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Izawa H, Eda R, Niida N, Nakamura M, Furukawa T, Sei K, Kubo M, Suzuki M, Maehana S. Genome sequences of Enterobacter asburiae mcr-9 harboring and Enterobacter roggenkampii mcr-10 harboring isolated from a wastewater treatment plant in Japan. Microbiol Resour Announc 2024:e0040724. [PMID: 39315836 DOI: 10.1128/mra.00407-24] [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: 04/17/2024] [Accepted: 07/19/2024] [Indexed: 09/25/2024] Open
Abstract
Severe infections caused by multi-drug-resistant Gram-negative rods pose a clinical threat due to their high mortality risk. The global spread of plasmid-mediated colistin-resistance genes has become a serious problem. In this study, we identified Enterobacter spp. harboring mcr-9 and mcr-10 from a wastewater treatment plant in Japan.
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Affiliation(s)
- Hiroki Izawa
- Laboratory of Environmental Microbiology, Graduate School of Medical Sciences, Kitasato University, Kanagawa, Japan
- Department of Clinical Laboratory, Kitasato University Hospital, Kanagawa, Japan
| | - Ryotaro Eda
- Laboratory of Environmental Microbiology, Graduate School of Medical Sciences, Kitasato University, Kanagawa, Japan
- Research Center for Biosafety, Laboratory Animal and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nagi Niida
- Laboratory of Environmental Microbiology, Graduate School of Medical Sciences, Kitasato University, Kanagawa, Japan
| | - Masaki Nakamura
- Department of Clinical Laboratory, Kitasato University Hospital, Kanagawa, Japan
- Department of Laboratory Medicine, School of Medicine, Kitasato University, Kanagawa, Japan
| | - Takashi Furukawa
- Department of Health Science, Laboratory of Environmental Hygiene, School of Allied Health Sciences, Kitasato University, Kanagawa, Japan
| | - Kazunari Sei
- Department of Health Science, Laboratory of Environmental Hygiene, School of Allied Health Sciences, Kitasato University, Kanagawa, Japan
| | - Makoto Kubo
- Laboratory of Environmental Microbiology, Graduate School of Medical Sciences, Kitasato University, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, Kanagawa, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shotaro Maehana
- Laboratory of Environmental Microbiology, Graduate School of Medical Sciences, Kitasato University, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, Kanagawa, Japan
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2
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Sukkar I, Valcek A, Dolejska M. VIM-1-producing Enterobacter asburiae with mobile colistin resistance genes from wastewaters. BMC Genomics 2024; 25:870. [PMID: 39300338 PMCID: PMC11411806 DOI: 10.1186/s12864-024-10780-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 09/06/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Wastewaters are considered as important players in the spread of antimicrobial resistance, thus affecting the health of humans and animals. Here, we focused on wastewaters as a possible source of carbapenemase-producing Enterobacterales for the environment. METHODS A total of 180 presumptive coliforms from hospital and municipal wastewaters, and a river in the Czech Republic were obtained by selective cultivation on meropenem-supplemented media and tested for presence of carbapenemase-encoding genes by PCR. Strains carrying genes of interest were characterized by testing antimicrobial susceptibility, carbapenemase production and combination of short- and long- read whole-genome sequencing. The phylogenetic tree including publicly available genomes of Enterobacter asburiae was conducted using Prokka, Roary and RAxML. RESULTS Three VIM-producing Enterobacter asburiae isolates, members of the Enterobacter cloacae complex, were detected from hospital and municipal wastewaters, and the river. The blaVIM-1 gene was located within a class 1 integron that was carried by different F-type plasmids and one non-typeable plasmid. Furthermore, one of the isolates carried plasmid-borne colistin-resistance gene mcr-10, while in another isolate chromosomally located mcr-9 without colistin resistance phenotype was detected. In addition, the analysis of 685 publicly available E. asburiae genomes showed they frequently carry carbapenemase genes, highlighting the importance of this species in the emergence of resistance to last-line antibiotics. CONCLUSION Our findings pointed out the important contribution of hospital and community wastewaters in transmission of multi-drug resistant pathogens.
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Affiliation(s)
- Iva Sukkar
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Adam Valcek
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Monika Dolejska
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic.
- Faculty of Medicine, Charles University, Pilsen, Czech Republic.
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic.
- Division of Clinical Microbiology and Immunology, Department of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic.
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3
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Alves GDSO, Canellas ALB, Gallo MN, Vinzon SB, Laport MS. In treacherous waters: detection of colistin-resistant bacteria in water and plastic litter from a recreational estuary. Lett Appl Microbiol 2024; 77:ovae082. [PMID: 39227173 DOI: 10.1093/lambio/ovae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/08/2024] [Accepted: 09/02/2024] [Indexed: 09/05/2024]
Abstract
Colistin resistance poses a major therapeutic challenge and resistant strains have now been reported worldwide. However, the occurrence of such bacteria in aquatic environments is considerably less understood. This study aimed to isolate and characterize colistin-resistant strains from water and plastic litter collected in an urban recreational estuary. Altogether, 64 strains with acquired colistin resistance were identified, mainly Acinetobacter spp. and Enterobacter spp. From these, 40.6% were positive for at least one mcr variant (1-9), 26.5% harbored, extended-spectrum beta-lactamases, 23.4% harbored, sulfonamide resistance genes, and 9.3% harbored, quinolone resistance genes. merA, encoding mercury resistance, was detected in 10.5% of these strains, most of which were also strong biofilm producers. The minimum inhibitory concentration toward colistin was determined for the mcr-positive strains and ranged from 2 to ≥512 µg ml-1. Our findings suggest that Gram-negative bacteria highly resistant to a last-resort antimicrobial can be found in recreational waters and plastic litter, thereby evidencing the urgency of the One Health approach to mitigate the antimicrobial resistance crisis.
