1
|
Knecht CA, García Allende N, Álvarez VE, Prack Mc Cormick B, Massó MG, Campos J, Fox B, Alonso FM, Donis N, Canigia LF, Quiroga MP, Centrón D. New sequence type of an Enterobacter cloacae complex strain with the potential to become a high-risk clone. J Glob Antimicrob Resist 2022; 31:162-164. [PMID: 36049730 DOI: 10.1016/j.jgar.2022.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/13/2022] [Accepted: 08/21/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Enterobacter cloacae complex (ECC) has awakened interest recently because of its increasing resistance to carbapenems codified by several genes all over the globe. Even though there are some sequence types (STs) which represent high-risk clones, there is substantial clonal diversity in the ECC. This work aimed to perform whole-genome sequencing (WGS), genomic analysis, and phylogenetic studies of a Klebsiella pneumoniae carbapenemase (KPC) -producing multidrug-resistant (MDR) ECC isolate from Argentina. METHODS We analysed the genome of an MDR KPC-producing ECC strain isolated from a urine sample from a patient in a hospital in Argentina. The WGS was done by Illumina MiSeq-I (Illumina, San Diego, CA). The genome was assembled with SPAdes 3.9.0, and annotated with PROKKA, RAST, and Blast. Plasmids were identified with PlasmidFinder. Antibiotic resistance genes were detected using RESfinder, CARD, and Blastn. STs were identified with pubMLST. RESULTS The strain was identified as Enterobacter hormaechei, an important emerging human pathogen. No ST could be assigned; six of seven alleles of multilocus sequence typing (MLST) were the same as for E. hormaechei ST66, which is a high-risk clone. We found multiple acquired antibiotic resistance genes, including blaKPC-2 in an IncM1 plasmid, and a secretion system VI, which can favour the prevalence of ECC strains while competing with other bacteria. CONCLUSION Because of its MLST profile being so close to that of E. hormaechei ST66, the acquisition of multiple resistance genes, and the presence of the secretion systems, the potential of this strain for becoming a new high-risk clone cannot be discarded.
Collapse
Affiliation(s)
- Camila A Knecht
- Research Laboratory on Antibiotic Resistance Mechanisms. Institute of Medical Microbiology and Parasitology, Faculty of Medicine, University of Buenos Aires-National Council for Scientific and Technological Research (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | | | - Verónica E Álvarez
- Research Laboratory on Antibiotic Resistance Mechanisms. Institute of Medical Microbiology and Parasitology, Faculty of Medicine, University of Buenos Aires-National Council for Scientific and Technological Research (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Bárbara Prack Mc Cormick
- Research Laboratory on Antibiotic Resistance Mechanisms. Institute of Medical Microbiology and Parasitology, Faculty of Medicine, University of Buenos Aires-National Council for Scientific and Technological Research (IMPaM, UBA-CONICET), Buenos Aires, Argentina; Faculty of Agricultural Sciences, National University of Lomas de Zamora, Argentina
| | - Mariana G Massó
- Research Laboratory on Antibiotic Resistance Mechanisms. Institute of Medical Microbiology and Parasitology, Faculty of Medicine, University of Buenos Aires-National Council for Scientific and Technological Research (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Josefina Campos
- Genomics and bioinformatics platform, INEI-ANLIS 'Dr. Carlos G. Malbran', Buenos Aires, Argentina
| | | | - Fernando Martín Alonso
- Research Laboratory on Antibiotic Resistance Mechanisms. Institute of Medical Microbiology and Parasitology, Faculty of Medicine, University of Buenos Aires-National Council for Scientific and Technological Research (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Nicolás Donis
- Research Laboratory on Antibiotic Resistance Mechanisms. Institute of Medical Microbiology and Parasitology, Faculty of Medicine, University of Buenos Aires-National Council for Scientific and Technological Research (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | | | - María Paula Quiroga
- Research Laboratory on Antibiotic Resistance Mechanisms. Institute of Medical Microbiology and Parasitology, Faculty of Medicine, University of Buenos Aires-National Council for Scientific and Technological Research (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Daniela Centrón
- Research Laboratory on Antibiotic Resistance Mechanisms. Institute of Medical Microbiology and Parasitology, Faculty of Medicine, University of Buenos Aires-National Council for Scientific and Technological Research (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| |
Collapse
|
2
|
Brovedan MA, Marchiaro PM, Díaz MS, Faccone D, Corso A, Pasteran F, Viale AM, Limansky AS. Pseudomonas putida group species as reservoirs of mobilizable Tn402-like class 1 integrons carrying bla VIM-2 metallo-β-lactamase genes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 96:105131. [PMID: 34748986 DOI: 10.1016/j.meegid.2021.105131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 01/22/2023]
Abstract
