspects -- Genetic aspects -- Testing, Beta lactamases -- Physiological aspects, Drug resistance in microorganisms -- Research, Enterobacter -- Physiological aspects -- Genetic aspects -- Testing, Microbiological research, Health
Abstract

Carbapenemase-producing Enterobacterales (CPEs) pose a considerable threat to public health because of antimicrobial resistance. In France, the most prevalent carbapenemases are OXA-48-like type. More than 55 variants of OXA-48-like enzymes [...]

Published
2024
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2. IMI-Type Carbapenemase-Producing Enterobacter cloacae Complex, France and Overseas Regions, 2012-2022

Author

Emeraud, Cecile, Girlich, Delphine, Deschamps, Manon, Rezzoug, Ines, Jacquemin, Aymeric, Jousset, Agnes B., Lecolant, Solene, Locher, Lucy, Birer, Aurelien, Naas, Thierry, Bonnin, Remy A., and Dortet, Laurent

Subjects
Enterobacteriaceae infections -- Drug therapy -- Genetic aspects, Drug resistance in microorganisms -- Genetic aspects, Genotype -- Identification and classification -- Health aspects, Health
Abstract

The Enterobacter cloacae complex (ECC) is highly diverse; its many species and subspecies can be distinguished by using phenotypic methods or matrix-assisted laser desorption/ionization time-offlight mass spectrometry. Whole-genome sequencing enables [...]

Published
2024
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3. Population Analysis of Escherichia coli Sequence Type 361 and Reduced Cefiderocol Susceptibility, France

Author

Jousset, Agnes B., Bouabdallah, Laura, Birer, Aurelien, Rosinski-Chupin, Isabelle, Mariet, Jean-Francois, Oueslati, Saoussen, Emeraud, Cecile, Girlich, Delphine, Glaser, Philippe, Naas, Thierry, Bonnin, Remy A., and Dortet, Laurent

Subjects
Beta lactamases -- Genetic aspects, Protein binding -- Genetic aspects, Imipenem, Infection -- Genetic aspects, Escherichia coli -- Genetic aspects, Health
Abstract

Few last-line antimicrobial agents effectively treat infections caused by New Delhi metallo-[beta]-lactamase (NDM)-producing Enterobacterales (1). Cefiderocol is a novel synthetic conjugate siderophore cephalosporin that is more stable against [beta]-lactamase hydrolysis [...]

Published
2023
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4. Spread of carbapenemase-producing Morganella spp from 2013 to 2021: a comparative genomic study

Author

Bonnin, Rémy A, Creton, Elodie, Perrin, Amandine, Girlich, Delphine, Emeraud, Cecile, Jousset, Agnès B, Duque, Mathilde, Jacquemin, Aymeric, Hopkins, Katie, Bogaerts, Pierre, Glupczynski, Youri, Pfennigwerth, Niels, Gniadkowski, Marek, Hendrickx, Antoni P A, van der Zwaluw, Kim, Apfalter, Petra, Hartl, Rainer, Studentova, Vendula, Hrabak, Jaroslav, Larrouy-Maumus, Gerald, Rocha, Eduardo P C, Naas, Thierry, and Dortet, Laurent

Published
2024
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6. Polyclonal Dissemination of OXA-232 Carbapenemase--Producing Klebsiella pneumoniae, France, 2013-2021

Author

Emeraud, Cecile, Birer, Aurelien, Girlich, Delphine, Jousset, Agnes B., Creton, Elodie, Naas, Thierry, Bonnin, Remy A., and Dortet, Laurent

Subjects
Klebsiella infections -- Risk factors -- Prevention, Beta lactam antibiotics -- Dosage and administration, Health
Abstract

The massive dissemination of carbapenemase-producing Enterobacterales poses a global threat to public health. Carbapenem antibiotics remain the last line of defense against highly resistant Enterobacterales. Carbapenemases have been identified in [...]

Published
2022
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8. Emergence and Polyclonal Dissemination of OXA-244--Producing Escherichia coli, France

Author

Emeraud, Cecile, Girlich, Delphine, Bonnin, Remy A., Jousset, Agnes B., Naas, Thierry, and Dortet, Laurent

Subjects
Oxacillin -- Genetic aspects, Escherichia coli -- Genetic aspects -- Identification and classification, Health
Abstract

Carbapenems are the last line antimicrobial drugs for treating infections caused by multidrug-resistant Enterobacterales. The global dissemination of carbapenemase-producing Enterobacterales (CPE; formerly known as carbapenemase-producing Enterobacteriaceae) pose a serious threat [...]