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Affiliation(s)
| | - Anna Luiza Bauer Canellas
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Marcos N Gallo
- Área de Engenharia Costeira e Oceanográfica, COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-598, Brazil
| | - Susana Beatriz Vinzon
- Área de Engenharia Costeira e Oceanográfica, COPPE, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-598, Brazil
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
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Santos da Costa B, Peixoto RS, da Conceição Neto OC, da Silva Pontes L, Tavares E Oliveira TR, Tavares Teixeira CB, de Oliveira Santos IC, Silveira MC, Silva Rodrigues DC, Pribul BR, Rocha-de-Souza CM, D 'Alincourt Carvalho-Assef AP. Polymyxin resistance in Enterobacter cloacae complex in Brazil: phenotypic and molecular characterization. Braz J Microbiol 2024:10.1007/s42770-024-01464-1. [PMID: 39210190 DOI: 10.1007/s42770-024-01464-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 07/04/2024] [Indexed: 09/04/2024] Open
Abstract
Enterobacter cloacae complex isolates have been reported as an important nosocomial multidrug resistance pathogen. In the present study, we investigated antimicrobial susceptibility and the colistin-resistance rates, their genetic determinants and clonality among clinical E. cloacae complex isolates from different Brazilian states. For this, an initial screening was carried out on 94 clinical isolates of E. clocacae complex received between 2016 and 2018 by LAPIH-FIOCRUZ, using EMB plates containing 4 μg/mL of colistin, followed MIC determination, resulting in the selection of 26 colistin-resistant isolates from the complex. The presence of carbapenemases encoding genes (blaKPC, blaNDM and blaOXA-48), plasmidial genes for resistance to polymyxins (mcr1-9) and mutations in chromosomal genes (pmrA, pmrB, phoP and phoQ) described as associated with resistance to polymyxin were screened by PCR and DNA sequencing. Finally, the hsp60 gene was sequenced to identify species of the E. cloacae complex and genetic diversity was evaluated by PFGE and MLST. The results have shown that among 94 E. cloacae complex isolates, 19 (20.2%) were colistin-resistant. The resistant strains exhibited MIC ranging from 4 to 128 µg / mL and E. hormaechei subsp. steigerwaltii was the prevalent species in the complex (31,6%), followed by E. cloacae subsp. cloacae (26,3%). The antimicrobials with the highest susceptibility rate were gentamicin (21%) and tigecycline (26%). Carbapenemases encoding genes (blaKPC n = 5, blaNDM n = 1) were detected in 6 isolates and mcr-9 in one. Among the modifications found in PmrA, PmrB, PhoP e PhoQ (two-component regulatory system), only the S175I substitution in PmrB found in E. cloacae subsp cloacae isolates were considered deleterious (according to the prediction of PROVEAN). By PFGE, 13 profiles were found among E. cloacae complex isolates, with EcD the most frequent. Furthermore, by MLST 10 ST's, and 1 new ST, were identified in E. cloacae. In conclusion, no prevalence of clones or association among carbapenemase production and polymyxin resistance was found between the E. cloacae. Thereby, the results suggest that the increased polymyxin-resistance is related to the selective pressure exerted by the indiscriminate use in hospitals. Lastly, this study highlights the urgent need to elucidate the mechanism involved in the resistance to polymyxin in the E. cloacae complex and the development of measures to control and prevent infections caused by these multiresistant bacteria.
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Affiliation(s)
- Bianca Santos da Costa
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
| | - Renata Stavracakis Peixoto
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
| | - Orlando Carlos da Conceição Neto
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
| | - Leilane da Silva Pontes
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
| | - Thamirys Rachel Tavares E Oliveira
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
| | - Camila Bastos Tavares Teixeira
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
| | - Ivson Cassiano de Oliveira Santos
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
| | - Melise Chaves Silveira
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
| | - Daiana Cristina Silva Rodrigues
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
| | - Bruno Rocha Pribul
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
- Coleção de Culturas de Bactérias de Origem Hospitalar (CCBH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Av. Brasil, Rio de Janeiro,RJ, 436521045900, Brazil
| | - Cláudio Marcos Rocha-de-Souza
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil
- Coleção de Culturas de Bactérias de Origem Hospitalar (CCBH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Av. Brasil, Rio de Janeiro,RJ, 436521045900, Brazil
| | - Ana Paula D 'Alincourt Carvalho-Assef
- Instituto Oswaldo Cruz - Fundação Oswaldo Cruz, Laboratório de Bacteriologia Aplicada a Saúde Única E Resistência Antimicrobiana, Av. Brasil, Rio de Janeiro, RJ, 436521045900, Brazil.
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Das S, Mallick A, Barik M, Sarkar S, Saha P. The emergence of clonally diverse carbapenem-resistant Enterobacter cloacae complex in West Bengal, India: a dockyard of β-lactamases periling nosocomial infections. Int Microbiol 2024; 27:1023-1033. [PMID: 37985632 DOI: 10.1007/s10123-023-00451-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023]
Abstract
Carbapenem-resistant Enterobacter cloacae complex (CRECC) constitutes a global public health threat challenging clinical treatment and infection control, especially in low- and middle-income countries such as India. We analyzed the antimicrobial susceptibility, major β-lactamase genes, plasmid profiles, and genetic relatedness to understand the molecular epidemiology of CRECC clinical isolates (n = 44) in West Bengal, India, during 2021-2022. The majority (> 55%) of the isolates were resistant to fluoroquinolones, aminoglycosides, and co-trimoxazole, even > 20% for tigecycline and > 35% were extensively drug-resistant. Co-β-lactamase production was categorized into twenty-seven types, importantly NDM (84%), OXA-48 (40%), TEM (61%), CTX-M (46%), OXA-1 (55%), and MIR (27%). The NDM-1 and OXA-181 were major variants with the first observations of NDM-24 and -29 variants in India. Wide-range of plasmids (2 to > 212 kb) were harbored by the β-lactamase-producing isolates: small (91%), medium (27%), large (9%), and mega (71%). IncX3, ColE1, and HI2 were noted in about 30% of isolates, while IncF and R were carried by < 20% of isolates. The clonally diverse CRECC isolates were noted to cause cross-infections, especially at superficial site, bloodstream, and urinary-tract. This is the first molecular surveillance on CRECC in India. The study isolates serve as the dockyard of NDM, TEM, and CTX-M harboring a wide range of plasmids. The outcomes of the study may strengthen local and national policies for infection prevention and control practices, clarifying the genetic diversity among CRECC. Extensive genomic study may further intersect the relationships between these different plasmids, especially with their sizes, types, and antibiotic resistance markers.
