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Vanparis O, Oueslati S, Girlich D, Jousset AB, Guyot C, Delaval A, Naas T, Dortet L, Bonnin RA. Genetic and biochemical characterization of OXA-1186, a novel OXA-198-type carbapenemase hydrolysing cephalosporins in Citrobacter freundii. J Antimicrob Chemother 2024:dkae339. [PMID: 39319679 DOI: 10.1093/jac/dkae339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 08/22/2024] [Indexed: 09/26/2024] Open
Abstract
OBJECTIVES This study described OXA-1186, a novel carbapenemase related to OXA-198 carbapenemase and produced by a clinical isolate of Citrobacter freundii. METHODS WGS was used to characterize the resistome, virulome and plasmid types of the C. freundii 315C8 isolate and to reconstruct the blaOXA-1186-carrying plasmid. Disc diffusion and broth microdilution assays were used to determine MICs. The blaOXA-1186 gene was cloned into plasmid pTOPO and then transformed into Escherichia coli TOP10 or HB4. It was also cloned in pET41b and transformed into E. coli BL21 DE3 for protein purification. Steady-state kinetic parameters were determined on purified OXA-1186. RESULTS C. freundii 315C8, belonging to ST8, was resistant to penicillins including temocillin and broad-spectrum cephalosporins and displayed reduced susceptibility to carbapenems. It was negative for one of the five main carbapenemases. WGS revealed that the blaOXA-1186 gene encoded a novel carbapenemase that shared 83% amino acid identity with OXA-198. The blaOXA-1186 gene was carried on an IncP6-type plasmid and was embedded within a class 1 integron. Cloning and expression in E. coli revealed that expression of the blaOXA-1186 gene conferred resistance to penicillins, cephalosporins and carbapenems, where it was associated with impaired outer membrane permeability. Kinetic parameters confirmed the hydrolysis of ceftazidime, cefepime and aztreonam, in addition to imipenem and meropenem. CONCLUSIONS Here, we described a novel carbapenemase, OXA-1186, identified in C. freundii. Unlike OXA-198, OXA-1186 is able to hydrolyse broad-spectrum cephalosporins. This carbapenemase was carried on a broad-spectrum IncP6 plasmid identified in other Citrobacter species and non-fermenters.
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Affiliation(s)
- Oceane Vanparis
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Saoussen Oueslati
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Delphine Girlich
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Agnès B Jousset
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Bicêtre Hosptial, Le Kremlin-Bicêtre, France
| | - Caroline Guyot
- Service de bactériologie, Groupe Hospitalier Intercommunal du Raincy-Montfermeil, Montfermeil, France
| | - Anne Delaval
- Service de bactériologie, Groupe Hospitalier Intercommunal du Raincy-Montfermeil, Montfermeil, France
| | - Thierry Naas
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Bicêtre Hosptial, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, Bicêtre Hosptial, Le Kremlin-Bicêtre, France
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Furlan JPR, Sellera FP, Gonzalez IHL, Ramos PL, Stehling EG. The curious case of the rare Citrobacter pasteurii isolated from an endangered primate in Brazil. Comp Immunol Microbiol Infect Dis 2024; 113:102234. [PMID: 39276760 DOI: 10.1016/j.cimid.2024.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024]
Abstract
The genus Citrobacter comprises clinically important human pathogens but has been less frequently associated with wildlife infections. Citrobacter pasteurii was first identified as causing human diarrhea and remains rarely documented. In this study, a Gram-negative bacterial strain, named A318, was identified as causing diarrhea in a black lion tamarin. This strain was biochemically identified as Trabulsiella guamensis, a species of unusual nature, and was submitted to whole-genome characterization. Curiously, phylogenomic analysis showed that A318 strain belonged to the genus Citrobacter, with confirmation of the species C. pasteurii by average nucleotide identity (99.02 %) and digital DNA-DNA hybridization (93.80 %) analyzes. Cases of misidentification of C. pasteurii as Citrobacter youngae were detected and corrected in this study. In addition to the genome sequence of the type strain of C. pasteurii, only two others from the Australian cockle and Portuguese silver gull are publicly available. Single nucleotide polymorphism differences among all C. pasteurii indicated a highly diverse population. No acquired antimicrobial resistance genes and plasmid replicons were found. Therefore, our findings emphasize the importance of gold-standard methods for accurate identification and underscores the importance of continued surveillance and research to mitigate the risks posed by zoonotic and zooanthroponotic pathogens.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil
| | - Fábio Parra Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Irys Hany Lima Gonzalez
- Wildlife Coordination, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Patrícia Locosque Ramos
- Wildlife Coordination, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil.