Published
2021
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9. Whole genome mapping of 5' RNA ends in bacteria by tagged sequencing : A comprehensive view in Enterococcus faecalis

Author

Innocenti, Nicolas, Golumbeanu, Monica, d'Hérouël, Aymeric Fouquier, Lacoux, Caroline, Bonnin, Rémy A., Kennedy, Sean P., Wessner, Françoise, Serror, Pascale, Bouloc, Philippe, Repoila, Francis, and Aurell, Erik

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Biomolecules, Quantitative Biology - Quantitative Methods
Abstract

Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first comprehensive view of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5'RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites and 352 processing sites in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding TSSs mapped. We discovered 95 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organisations. Presented data constitute a significant insight into bacterial RNA landscapes and a step towards the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.

Published
2014
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10. Emergence of New Non-Clonal Group 258 High-Risk Clones among Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Isolates, France

Author

Bonnin, Remy A., Jousset, Agnes B., Chiarelli, Adriana, Emeraud, Cecile, Glaser, Philippe, Naas, Thierry, and Dortet, Laurent

Subjects
Imipenem, Pneumonia, Tigecycline, Genomes, Epidemiology, Genomics, Meropenem, Health
Abstract

In Klebsiella pneumoniae bacteria, resistance to carbapenems results in 2 main mechanisms: the production of an extended spectrum [beta]-lactamase or plasmid-borne cephalosporinase associated with a decrease in permeability of the [...]

Published
2020
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13. Structural and Biochemical Features of OXA-517: a Carbapenem and Expanded-Spectrum Cephalosporin Hydrolyzing OXA-48 Variant

Author

Dabos, Laura, primary, Raczynska, Joanna E., additional, Bogaerts, Pierre, additional, Zavala, Agustin, additional, Girlich, Delphine, additional, Bonnin, Remy A., additional, Dortet, Laurent, additional, Peyrat, Aurélie, additional, Retailleau, Pascal, additional, Iorga, Bogdan I., additional, Jaskólski, Mariusz, additional, Glupczynski, Youri, additional, and Naas, Thierry, additional

Published
2023
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14. Evaluation of ceftolozane-tazobactam susceptibility on a French nationwide collection of Enterobacterales

Author

Jousset, Agnès B., Bernabeu, Sandrine, Emeraud, Cécile, Bonnin, Rémy A., Lomont, Alexandra, Zahar, Jean Ralph, Merens, Audrey, Isnard, Christophe, Soismier, Nathalie, Farfour, Eric, Fihman, Vincent, Yin, Nicolas, Barraud, Olivier, Jacquier, Hervé, Ranc, Anne-Gaëlle, Laurent, Frédéric, Corvec, Stéphane, d'Epenoux, Louise Ruffier, Bille, Emmanuelle, Degand, Nicolas, Plouzeau, Chloé, Guillard, Thomas, Cattoir, Vincent, Mizrahi, Asaf, Grillon, Antoine, Janvier, Frédéric, Brun, Cécile Le, Amara, Marlène, Bastide, Mathilda, Lemonnier, Alban, and Dortet, Laurent

Published
2023
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18. Temporal Variation in Antibiotic Resistance of Acinetobacter baumannii in a Teaching Hospital in Tunisia: Correlation with Antimicrobial Consumption

Author

Bouallegue Olfa, Naas Thierry, Chaouch Cherifa, Jaidane Nadia, Kalboussi Nesrine, Golli Rachida, Ghardallou Meriam, Mansour Wejdene, Boujaafar Noureddine, and Bonnin Remy A.

Subjects
0301 basic medicine, Imipenem, Veterinary medicine, General Immunology and Microbiology, biology, business.industry, 030106 microbiology, Antimicrobial, biology.organism_classification, Acinetobacter baumannii, Teaching hospital, 03 medical and health sciences, 0302 clinical medicine, Antibiotic resistance, Medicine, 030212 general & internal medicine, business, medicine.drug
Abstract

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.