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Affiliation(s)
- Surojit Das
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Abhi Mallick
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Mili Barik
- Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Soma Sarkar
- Department of Microbiology at Nil Ratan Sirkar Medical College Hospital, Kolkata, West Bengal, India
- Department of Microbiology at Infectious Diseases & Beleghata General Hospital, Kolkata, West Bengal, India
| | - Puranjoy Saha
- Department of Microbiology, Malda Medical College and Hospital, Malda, West Bengal, India
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6
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Wan Y, Myall AC, Boonyasiri A, Bolt F, Ledda A, Mookerjee S, Weiße AY, Getino M, Turton JF, Abbas H, Prakapaite R, Sabnis A, Abdolrasouli A, Malpartida-Cardenas K, Miglietta L, Donaldson H, Gilchrist M, Hopkins KL, Ellington MJ, Otter JA, Larrouy-Maumus G, Edwards AM, Rodriguez-Manzano J, Didelot X, Barahona M, Holmes AH, Jauneikaite E, Davies F. Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes. J Infect Dis 2024; 230:e159-e170. [PMID: 39052705 PMCID: PMC11272044 DOI: 10.1093/infdis/jiae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/02/2024] [Accepted: 01/19/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)-encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network. METHODS We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE-positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events. RESULTS Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations. CONCLUSIONS Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.SummaryThis was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ashleigh C Myall
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Frances Bolt
- Department of Infectious Diseases, Imperial College Healthcare NHS Trust, London, United Kingdom
- Centre for Antimicrobial Optimisation, Hammersmith Hospital, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Alice Ledda
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
| | - Siddharth Mookerjee
- Department of Infectious Diseases, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Andrea Y Weiße
- School of Biological Sciences, University of Edinburgh, Scotland, United Kingdom
- School of Informatics, University of Edinburgh, Scotland, United Kingdom
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jane F Turton
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
| | - Hala Abbas
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Microbiology, North West London Pathology, London, United Kingdom
| | - Ruta Prakapaite
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Akshay Sabnis
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Alireza Abdolrasouli
- Department of Infectious Diseases, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Kenny Malpartida-Cardenas
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Luca Miglietta
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Hugo Donaldson
- Department of Microbiology, North West London Pathology, London, United Kingdom
| | - Mark Gilchrist
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Diseases, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Katie L Hopkins
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom
| | - Matthew J Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Reference Services Division, UK Health Security Agency, London, United Kingdom
| | - Jonathan A Otter
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gerald Larrouy-Maumus
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Andrew M Edwards
- MRC Centre for Molecular Bacteriology and Infection, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jesus Rodriguez-Manzano
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Centre for Antimicrobial Optimisation, Hammersmith Hospital, Imperial College London, London, United Kingdom
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Alison H Holmes
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Diseases, Imperial College Healthcare NHS Trust, London, United Kingdom
- Centre for Antimicrobial Optimisation, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Frances Davies
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Diseases, Imperial College Healthcare NHS Trust, London, United Kingdom
- Department of Microbiology, North West London Pathology, London, United Kingdom
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7
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Baek JY, Yang J, Ko JH, Cho SY, Huh K, Chung DR, Peck KR, Ko KS, Kang CI. Extensively drug-resistant Enterobacter ludwigii co-harbouring MCR-9 and a multicopy of bla IMP-1 in South Korea. J Glob Antimicrob Resist 2024; 36:217-222. [PMID: 38157935 DOI: 10.1016/j.jgar.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024] Open
Abstract
In this study, we describe an Enterobacter ludwigii clinical isolate that is resistant to both carbapenems and colistin in South Korea. Antimicrobial susceptibility testing revealed that E. ludwigii CRE2104-31 was non-susceptible to all tested antibiotics except fosfomycin. Whole genome sequencing identified a 323-kbp IncHI2 plasmid, pCRE2104-31a, that was co-harbouring mobile colistin resistance (mcr)-9.1 and blaIMP-1. In comparison with other full plasmids, pCRE2104-31a exhibited the closest similarity to a plasmid from the Klebsiella pneumoniae strain CNR48 from France, with 19.9% query coverage and 99% identity. Notably, we observed five tandem repeats of blaIMP-1 and aac(6')-Il genes, accompanied by multiple attCs within a class I integron on the Tn402-like transposon. The unit of blaIMP-1-attC-aac(6')-Il-attC might have accumulated due to multiple convergent events. In addition to mcr-9.1 and blaIMP-1, various other antibiotic resistance-associated genes were identified in the plasmid, as follows: blaTEM-1B, aph(3')-I, aph(3')-Ia, aac(6')-Il, aac(6')-IIc, aac(6')-IIa, aph(6)-Id, aph(3'')-Ib, aadA2b, aac(6')-Ib3, sul, dfrA19, qnrB2, aac(6')-Ib-cr, ere(A), and qacE. A conjugation assay showed that the mcr-9.1/blaIMP-1-co-bearing plasmid was self-transmissible to E. coli J53. However, colistin and carbapenem resistance could not be transferred to E. coli due to high incompatibility. The convergence of mcr and carbapenemase genes is thought to be host-dependent among Enterobacteriaceae. The emergence of extensively drug-resistant E. ludwigii co-harbouring MCR-9.1 and a multicopy of blaIMP-1 would pose a significant threat within the compatible Enterobacteriaceae.