The Pseudomonas putida group (P. putida G) is composed of at least 21 species associated with a wide range of environments, including the clinical setting. Here, we characterized 13 carbapenem-resistant P. putida G clinical isolates bearing class 1 integrons/transposons (class 1 In/Tn) carrying blaVIM-2 metallo-β-lactamase gene cassettes obtained from hospitals of Argentina. Multilocus sequencing (MLSA) and phylogenetic analyses based on 16S rDNA, gyrB and rpoD sequences distinguished 7 species among them. blaVIM-2 was found in three different cassette arrays: In41 (blaVIM-2-aacA4), In899 (only blaVIM-2), and In528 (dfrB1-aacA4-blaVIM-2). In41 and In899 were associated with complete tniABQC transposition modules and IRi/IRt boundaries characteristic of the Tn5053/Tn402 transposons, which were designated Tn6335 and Tn6336, respectively. The class 1 In/Tn element carrying In528, however, exhibited a defective tni module bearing only the tniC (transposase) gene, associated with a complete IS6100 bounded with two oppositely-oriented IRt end regions. In some P. putida G isolates including P. asiatica, P. juntendi, P. putida G/II, and P. putida G/V, Tn6335/Tn6336 were carried by pLD209-type conjugative plasmids capable of self-mobilization to P. aeruginosa or Escherichia coli. In other isolates of P. asiatica, P. putida G/II, and P. monteiliieilii, however, these blaVIM-2-containing class 1 In/Tn elements were found inserted into the res regions preceding the tnpR (resolvase) gene of particular Tn21 subgroup members of Tn3 transposons. The overall results reinforce the notion of P. putida G members as blaVIM-2 reservoirs, and shed light on the mechanisms of dissemination of carbapenem resistance genes to other pathogenic bacteria in the clinical setting.
Collapse
Affiliation(s)
- Marco A Brovedan
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Patricia M Marchiaro
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María S Díaz
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Diego Faccone
- Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando Pasteran
- Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro M Viale
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
| | - Adriana S Limansky
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
| |
Collapse
|
3
|
Miltgen G, Garrigos T, Cholley P, Deleume M, Allou N, Allyn J, Wilkinson DA, Lugagne N, Belmonte O, Bertrand X, Hocquet D, Mavingui P. Nosocomial cluster of carbapenemase-producing Enterobacter cloacae in an intensive care unit dedicated COVID-19. Antimicrob Resist Infect Control 2021; 10:151. [PMID: 34674756 PMCID: PMC8529563 DOI: 10.1186/s13756-021-01022-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022] Open
Abstract
Concomitant prevention of SARS-CoV-2 and extensively drug-resistant bacteria transmission is a difficult challenge in intensive care units dedicated to COVID-19 patients. We report a nosocomial cluster of four patients carrying NDM-1 plasmid-encoded carbapenemase-producing Enterobacter cloacae. Two main factors may have contributed to cross-transmission: misuse of gloves and absence of change of personal protective equipment, in the context of COVID-19-associated shortage. This work highlights the importance of maintaining infection control measures to prevent CPE cross-transmission despite the difficult context and that this type of outbreak can potentially involve several species of Enterobacterales.
Collapse
Affiliation(s)
- Guillaume Miltgen
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France. .,UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France.
| | - Thomas Garrigos
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Pascal Cholley
- Service d'Hygiène Hospitalière, CHU Jean Minjoz, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Marine Deleume
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Nicolas Allou
- Service de Réanimation Polyvalente, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Jérôme Allyn
- Service de Réanimation Polyvalente, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - David A Wilkinson
- UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | - Nathalie Lugagne
- Service d'hygiène hospitalière, CHU Félix Guyon, Saint-Denis, La Réunion, France
| | - Olivier Belmonte
- Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400, Saint-Denis, La Réunion, France
| | - Xavier Bertrand
- Service d'Hygiène Hospitalière, CHU Jean Minjoz, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- Service d'Hygiène Hospitalière, CHU Jean Minjoz, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Patrick Mavingui
- UMR PIMIT, Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| |
Collapse
|
4
|
Zhu Y, Liu W, Schwarz S, Wang C, Yang Q, Luan T, Wang L, Liu S, Zhang W. Characterization of a blaNDM-1-carrying IncHI5 plasmid from Enterobacter cloacae complex of food-producing animal origin. J Antimicrob Chemother 2021; 75:1140-1145. [PMID: 32016414 DOI: 10.1093/jac/dkaa010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To characterize an NDM-1-encoding multiresistance IncHI5 plasmid from Enterobacter cloacae complex of chicken origin. METHODS Carbapenemase genes were detected by PCR and Sanger sequencing. The MICs for the E. cloacae complex isolate and its transformant were determined by the agar dilution and broth microdilution methods. Conjugation and electrotransformation were performed to assess the horizontal transferability of the carbapenemase plasmid. Plasmid DNA was isolated from the transformant and fully sequenced using Illumina HiSeq and PacBio platforms. Plasmid stability was investigated by sequential passages on antibiotic-free medium. A circular intermediate was detected by inverse PCR and Sanger sequencing. RESULTS Plasmid pNDM-1-EC12 carried a conserved IncHI5 backbone and exhibited an MDR phenotype. All antimicrobial resistance genes were clustered in a single MDR region. Genetic environment analysis revealed that the blaNDM-1 gene was in a novel complex integron, In469. Based on sequence analysis, the blaNDM-1-carrying region was thought to be inserted by homologous recombination. Inverse PCR indicated that an ISCR1-mediated circular intermediate can be formed. Plasmid pNDM-1-EC12 was stably maintained both in the parental strain and the transformant without selective pressure. Comprehensive analysis of IncHI5-type plasmids suggested that they may become another key vehicle for rapid transmission of carbapenemase genes. CONCLUSIONS To the best of our knowledge, this is the first report of a fully sequenced IncHI5 plasmid recovered from an E. cloacae complex strain of food-producing animal origin. Co-occurrence of blaNDM-1 with genes encoding resistance to other antimicrobial agents on the same IncHI5 plasmid may result in the co-selection of blaNDM-1 and facilitates its persistence and rapid dissemination.