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Jacquemin A, Naas T, Dortet L, Bonnin RA. Accumulibacter spp. as the origin of the OXA-198 carbapenemase gene cassette. J Antimicrob Chemother 2024; 79:1466-1468. [PMID: 38619055 DOI: 10.1093/jac/dkae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Affiliation(s)
- Aymeric Jacquemin
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, 78 rue du Général Leclerc, 94275, Le Kremlin-Bicêtre Cedex, France
| | - Thierry Naas
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, 78 rue du Général Leclerc, 94275, Le Kremlin-Bicêtre Cedex, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, 78 rue du Général Leclerc, 94275, Le Kremlin-Bicêtre Cedex, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- Team 'Resist' UMR1184 'Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)', INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, 78 rue du Général Leclerc, 94275, Le Kremlin-Bicêtre Cedex, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Bicêtre Hospital, Le Kremlin-Bicêtre, France
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Kvesić M, Šamanić I, Novak A, Fredotović Ž, Dželalija M, Kamenjarin J, Goić Barišić I, Tonkić M, Maravić A. Submarine Outfalls of Treated Wastewater Effluents are Sources of Extensively- and Multidrug-Resistant KPC- and OXA-48-Producing Enterobacteriaceae in Coastal Marine Environment. Front Microbiol 2022; 13:858821. [PMID: 35602062 PMCID: PMC9121779 DOI: 10.3389/fmicb.2022.858821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid and ongoing spread of carbapenemase-producing Enterobacteriaceae has led to a global health threat. However, a limited number of studies have addressed this problem in the marine environment. We investigated their emergence in the coastal waters of the central Adriatic Sea (Croatia), which are recipients of submarine effluents from two wastewater treatment plants. Fifteen KPC-producing Enterobacteriaceae (nine Escherichia coli, four Klebsiella pneumoniae and two Citrobacter freundii) were recovered, and susceptibility testing to 14 antimicrobials from 10 classes showed that four isolates were extensively drug resistant (XDR) and two were resistant to colistin. After ERIC and BOX-PCR typing, eight isolates were selected for whole genome sequencing. The E. coli isolates belonged to serotype O21:H27 and sequence type (ST) 2795, while K. pneumoniae isolates were assigned to STs 37 and 534. Large-scale genome analysis revealed an arsenal of 137 genes conferring resistance to 19 antimicrobial drug classes, 35 genes associated with virulence, and 20 plasmid replicons. The isolates simultaneously carried 43–90 genes encoding for antibiotic resistance, while four isolates co-harbored carbapenemase genes blaKPC-2 and blaOXA-48. The blaOXA-48 was associated with IncL-type plasmids in E. coli and K. pneumoniae. Importantly, the blaKPC-2 in four E. coli isolates was located on ~40 kb IncP6 broad-host-range plasmids which recently emerged as blaKPC-2 vesicles, providing first report of these blaKPC-2-bearing resistance plasmids circulating in E. coli in Europe. This study also represents the first evidence of XDR and potentially virulent strains of KPC-producing E. coli in coastal waters and the co-occurrence of blaKPC-2 and blaOXA-48 carbapenemase genes in this species. The leakage of these strains through submarine effluents into coastal waters is of concern, indicating a reservoir of this infectious threat in the marine environment.
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Affiliation(s)
- Marija Kvesić
- Center of Excellence for Science and Technology, Integration of Mediterranean Region, University of Split, Split, Croatia
- Doctoral Study of Biophysics, Faculty of Science, University of Split, Split, Croatia
| | - Ivica Šamanić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Anita Novak
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Željana Fredotović
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Mia Dželalija
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Juraj Kamenjarin
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Ivana Goić Barišić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Marija Tonkić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
- *Correspondence: Ana Maravić,
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Abstract
Class D β-lactamases are composed of 14 families and the majority of the member enzymes are included in the OXA family. The genes for class D β-lactamases are frequently identified in the chromosome as an intrinsic resistance determinant in environmental bacteria and a few of these are found in mobile genetic elements carried by clinically significant pathogens. The most dominant OXA family among class D β-lactamases is superheterogeneous and the family needs to have an updated scheme for grouping OXA subfamilies through phylogenetic analysis. The OXA enzymes, even the members within a subfamily, have a diverse spectrum of resistance. Such varied activity could be derived from their active sites, which are distinct from those of the other serine β-lactamases. Their substrate profile is determined according to the size and position of the P-, Ω- and β5-β6 loops, assembling the active-site channel, which is very hydrophobic. Also, amino acid substitutions occurring in critical structures may alter the range of hydrolysed substrates and one subfamily could include members belonging to several functional groups. This review aims to describe the current class D β-lactamases including the functional groups, occurrence types (intrinsic or acquired) and substrate spectra and, focusing on the major OXA family, a new model for subfamily grouping will be presented.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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6
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Emeraud C, Girlich D, Bonnin RA, Jousset AB, Naas T, Dortet L. Emergence and Polyclonal Dissemination of OXA-244-Producing Escherichia coli, France. Emerg Infect Dis 2021; 27:1206-1210. [PMID: 33755001 PMCID: PMC8007313 DOI: 10.3201/eid2704.204459] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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.