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Affiliation(s)
- Jin Yang Baek
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea
| | - Jinyoung Yang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jae-Hoon Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sun Young Cho
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kwan Soo Ko
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
| | - Cheol-In Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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Xedzro C, Shimamoto T, Yu L, Zuo H, Sugawara Y, Sugai M, Shimamoto T. Emergence of colistin-resistant Enterobacter cloacae and Raoultella ornithinolytica carrying the phosphoethanolamine transferase gene, mcr-9, derived from vegetables in Japan. Microbiol Spectr 2023; 11:e0106323. [PMID: 37909761 PMCID: PMC10714742 DOI: 10.1128/spectrum.01063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/17/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Plasmid-mediated mobile colistin-resistance genes have been recognized as a global threat because they jeopardize the efficacy of colistin in therapeutic practice. Here, we described the genetic features of two mcr-9.1-carrying Gram-negative bacteria with a colistin-resistant phenotype derived from vegetables in Japan. The colistin-resistant mcr-9.1, which has never been detected in vegetables, was located on a large plasmid in Enterobacter cloacae CST17-2 and Raoultella ornithinolytica CST129-1, suggesting a high chance of horizontal gene transfer. To the best of our knowledge, this is the first report of mcr-9 in R. ornithinolytica. This study indicates that fresh vegetables might be a potential source for the transmission of mcr-9 genes encoding resistance to frontline (colistin) and clinically relevant antimicrobials. The study also provides additional consideration for colistin use and the relevance of routine surveillance in epidemiological perspective to curb the continuous spread of mcr alleles.
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Affiliation(s)
- Christian Xedzro
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Toshi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Liansheng Yu
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Hui Zuo
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Tadashi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
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9
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Wu W, Wang J, Zhang P, Wang N, Yuan Q, Shi W, Zhang X, Li X, Qu T. Emergence of carbapenem-resistant Enterobacter hormaechei ST93 plasmids co-harbouring bla NDM-1, bla KPC-2, and mcr-9 in bloodstream infection. J Glob Antimicrob Resist 2023; 34:67-73. [PMID: 37369326 DOI: 10.1016/j.jgar.2023.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/05/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
OBJECTIVES We isolated a strain of Enterobacter hormaechei, ECC2783, co-harbouring blaNDM-1, blaKPC-2 and mcr-9 plasmids from a bloodstream infection and investigated its biological features. METHODS The presence of carbapenemase genes and mcr-9 was confirmed by polymerase chain reaction amplification. Whole genome sequencing and genomic analysis were performed on ECC2783. Experiments assessing the conjugation and stability of plasmids carrying the carbapenemase gene were performed. We also performed a colistin resistance induction experiment and studied the fitness cost of transconjugants. RESULTS ECC2783 has an extensive drug resistance phenotype. Multilocus sequence typing analysis results showed that ECC2783 belongs to sequence type 93. Bioinformatics analysis confirmed that ECC2783 has four plasmids, of which pECC2783_a, carrying mcr-9, is the IncHI2 type, and pECC2783_c, carrying blaNDM-1, is the IncX3 type. pECC2783_d, carrying blaKPC-2, is an unclassified type. We successfully obtained two transconjugants (J53/ECC2783_1, carrying blaNDM-1, and J53/ECC2783_2, carrying blaKPC-2 and blaNDM-1). There was no statistically significant difference in the relative growth rate between J53 and J53/ECC2783_2. CONCLUSION For the first time, we isolated carbapenem-resistant E. hormaechei plasmids co-harbouring blaNDM-1, blaKPC-2, and mcr-9 from a patient with a blood stream infection. This isolate has a survival advantage in a hospital environment, and its clinical monitoring should be strengthened.
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Affiliation(s)
- Wenhao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Wang
- Respiratory Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Piaopiao Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nanfei Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qing Yuan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weixiao Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaofan Zhang
- Laboratory Medicine Centre, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xi Li
- Laboratory Medicine Centre, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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10
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Li X, Jiang T, Wu C, Kong Y, Ma Y, Wu J, Xie X, Zhang J, Ruan Z. Molecular epidemiology and genomic characterization of a plasmid-mediated mcr-10 and blaNDM-1 co-harboring multidrug-resistant Enterobacter asburiae. Comput Struct Biotechnol J 2023; 21:3885-3893. [PMID: 37602227 PMCID: PMC10433016 DOI: 10.1016/j.csbj.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 07/29/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023] Open
Abstract
Colistin is considered as one of the last-resort antimicrobial agents for treating multidrug-resistant bacterial infections. Multidrug-resistant E. asburiae has been increasingly isolated from clinical patients, which posed a great challenge for antibacterial treatment. This study aimed to report a mcr-10 and blaNDM-1 co-carrying E. asburiae clinical isolate 5549 conferred a high-level resistance against colistin. Antibiotic susceptibility testing was performed using the microdilution broth method. Transferability of mcr-10 and blaNDM-1-carrying plasmids were investigated by conjugation experiments. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to identify modifications in lipid A. Whole genome sequencing and phylogenetic analysis between strain 5549 and a total of 301 E. asburiae genomes retrieved from NCBI database were performed. The genetic characteristics of mcr-10 and blaNDM-1-bearing plasmids were also analyzed. Our study indicated that strain 5549 showed extensively antibiotic-resistant trait, including colistin and carbapenem resistance. The mcr-10 and blaNDM-1 were carried by IncFIB/IncFII type p5549_mcr-10 (159417 bp) and IncN type p5549_NDM-1 (63489 bp), respectively. Conjugation assays identified that only the blaNDM-1-carrying plasmid could be successfully transferred to E. coli J53. Interestingly, mcr-10 did not mediate colistin resistance when it was cloned into E. coli DH5α. Mass spectrometry analysis showed the lipid A palmitoylation of the C-lacyl-oxo-acyl chain to the chemical structure of lipid A at m/z 2063 in strain 5549. In summary, this study is the first to report a mcr-10 and blaNDM-1 co-occurrence E. asburiae recovered from China. Our investigation revealed the distribution of different clonal lineage of E. asburiae with epidemiology perspective and the underlying mechanisms of colistin resistance. Active surveillance is necessary to control the further dissemination of multidrug-resistant E. asburiae.