Collapse
Affiliation(s)
- Yao Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wenyu Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Changzhen Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Qin Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Tian Luan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Lingli Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Dissemination of a 'rare' extended-spectrum β-lactamase gene bla SFO-1 mediated by epidemic clones of carbapenemase-producing Enterobacter hormaechei in China. Int J Antimicrob Agents 2020; 56:106079. [PMID: 32634604 DOI: 10.1016/j.ijantimicag.2020.106079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/16/2020] [Accepted: 06/28/2020] [Indexed: 12/17/2022]
Abstract
An increasing trend of the coexistence of a rare extended-spectrum β-lactamase gene blaSFO-1 and carbapenemase genes in Enterobacteriaceae has recently been noted. This study aimed to determine the epidemiological and genetic characterisation of SFO-1-positive carbapenem-resistant Enterobacter cloacae complex (CREC) isolates. A total of 61 CREC clinical isolates were collected in the framework of a national surveillance for carbapenem-resistant Enterobacteriaceae during 2011-2015 in China. Seven SFO-1-positive CREC isolates (11.5%) were identified in four provinces, suggesting a wide dissemination of the blaSFO-1 gene among the CREC population in China. Five SFO-1-positive CREC isolates were further identified by screening 1625 genomes of E. cloacae complex strains retrieved from GenBank. The 12 SFO-1-positive CREC isolates were further identified as Enterobacter hormaechei, of which 10 belonged to epidemic clones (ST93, ST114 and ST418), indicating that these clones might largely contribute to the dissemination of blaSFO-1. Phylogenomics analysis further identified the occurrence of clonal dissemination in the community setting. The blaSFO-1-bearing plasmids were assigned to various incompatibility groups with highly diverse sizes (~104-370 kb), suggesting a wide vector range of blaSFO-1. Two types of genetic context, with and without insertion sequence IS26, were identified for the blaSFO-1 gene. The genetic context flanked by IS26 was more prevalent, thus largely facilitating the mobility of blaSFO-1. This study revealed that the blaSFO-1 gene is not as rare as previously found and that epidemic clones of CREC are responsible for its dissemination in China. These findings highlight the potential of wide dissemination of low-prevalence antimicrobial resistance genes.
Collapse
|
7
|
Reyes JA, Melano R, Cárdenas PA, Trueba G. Mobile genetic elements associated with carbapenemase genes in South American Enterobacterales. Braz J Infect Dis 2020; 24:231-238. [PMID: 32325019 PMCID: PMC9392046 DOI: 10.1016/j.bjid.2020.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/11/2020] [Accepted: 03/21/2020] [Indexed: 01/04/2023] Open
Abstract
Introduction Carbapenem resistance in members of order Enterobacterales is a growing public health problem causing high mortality in developing and industrialized countries. Its emergence and rapid propagation worldwide was due to both intercontinental spread of pandemic strains and horizontal dissemination via mobile genetic elements (MGE) such as plasmids and transposons. Objective To describe MGE carrying carbapenem resistance genes in Enterobacterales which have been reported in South America. Search strategy and selection criteria A search of the literature in English or Spanish published until 2019 in PubMed, Google Scholar, LILACS and SciELO databases was performed for studies of MGE in Enterobacterales reported in South American countries. Results Seven South American countries reported MGE related to carbapenemases. Carbapenemase-producing Klebsiella pneumoniae belonging to clonal complex 258 were the most prevalent pathogens reported; others carbapenemase-producing Enterobacterales such as Escherichia coli, Serratia marcescens, and Providencia rettgeri also have been reported. The MGE implicated in the spread of the most prevalent carbapenemase genes are Tn4401 and non-Tn4401 elements for blaKPC and ISAba125 for blaNDM, located in different plasmid incompatibility groups, i.e. L/M, A/C, FII and bacterial clones. Conclusion This review indicates that, like in other parts of the world, the most commonly reported carbapenemases in Enterobacterales from South America are being disseminated through clones, plasmids, and transposons which have been previously reported in other parts of the world.