Published
2019

19. MOESM3 of Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli

Author

PatiñO-Navarrete, Rafael, Rosinski-Chupin, Isabelle, Cabanel, Nicolas, Lauraine Gauthier, Takissian, Julie, Jean-Yves Madec, Monzer Hamze, Bonnin, Remy, Naas, Thierry, and Glaser, Philippe

Abstract

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.

Published
2020
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20. Dynamic insights on transcription initiation and RNA processing during bacterial adaptation

Author

Lacoux, Caroline, D'Herouel, Aymeric Fouquier, Wessner-Le Bohec, Francoise, Innocenti, Nicolas, Bohn, Chantal, Kennedy, Sean P., Rochat, Tatiana, Bonnin, Remy A., Serror, Pascale, Aurell, Erik, Bouloc, Philippe, Repoila, Francis, Lacoux, Caroline, D'Herouel, Aymeric Fouquier, Wessner-Le Bohec, Francoise, Innocenti, Nicolas, Bohn, Chantal, Kennedy, Sean P., Rochat, Tatiana, Bonnin, Remy A., Serror, Pascale, Aurell, Erik, Bouloc, Philippe, and Repoila, Francis

Abstract

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled sigma(E) system in E. coli was coupled to our previously described tag RNAseq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5' RNA tags. Changes in TIF showed a binary increased/decreased pattern that alternated between transcriptionally activated and repressed promoters, providing the bacterial population with transcriptional oscillation. PF variation fell into three categories of cleavage activity: (i) constant and independent of RNA levels, (ii) increased once RNA has accumulated, and (iii) positively correlated to changes in TIF. This work provides a comprehensive and dynamic view of major events leading to transcriptomic reshaping during bacterial adaptation. It unveils an interplay between transcription initiation and the activity of specific RNA cleavage sites. This study utilized a well-known genetic system to analyze fundamental processes and can serve as a blueprint for comprehensive studies that exploit the RNA metabolism to decipher and understand bacterial gene expression control., QC 20200407

Published
2020
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21. Carbapenemase-producing Acinetobacter spp. in Cattle, France

Author

Poirel, Laurent, Bercot, Beatrice, Millemann, Yves, Bonnin, Remy A., Pannaux, Glenn, and Nordmann, Patrice

Subjects
Drug resistance in microorganisms -- Research, Carbapenems -- Research, Acinetobacter -- Research, Health
Abstract

To the Editor: Multidrug resistance in bacteria isolated from animals is an emerging phenomenon, mirroring what is happening among humans. During the past decade, expanded-spectrum [beta]-lactamases in Enterobacteriaceae from humans [...]

Published
2012
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25. Multidrug-resistant Acinetobacter baumannii clone, France

Author

Bonnin, Remy A., Cuzon, Gaelle, Poirel, Laurent, and Nordmann, Patrice

Subjects
Bacterial pneumonia -- Causes of -- Control, Acinetobacter baumannii -- Health aspects -- Care and treatment -- Control, Drug resistance -- Control -- Health aspects, Pneumonia -- Causes of -- Control, Health
Abstract

To the Editor: Acinetobacter baumannii is an opportunistic pathogen that is a source of nosocomial infections, mostly pneumonia (7). Treatment of infections caused by A. baumannii is becoming a serious [...]

Published
2013

26. Characterization of bla(OXA-143) Variants in Acinetobacter baumannii and Acinetobacter pittii

Author

Zander, Esther, Bonnin, Remy A., Seifert, Harald, Higgins, Paul G., Zander, Esther, Bonnin, Remy A., Seifert, Harald, and Higgins, Paul G.

Abstract

The acquired carbapenem- hydrolyzing oxacillinase ( OXA) OXA- 143 has thus far been detected only in Acinetobacter baumannii isolates from Brazil. The aim of this study was to characterize three OXA- 143 variants: OXA- 231 and OXA- 253 from carbapenem-resistant A. baumannii isolates and OXA- 255 in a carbapenem- susceptible Acinetobacter pittii isolate originating from Brazil, Honduras, and the United States, respectively. The 5' rapid amplification of cDNA ends ( RACE) technique identified the same transcription initiation site for all bla(OXA-143-like) genes and revealed differences in the putative promoter regions. However, all cloned OXA- 143 variants conferred carbapenem resistance on A. baumannii ATCC 17978 and OXA- 255 conferred carbapenem resistance on A. pittii SH024, which was correlated with blaOXA- 255 gene expression. This is the first description of OXA- 143- like outside A. baumannii. Detection of OXA- 143- like in the United States and Honduras indicates its dissemination through the American continent.