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Affiliation(s)
- Xinyang Li
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tian Jiang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Taizhou, China
| | - Chenghao Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingying Kong
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Yilei Ma
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Jianyong Wu
- Department of Clinical Laboratory, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Xinyou Xie
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Jun Zhang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
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11
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Hu S, Xie W, Cheng Q, Zhang X, Dong X, Jing H, Wang J. Molecular eidemiology of carbapenem-resistant Enterobacter cloacae complex in a tertiary hospital in Shandong, China. BMC Microbiol 2023; 23:177. [PMID: 37407923 DOI: 10.1186/s12866-023-02913-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND The increasing incidence and prevalence of carbapenem-resistant Enterobacter cloacae complex (CREC) poses great challenges to infection prevention and disease treatment. However, much remains unknown about the clinical characteristics of CREC isolates. Our objective was to characterize antimicrobial resistance and, carbapenemase production in CREC with 36 CREC isolates collected from a tertiary hospital in Shandong, China. RESULTS Three types of carbapenemases (NDM, IMP and VIM) were detected in these isolates. Among them, NDM carbapenemases were most prevalent, with a 61.2% (22/36) detection rate for NDM-1, 27.8% (10/36) for NDM-5 and 2.8% (1/36) for NDM-7. IMP-4 was found in two isolates and VIM-1 in only one isolate. The MLST analysis identified 12 different sequence types (STs), of which ST171 (27.8%) was the most prevalent, followed by ST418 (25.0%). ST171 isolates had significantly higher rates of resistance than other STs to gentamicin and tobramycin (Ps < 0.05), and lower rates of resistance to aztreonam than ST418 and other STs (Ps < 0.05). Among 17 carbapenemase-encoding genes, the blaNDM-5 gene was more frequently detected in ST171 than in ST418 and other isolates (Ps < 0.05). In contrast, the blaNDM-1 gene was more frequently seen in ST418 than in ST171 isolates. One novel ST (ST1965) was identified, which carried the blaNDM-1 gene. CONCLUSION NDM-5 produced by ST171 and NDM-1 carbapenemase produced by ST418 were the leading cause of CREC in this hospital. This study enhances the understanding of CREC strains and helps improve infection control and treatment in hospitals.
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Affiliation(s)
- Shengnan Hu
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Wenyan Xie
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Qiwen Cheng
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, 85287, USA
| | - Xiaoning Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Xiutao Dong
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China
| | - Huaiqi Jing
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, 102206, People's Republic of China
| | - Jiazheng Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, Shandong, China.
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12
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Cahill N, Hooban B, Fitzhenry K, Joyce A, O'Connor L, Miliotis G, McDonagh F, Burke L, Chueiri A, Farrell ML, Bray JE, Delappe N, Brennan W, Prendergast D, Gutierrez M, Burgess C, Cormican M, Morris D. First reported detection of the mobile colistin resistance genes, mcr-8 and mcr-9, in the Irish environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162649. [PMID: 36906027 DOI: 10.1016/j.scitotenv.2023.162649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eight mcr positive Enterobacterales (one mcr-8 and seven mcr-9) were recovered from six samples (freshwater (n = 2), healthcare facility wastewater (n = 2), wastewater treatment plant influent (n = 1) and integrated constructed wetland influent (piggery farm waste) (n = 1)). While the mcr-8 positive K. pneumoniae displayed resistance to colistin, all seven mcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 ± 4.1 (10-61), including the carbapenemases, blaOXA-48 (n = 2) and blaNDM-1 (n = 1), which were harboured by three of the isolates. The mcr genes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs of mcr genes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.
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Affiliation(s)
- Niamh Cahill
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland.
| | - Brigid Hooban
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Kelly Fitzhenry
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Aoife Joyce
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Liam Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Alexandra Chueiri
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Maeve Louise Farrell
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - James E Bray
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Niall Delappe
- National Carbapenemase-Producing Enterobacterales Reference Laboratory, National Salmonella, Shigella and Listeria Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Wendy Brennan
- National Carbapenemase-Producing Enterobacterales Reference Laboratory, National Salmonella, Shigella and Listeria Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Deirdre Prendergast
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland
| | | | - Catherine Burgess
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland; National Carbapenemase-Producing Enterobacterales Reference Laboratory, National Salmonella, Shigella and Listeria Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
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13
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Lee KY, Lavelle K, Huang A, Atwill ER, Pitesky M, Li X. Assessment of Prevalence and Diversity of Antimicrobial Resistant Escherichia coli from Retail Meats in Southern California. Antibiotics (Basel) 2023; 12:antibiotics12040782. [PMID: 37107144 PMCID: PMC10135137 DOI: 10.3390/antibiotics12040782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/10/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Retail meat products may serve as reservoirs and conduits for antimicrobial resistance, which is frequently monitored using Escherichia coli as indicator bacteria. In this study, E. coli isolation was conducted on 221 retail meat samples (56 chicken, 54 ground turkey, 55 ground beef, and 56 pork chops) collected over a one-year period from grocery stores in southern California. The overall prevalence of E. coli in retail meat samples was 47.51% (105/221), with E. coli contamination found to be significantly associated with meat type and season of sampling. From antimicrobial susceptibility testing, 51 isolates (48.57%) were susceptible to all antimicrobials tested, 54 (51.34%) were resistant to at least 1 drug, 39 (37.14%) to 2 or more drugs, and 21 (20.00%) to 3 or more drugs. Resistance to ampicillin, gentamicin, streptomycin, and tetracycline were significantly associated with meat type, with poultry counterparts (chicken or ground turkey) exhibiting higher odds for resistance to these drugs compared to non-poultry meats (beef and pork). From the 52 E. coli isolates selected to undergo whole-genome sequencing (WGS), 27 antimicrobial resistance genes (ARGs) were identified and predicted phenotypic AMR profiles with an overall sensitivity and specificity of 93.33% and 99.84%, respectively. Clustering assessment and co-occurrence networks revealed that the genomic AMR determinants of E. coli from retail meat were highly heterogeneous, with a sparsity of shared gene networks.