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7
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Girlich D, Bogaerts P, Bouchahrouf W, Bernabeu S, Langlois I, Begasse C, Arangia N, Dortet L, Huang TD, Glupczynski Y, Naas T. Evaluation of the Novodiag CarbaR+, a Novel Integrated Sample to Result Platform for the Multiplex Qualitative Detection of Carbapenem and Colistin Resistance Markers. Microb Drug Resist 2021; 27:170-178. [DOI: 10.1089/mdr.2020.0132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Delphine Girlich
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB),” INSERM, Université Paris-Saclay, CEA, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur–APHP–Université Paris-Sud, Paris, France
| | - Pierre Bogaerts
- Laboratory of Clinical Microbiology, National Reference Center for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Warda Bouchahrouf
- Laboratory of Clinical Microbiology, National Reference Center for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Sandrine Bernabeu
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB),” INSERM, Université Paris-Saclay, CEA, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur–APHP–Université Paris-Sud, Paris, France
- Bacteriology-Hygiene Unit, Assistance Publique–Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Isabelle Langlois
- Bacteriology-Hygiene Unit, Assistance Publique–Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Christine Begasse
- Bacteriology-Hygiene Unit, Assistance Publique–Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Nicolas Arangia
- Bacteriology-Hygiene Unit, Assistance Publique–Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB),” INSERM, Université Paris-Saclay, CEA, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur–APHP–Université Paris-Sud, Paris, France
- Bacteriology-Hygiene Unit, Assistance Publique–Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Te-Din Huang
- Laboratory of Clinical Microbiology, National Reference Center for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Youri Glupczynski
- Laboratory of Clinical Microbiology, National Reference Center for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, Yvoir, Belgium
| | - Thierry Naas
- Team “Resist” UMR1184 “Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB),” INSERM, Université Paris-Saclay, CEA, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur–APHP–Université Paris-Sud, Paris, France
- Bacteriology-Hygiene Unit, Assistance Publique–Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
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Bonnin RA, Girlich D, Jousset AB, Emeraud C, Creton E, Gauthier L, Jové T, Dortet L, Naas T. Genomic analysis of VIM-2-producing Enterobacter hormaechei subsp. steigerwaltii. Int J Antimicrob Agents 2021; 57:106285. [PMID: 33493673 DOI: 10.1016/j.ijantimicag.2021.106285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/24/2020] [Accepted: 01/03/2021] [Indexed: 11/15/2022]
Abstract
Carbapenemase-producing Enterobacterales (CPE) is a major public-health concern. Here we describe the occurrence of blaVIM-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.
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Affiliation(s)
- Rémy A Bonnin
- Team Resist, UMR-1184 (INSERM - Université Paris-Saclay - CEA), LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; EERA 'Evolution and Ecology of Resistance to Antibiotics' Unit, (Institut Pasteur - APHP - Université Paris Saclay), Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance 'Carbapenemase-producing Enterobacteriaceae', Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Delphine Girlich
- Team Resist, UMR-1184 (INSERM - Université Paris-Saclay - CEA), LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; EERA 'Evolution and Ecology of Resistance to Antibiotics' Unit, (Institut Pasteur - APHP - Université Paris Saclay), Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance 'Carbapenemase-producing Enterobacteriaceae', Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Agnès B Jousset
- Team Resist, UMR-1184 (INSERM - Université Paris-Saclay - CEA), LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; EERA 'Evolution and Ecology of Resistance to Antibiotics' Unit, (Institut Pasteur - APHP - Université Paris Saclay), Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance 'Carbapenemase-producing Enterobacteriaceae', Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Cecile Emeraud
- Team Resist, UMR-1184 (INSERM - Université Paris-Saclay - CEA), LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; EERA 'Evolution and Ecology of Resistance to Antibiotics' Unit, (Institut Pasteur - APHP - Université Paris Saclay), Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance 'Carbapenemase-producing Enterobacteriaceae', Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Elodie Creton
- Team Resist, UMR-1184 (INSERM - Université Paris-Saclay - CEA), LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance 'Carbapenemase-producing Enterobacteriaceae', Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Lauraine Gauthier
- Team Resist, UMR-1184 (INSERM - Université Paris-Saclay - CEA), LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; EERA 'Evolution and Ecology of Resistance to Antibiotics' Unit, (Institut Pasteur - APHP - Université Paris Saclay), Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance 'Carbapenemase-producing Enterobacteriaceae', Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, University of Limoges, Limoges, France
| | - Laurent Dortet
- Team Resist, UMR-1184 (INSERM - Université Paris-Saclay - CEA), LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; EERA 'Evolution and Ecology of Resistance to Antibiotics' Unit, (Institut Pasteur - APHP - Université Paris Saclay), Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance 'Carbapenemase-producing Enterobacteriaceae', Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Team Resist, UMR-1184 (INSERM - Université Paris-Saclay - CEA), LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France; EERA 'Evolution and Ecology of Resistance to Antibiotics' Unit, (Institut Pasteur - APHP - Université Paris Saclay), Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance 'Carbapenemase-producing Enterobacteriaceae', Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, France.