Published
2014

27. Susceptibility Testing Is Key for the Success of Cefiderocol Treatment: A Retrospective Cohort Study.

Author

Bleibtreu, Alexandre, Dortet, Laurent, Bonnin, Remy A., Wyplosz, Benjamin, Sacleux, Sophie-Caroline, Mihaila, Liliana, Dupont, Hervé, Junot, Helga, Bunel, Vincent, Grall, Nathalie, Razazi, Keyvan, Duran, Clara, Tattevin, Pierre, Dinh, Aurélien, and Costa-de-Oliveira, Sofia

Subjects
PSEUDOMONAS aeruginosa, RESPIRATORY infections, GRAM-negative bacteria, ACINETOBACTER baumannii, PSEUDOMONAS aeruginosa infections, COHORT analysis, KLEBSIELLA pneumoniae
Abstract

Cefiderocol is a novel siderophore cephalosporin, which has proven in vitro activity against carbapenem-resistant (CR) Gram-negative pathogens and stability towards all carbapenemases. The aim of this study was to describe the first cases of prescriptions and the efficacy of cefiderocol for compassionate use in the 2 months following its access in France. We performed a national retrospective study of all patients who received at least one dose of cefiderocol from 2 November 2018 to 5 November 2019. We collected clinical characteristics and outcome through a standard questionnaire. Bacterial isolates from 12 patients were centralized and analyzed in the French National Reference Center for Antimicrobial Resistance, and sequenced using Illumina technology. Finally, 13 patients from 7 French university hospitals were included in the study. The main type of infection treated by cefiderocol was respiratory tract infections (RTI, n = 10). The targeted bacteria were Pseudomonas aeruginosa (n = 12), including carbapenemase-producing P. aeruginosa (n = 9), Acinetobacter baumannii (n = 2), Klebsiella pneumoniae (n = 1), and Enterobacter hormaechei (n = 1). Overall, of the 12 patients whose samples were analyzed, 5 P. aeruginosa strains were not susceptible to cefiderocol (4 categorized as resistant and 1 as intermediate) according to Clinical and Laboratory Standards Institute (CLSI) breakpoints. If considering susceptible strains, the cure rate was 6/7, while being 0/5 among not-susceptible strains. This study underlines the necessity to test strains in adequate conditions. [ABSTRACT FROM AUTHOR]

Published
2021
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28. MOESM4 of Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli

Author

PatiñO-Navarrete, Rafael, Rosinski-Chupin, Isabelle, Cabanel, Nicolas, Lauraine Gauthier, Takissian, Julie, Jean-Yves Madec, Monzer Hamze, Bonnin, Remy, Naas, Thierry, and Glaser, Philippe

Subjects
2. Zero hunger
Abstract

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.

29. MOESM4 of Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli

Author

PatiñO-Navarrete, Rafael, Rosinski-Chupin, Isabelle, Cabanel, Nicolas, Lauraine Gauthier, Takissian, Julie, Jean-Yves Madec, Monzer Hamze, Bonnin, Remy, Naas, Thierry, and Glaser, Philippe

Subjects
2. Zero hunger
Abstract

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.

30. First report of OXA-48-producing Klebsiella pneumoniae strains in Iran

Author

Azimi, Leila, Nordmann, Patrice, Lari, Abdolaziz Rastegar, and Bonnin, Rémy A.

Subjects
carbapenem, Klebsiella pneumoniae, CarbaNP test, MHT, OXA-48, Medicine, Public aspects of medicine, RA1-1270, Microbiology, QR1-502
Abstract

[english] Carbapenem-resistant are increasingly reported worldwide and cause therapeutic problem in health care facilities. In this study 28 imipenem-resistant were examined for expression of carbapenemases by phenotypic and genotypic methods. Modified Hodge Test (MHT), CarbaNP test were used for phenotypic detection, and PCR using specific primers for the detection of and type carbapenemases with specific primers were performed. MHT and CarbaNP tests were positive for all of imipenem-resistant . The gene was detected in 27/28 isolates. One isolate was positive for the presence of the gene. According to our results NP test and MHT have high sensitivity and specificity for detection of those carbapenemases. This study reports the first cases of OXA-48-producing in Iran.

Published
2014
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