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Affiliation(s)
- Katie Yen Lee
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
- Western Institute for Food Safety and Security, University of California, Davis, Davis, CA 95616, USA
| | - Kurtis Lavelle
- Western Institute for Food Safety and Security, University of California, Davis, Davis, CA 95616, USA
| | - Anny Huang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Edward Robert Atwill
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Maurice Pitesky
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Xunde Li
- Western Institute for Food Safety and Security, University of California, Davis, Davis, CA 95616, USA
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14
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Zhou K, Zhou Y, Xue CX, Xu T, Chen Y, Shen P, Xiao Y. Bloodstream infections caused by Enterobacter hormaechei ST133 in China, 2010-22. THE LANCET. MICROBE 2023; 4:e13. [PMID: 36029774 DOI: 10.1016/s2666-5247(22)00226-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 01/04/2023]
Affiliation(s)
- Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China; First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yanzi Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, Zhejiang, China
| | - Chun-Xu Xue
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China; First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, China; First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, Zhejiang, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, Zhejiang, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, Zhejiang, China.
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15
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Han M, Liu C, Xie H, Zheng J, Zhang Y, Li C, Shen H, Cao X. Genomic and clinical characteristics of carbapenem-resistant Enterobacter cloacae complex isolates collected in a Chinese tertiary hospital during 2013-2021. Front Microbiol 2023; 14:1127948. [PMID: 36896426 PMCID: PMC9989974 DOI: 10.3389/fmicb.2023.1127948] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Objective To analyze the molecular epidemiology of carbapenem-resistant Enterobacter cloacae complex (CREC) by whole-genome sequencing and to explore its clinical characteristics. Methods Enterobacter cloacae complex isolates collected in a tertiary hospital during 2013-2021 were subjected to whole-genome sequencing to determine the distribution of antimicrobial resistance genes (ARGs), sequence types (STs), and plasmid replicons. A phylogenetic tree of the CREC strains was constructed based on the whole-genome sequences to analyze their relationships. Clinical patient information was collected for risk factor analysis. Results Among the 51 CREC strains collected, blaNDM-1 (n = 42, 82.4%) was the main carbapenem-hydrolyzing β-lactamase (CHβL), followed by blaIMP-4 (n = 11, 21.6%). Several other extended-spectrum β-lactamase-encoding genes were also identified, with blaSHV-12 (n = 30, 58.8%) and blaTEM-1B (n = 24, 47.1%) being the predominant ones. Multi-locus sequence typing revealed 25 distinct STs, and ST418 (n = 12, 23.5%) was the predominant clone. Plasmid analysis identified 15 types of plasmid replicons, among which IncHI2 (n = 33, 64.7%) and IncHI2A (n = 33, 64.7%) were the main ones. Risk factor analysis showed that intensive care unit (ICU) admission, autoimmune disease, pulmonary infection, and previous corticosteroid use within 1 month were major risk factors for acquiring CREC. Logistic regression analysis showed that ICU admission was an independent risk factor for CREC acquisition and was closely related with acquiring infection by CREC with ST418. Conclusion BlaNDM-1 and blaIMP-4 were the predominant carbapenem resistance genes. ST418 carrying BlaNDM-1 not only was the main clone, but also circulated in the ICU of our hospital during 2019-2021, which highlights the necessity for surveillance of this strain in the ICU. Furthermore, patients with risk factors for CREC acquisition, including ICU admission, autoimmune disease, pulmonary infection, and previous corticosteroid use within 1 month, need to be closely monitored for CREC infection.
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Affiliation(s)
- Mei Han
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chang Liu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hui Xie
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jie Zheng
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Yan Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chuchu Li
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
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Yuan Q, Xia P, Xiong L, Xie L, Lv S, Sun F, Feng W. First report of coexistence of bla KPC-2-, bla NDM-1- and mcr-9-carrying plasmids in a clinical carbapenem-resistant Enterobacter hormaechei isolate. Front Microbiol 2023; 14:1153366. [PMID: 37032905 PMCID: PMC10076803 DOI: 10.3389/fmicb.2023.1153366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Colistin is regarded as one of the last-resort antibiotics against severe infections caused by carbapenem-resistant Enterobacteriaceae. Strains with cooccurrence of mcr-9 and carbapenemase genes are of particular concern. This study aimed to investigate the genetic characteristics of a bla KPC-2-carrying plasmid, bla NDM-1-carrying plasmid and mcr-9-carrying plasmid coexisting in a carbapenem-resistant Enterobacter hormaechei isolate. Methods E. hormaechei strain E1532 was subjected to whole-genome sequencing, and the complete nucleotide sequences of three resistance plasmids identified in the strain were compared with related plasmid sequences. The resistance phenotypes mediated by these plasmids were analyzed by plasmid transfer, carbapenemase activity and antimicrobial susceptibility testing. Results Whole-genome sequencing revealed that strain E1532 carries three different resistance plasmids, pE1532-KPC, pE1532-NDM and pE1532-MCR. pE1532-KPC harboring bla KPC-2 and pE1532-NDM harboring bla NDM-1 are highly identical to the IncR plasmid pHN84KPC and IncX3 plasmid pNDM-HN380, respectively. The mcr-9-carrying plasmid pE1532-MCR possesses a backbone highly similar to that of the IncHI2 plasmids R478 and p505108-MDR, though their accessory modules differ. These three coexisting plasmids carry a large number of resistance genes and contribute to high resistance to almost all antibiotics tested, except for amikacin, trimethoprim/sulfamethoxazole, tigecycline and polymyxin B. Most of the plasmid-mediated resistance genes are located in or flanked by various mobile genetic elements, facilitating horizontal transfer of antibiotic resistance genes. Discussion This is the first report of a single E. hormaechei isolate with coexistence of three resistance plasmids carrying mcr-9 and the two most common carbapenemase genes, bla KPC-2 and bla NDM-1. The prevalence and genetic features of these coexisting plasmids should be monitored to facilitate the establishment of effective strategies to control their further spread.