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9
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Bonnin RA, Jousset AB, Emeraud C, Oueslati S, Dortet L, Naas T. Genetic Diversity, Biochemical Properties, and Detection Methods of Minor Carbapenemases in Enterobacterales. Front Med (Lausanne) 2021; 7:616490. [PMID: 33553210 PMCID: PMC7855592 DOI: 10.3389/fmed.2020.616490] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/09/2020] [Indexed: 01/05/2023] Open
Abstract
Gram-negative bacteria, especially Enterobacterales, have emerged as major players in antimicrobial resistance worldwide. Resistance may affect all major classes of anti-gram-negative agents, becoming multidrug resistant or even pan-drug resistant. Currently, β-lactamase-mediated resistance does not spare even the most powerful β-lactams (carbapenems), whose activity is challenged by carbapenemases. The dissemination of carbapenemases-encoding genes among Enterobacterales is a matter of concern, given the importance of carbapenems to treat nosocomial infections. Based on their amino acid sequences, carbapenemases are grouped into three major classes. Classes A and D use an active-site serine to catalyze hydrolysis, while class B (MBLs) require one or two zinc ions for their activity. The most important and clinically relevant carbapenemases are KPC, IMP/VIM/NDM, and OXA-48. However, several carbapenemases belonging to the different classes are less frequently detected. They correspond to class A (SME-, Nmc-A/IMI-, SFC-, GES-, BIC-like…), to class B (GIM, TMB, LMB…), class C (CMY-10 and ACT-28), and to class D (OXA-372). This review will address the genetic diversity, biochemical properties, and detection methods of minor acquired carbapenemases in Enterobacterales.
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Affiliation(s)
- Rémy A Bonnin
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France
| | - Agnès B Jousset
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Cécile Emeraud
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Saoussen Oueslati
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France
| | - Laurent Dortet
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Team "Resist" UMR1184 "Immunology of Viral, Auto-Immune, Hematological and Bacterial diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP-Université Paris-Sud, Paris, France.,Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
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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, Naas T. A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales. Sci Rep 2020; 10:9160. [PMID: 32514057 PMCID: PMC7280188 DOI: 10.1038/s41598-020-66161-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 05/13/2020] [Indexed: 12/22/2022] Open
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 blaOXA-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.
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Affiliation(s)
- Rémy A Bonnin
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
| | - Delphine Girlich
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
| | - Agnès B Jousset
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Lauraine Gauthier
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Gaëlle Cuzon
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Pierre Bogaerts
- Belgian National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, B-5530, Yvoir, Belgium
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - ANSES Laboratoire de Lyon, 31 avenue Tony Garnier, 69364, Lyon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - ANSES Laboratoire de Lyon, 31 avenue Tony Garnier, 69364, Lyon, France
| | | | - Olivier Barraud
- Université de Limoges, INSERM, CHU Limoges, UMR 1092, Limoges, France
| | - Nicolas Fortineau
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Philippe Glaser
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
| | - Youri Glupczynski
- Belgian National Reference Laboratory for Monitoring of Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, B-5530, Yvoir, Belgium
| | - Laurent Dortet
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- UMR 1184, Team Resist, INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.
- French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.
- Joint research Unit EERA « Evolution and Ecology of Resistance to Antibiotics », Institut Pasteur-APHP-University Paris Sud, Paris, France.
- Bacteriology-Hygiene unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.
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