Collapse
|
8
|
Izdebski R, Baraniak A, Zabicka D, Sekowska A, Gospodarek-Komkowska E, Hryniewicz W, Gniadkowski M. VIM/IMP carbapenemase-producing Enterobacteriaceae in Poland: epidemic Enterobacter hormaechei and Klebsiella oxytoca lineages. J Antimicrob Chemother 2019; 73:2675-2681. [PMID: 29986025 DOI: 10.1093/jac/dky257] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/06/2018] [Indexed: 12/23/2022] Open
Abstract
Objectives To analyse VIM/IMP-type MBL-producing Enterobacteriaceae isolates identified in Poland during 2006-12. Methods Isolates were typed by PFGE, followed by MLST. blaVIM/IMP genes were amplified and sequenced within class 1 integrons. Their plasmidic versus chromosomal location was assessed by nuclease S1 and I-CeuI plus hybridization experiments. Plasmids were characterized by transfer assays and PCR-based replicon typing. Results One hundred and nineteen VIM/IMP-positive Enterobacteriaceae cases were reported in Poland from the first case in 2006 until 2012. The patients were in 54 hospitals and were infected or colonized by 121 organisms, including Enterobacter cloacae complex (n = 64), Klebsiella oxytoca (n = 23), Serratia marcescens (n = 20) and Klebsiella pneumoniae (n = 11). The isolates represented numerous pulsotypes and mainly original STs, and carried eight integrons with blaVIM-1-like genes (blaVIM-1/-4/-28/-37/-40; n = 101), three with blaVIM-2 variants (blaVIM-2/-20; n = 17) and one with blaIMP-19 (n = 3). Six integrons were new, and five and two formed prevalent families of In238-like (n = 96) and In1008-like (n = 16) elements, respectively. In238 (aacA4-blaVIM-4rpt) and In1008 (blaVIM-2-aacA4) had been originally observed in Polish Pseudomonas aeruginosa, suggestive of their transfer to enterobacteria, followed by spread and diversification. Four organisms have disseminated inter-regionally, i.e. Enterobacter hormaechei ST90 with plasmidic In238/In238a integrons (n = 36), K. oxytoca ST145 with a chromosomal In237-like element (n = 18) and two subclones of E. hormaechei ST89 with In1008- or In238-type variants (n = 8 and n = 7, respectively). Conclusions The epidemiology of VIM/IMP-producing Enterobacteriaceae in Poland has revealed a remarkable number of specific or novel characteristics of the organisms, with some possible links to other mid-southern European countries.
Collapse
Affiliation(s)
- R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - D Zabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - A Sekowska
- Department of Microbiology, Nicolas Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - E Gospodarek-Komkowska
- Department of Microbiology, Nicolas Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| |
Collapse
|
9
|
Peirano G, Matsumura Y, Adams MD, Bradford P, Motyl M, Chen L, Kreiswirth BN, Pitout JDD. Genomic Epidemiology of Global Carbapenemase-Producing Enterobacter spp., 2008-2014. Emerg Infect Dis 2019; 24:1010-1019. [PMID: 29774858 PMCID: PMC6004858 DOI: 10.3201/eid2406.171648] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We performed whole-genome sequencing on 170 clinical carbapenemase-producing Enterobacter spp. isolates collected globally during 2008-2014. The most common carbapenemase was VIM, followed by New Delhi metallo-β-lactamase (NDM), Klebsiella pneumoniae carbapenemase, oxacillin 48, and IMP. The isolates were of predominantly 2 species (E. xiangfangensis and E. hormaechei subsp. steigerwaltii) and 4 global clones (sequence type [ST] 114, ST93, ST90, and ST78) with different clades within ST114 and ST90. Particular genetic structures surrounding carbapenemase genes were circulating locally in various institutions within the same or between different STs in Greece, Guatemala, Italy, Spain, Serbia, and Vietnam. We found a common NDM genetic structure (NDM-GE-U.S.), previously described on pNDM-U.S. from Klebsiella pneumoniae ATCC BAA-214, in 14 different clones obtained from 6 countries spanning 4 continents. Our study highlights the importance of surveillance programs using whole-genome sequencing in providing insight into the molecular epidemiology of carbapenemase-producing Enterobacter spp.
Collapse
|