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Modified Drug-Susceptibility Testing and Screening Culture Agar for Colistin-Susceptible Enterobacteriaceae Isolates Harboring a Mobilized Colistin Resistance Gene mcr-9. J Clin Microbiol 2022; 60:e0139922. [PMID: 36445156 PMCID: PMC9769915 DOI: 10.1128/jcm.01399-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Three isolates of the Enterobacter cloacae complex harboring mcr-9, a member of the colistin resistance mcr gene family encoded on plasmids, were susceptible to colistin, with MICs of 0.125 to 0.5 μg/mL in standard broth microdilution (BMD) tests using cation-adjusted Mueller-Hinton broth (CA-MHB) in accordance with European Committee on Antimicrobial Susceptibility Testing guidelines. In contrast, their MICs for colistin were significantly higher (4 to 128 μg/mL) when BMD tests were performed using brain-heart infusion (BHI) medium, Luria-Bertani (LB) broth, tryptic soy broth (TSB), or CA-MHB supplemented with casein, tryptonen or peptone. Colistin significantly induced mcr-9 expression in a dose-dependent manner when these mcr-9-positive isolates were cultured in BHI or CA-MHB supplemented with peptone/casein. Pretreatment of mcr-9-positive isolates and Escherichia coli DH5α harboring mcr-9 with colistin significantly increased their survival rates against LL-37, a human antimicrobial peptide. Electrospray ionization time-of-flight mass spectrometry analysis showed that a lipid A moiety of lipopolysaccharide was partially modified by phosphoethanolamine in E. coli DH5α harboring mcr-9 when treated with colistin. Of 93 clinical isolates of Enterobacteriaceae, only the mcr-9-positive isolates showed MICs to colistin that were at least 32 times higher in BHI than in CA-MHB. These mcr-9-positive isolates grew on a modified BHI agar, MCR9-JU, containing 3 μg/mL colistin. These results suggest that the BMD method using BHI is useful when performed together with the BMD method using CA-MHB to detect mcr-9-positive isolates and that MCR9-JU agar is useful in screening for Enterobacteriaceae isolates harboring mcr-9 and other colistin-resistant isolates.
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Ryu EJ, Choi JG, Yoon JW, Lee EK, Kim JH, Park IH, Lee W, Lee SW, Kim YS. Identification of three Enterobacter asburiae isolates co-resistant to carbapenem and colistin in a hospital in Gangwon Province, South Korea. J Glob Antimicrob Resist 2022; 31:321-322. [PMID: 36347495 DOI: 10.1016/j.jgar.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/12/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Eun Jeong Ryu
- Infection Epidemiology Division, Gangwon Institute of Health and Environment, Gangwon-do, Republic of Korea.
| | - Jong Gil Choi
- Infection Epidemiology Division, Gangwon Institute of Health and Environment, Gangwon-do, Republic of Korea
| | - Jang Won Yoon
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Gangwon-do, Republic of Korea
| | - Eun-Kyoung Lee
- Infection Epidemiology Division, Gangwon Institute of Health and Environment, Gangwon-do, Republic of Korea
| | - Ji Hwan Kim
- Infection Epidemiology Division, Gangwon Institute of Health and Environment, Gangwon-do, Republic of Korea
| | - In Hee Park
- Infection Epidemiology Division, Gangwon Institute of Health and Environment, Gangwon-do, Republic of Korea
| | - Woan Lee
- Infection Epidemiology Division, Gangwon Institute of Health and Environment, Gangwon-do, Republic of Korea
| | - Soon-Won Lee
- Infection Epidemiology Division, Gangwon Institute of Health and Environment, Gangwon-do, Republic of Korea
| | - Young-Soo Kim
- Infection Epidemiology Division, Gangwon Institute of Health and Environment, Gangwon-do, Republic of Korea
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Boueroy P, Wongsurawat T, Jenjaroenpun P, Chopjitt P, Hatrongjit R, Jittapalapong S, Kerdsin A. Plasmidome in mcr-1 harboring carbapenem-resistant enterobacterales isolates from human in Thailand. Sci Rep 2022; 12:19051. [PMID: 36351969 PMCID: PMC9646850 DOI: 10.1038/s41598-022-21836-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022] Open
Abstract
The emergence of the mobile colistin-resistance genes mcr-1 has attracted significant attention worldwide. This study aimed to investigate the genetic features of mcr-1-carrying plasmid among carbapenem-resistant Enterobacterales (CRE) isolates and the potential genetic basis governing transmission. Seventeen mcr-harboring isolates were analyzed based on whole genome sequencing using short-read and long-read platforms. All the mcr-1-carrying isolates could be conjugatively transferred into a recipient Escherichia coli UB1637. Among these 17 isolates, mcr-1 was located on diverse plasmid Inc types, consisting of IncX4 (11/17; 64.7%), IncI2 (4/17; 23.53%), and IncHI/IncN (2/17; 11.76%). Each of these exhibited remarkable similarity in the backbone set that is responsible for plasmid replication, maintenance, and transfer, with differences being in the upstream and downstream regions containing mcr-1. The IncHI/IncN type also carried other resistance genes (blaTEM-1B or blaTEM-135). The mcr-1-harboring IncX4 plasmids were carried in E. coli ST410 (7/11; 63.6%) and ST10 (1/11; 9.1%) and Klebsiella pneumoniae ST15 (1/11; 9.1%), ST336 (1/11; 9.1%), and ST340 (1/11; 9.1%). The IncI2-type plasmid was harbored in E. coli ST3052 (1/4; 25%) and ST1287 (1/4; 25%) and in K. pneumoniae ST336 (2/4; 50%), whereas IncHI/IncN were carried in E. coli ST6721 (1/2; 50%) and new ST (1/2; 50%). The diverse promiscuous plasmids may facilitate the spread of mcr-1 among commensal E. coli or K. pneumoniae strains in patients. These results can provide information for a surveillance system and infection control for dynamic tracing.
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Affiliation(s)
- Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand.
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Rujirat Hatrongjit
- Department of General Sciences, Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Sathaporn Jittapalapong
- Department of Parasitology, Faculty of Veterinary Medicine, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
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Hu J, Li J, Liu C, Zhang Y, Xie H, Li C, Shen H, Cao X. Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysis. BMC Microbiol 2022; 22:255. [PMID: 36266616 DOI: 10.1186/s12866-022-02667-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To analyze the characteristics of global β-lactamase-producing Enterobacter cloacae including the distribution of β-lactamase, sequence types (STs) as well as plasmid replicons. METHODS All the genomes of the E. cloacae were downloaded from GenBank. The distribution of β-lactamase encoding genes were investigated by genome annotation after the genome quality was checked. The STs of these strains were analyzed by multi-locus sequence typing (MLST). The distribution of plasmid replicons was further explored by submitting these genomes to the genome epidemiology center. The isolation information of these strains was extracted by Per program from GenBank. RESULTS A total of 272 out of 276 strains were found to carry β-lactamase encoding genes. Among them, 23 varieties of β-lactamase were identified, blaCMH (n = 130, 47.8%) and blaACT (n = 126, 46.3%) were the most predominant ones, 9 genotypes of carbapenem-hydrolyzing β-lactamase (CHβLs) were identified with blaVIM (n = 29, 10.7%) and blaKPC (n = 24, 8.9%) being the most dominant ones. In addition, 115 distinct STs for the 272 ß-lactamase-carrying E. cloacae and 48 different STs for 106 CHβLs-producing E. cloacae were detected. ST873 (n = 27, 9.9%) was the most common ST. Furthermore, 25 different plasmid replicons were identified, IncHI2 (n = 65, 23.9%), IncHI2A (n = 64, 23.5%) and IncFII (n = 62, 22.8%) were the most common ones. Notably, the distribution of plasmid replicons IncHI2 and IncHI2A among CHβLs-producing strains were significantly higher than theat among non-CHβLs-producing strains (p < 0.05). CONCLUSION Almost all the E. cloacae contained β-lactamase encoding gene. Among the global E. cloacae, blaCMH and blaACT were main blaAmpC genes. BlaTEM and blaCTX-M were the predominant ESBLs. BlaKPC, blaVIM and blaNDM were the major CHβLs. Additionally, diversely distinct STs and different replicons were identified.
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Affiliation(s)
- Jincao Hu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Jia Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Chang Liu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Yan Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Hui Xie
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Chuchu Li
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China.
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China.
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21
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Miyazato Y, Iwamoto N, Usui M, Sato T, Miyoshi-Akiyama T, Nagashima M, Mezaki K, Hayakawa K, Ohmagari N. Chromosomal coharboring of bla IMP-60 and mcr-9 in Enterobacter asburiae isolated from a Japanese woman with empyema: a case report. BMC Infect Dis 2022; 22:762. [PMID: 36180829 PMCID: PMC9523918 DOI: 10.1186/s12879-022-07730-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/14/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Polymyxin E (colistin) is a last-resort antibiotic to treat infections caused by carbapenemase-producing Enterobacteriaceae (CPE). However, reports of CPEs resistant to colistin have been increasing, and the mcr genes are emerging as resistance mechanisms. Among them, plasmid-mediate mcr-9 is known to be associated with colistin resistance, whereas reports on chromosomal mcr-9 and its association with colistin resistance in humans are few. CASE PRESENTATION We identified Enterobacter asburiae harboring mcr-9 and blaIMP-60 in the pleural fluid of a patient with empyema. The long-read sequencing technique revealed that these genes were located on its chromosome. Despite the lack of exposure to colistin, the organism showed microcolonies in the inhibition circle in the E-test and disk diffusion test. Antibiotic susceptibility testing by broth microdilution confirmed its resistance to colistin. CONCLUSION Our case report showed that mcr-9 can be present not only on plasmids but also on the chromosome in E. asburiae, and that the presence of mcr-9 on its chromosome may influence its susceptibility to colistin.
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Affiliation(s)
- Yusuke Miyazato
- grid.45203.300000 0004 0489 0290Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Noriko Iwamoto
- grid.45203.300000 0004 0489 0290Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masaru Usui
- grid.412658.c0000 0001 0674 6856Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
| | - Toyotaka Sato
- grid.39158.360000 0001 2173 7691Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan ,grid.39158.360000 0001 2173 7691Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
| | - Tohru Miyoshi-Akiyama
- grid.45203.300000 0004 0489 0290Pathogenic Microbe Laboratory, National Center for Global Health and Medicine, Tokyo, Japan
| | - Maki Nagashima
- grid.45203.300000 0004 0489 0290Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuhisa Mezaki
- grid.45203.300000 0004 0489 0290Department of Clinical Laboratory, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kayoko Hayakawa
- grid.45203.300000 0004 0489 0290Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Norio Ohmagari
- grid.45203.300000 0004 0489 0290Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
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Štefánek M, Wenner S, Borges V, Pinto M, Gomes JP, Rodrigues J, Faria I, Pessanha MA, Martins F, Sabino R, Veríssimo C, Nogueira ID, Carvalho PA, Bujdáková H, Jordao L. Antimicrobial Resistance and Biofilms Underlying Catheter-Related Bloodstream Coinfection by Enterobacter cloacae Complex and Candida parapsilosis. Antibiotics (Basel) 2022; 11:antibiotics11091245. [PMID: 36140024 PMCID: PMC9495738 DOI: 10.3390/antibiotics11091245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Biofilm-associated infections are a public health concern especially in the context of healthcare-associated infections such as catheter-related bloodstream infections (CRBSIs). We evaluated the biofilm formation and antimicrobials resistance (AMR) of Enterobacter cloacae complex and Candida parapsilosis co-isolated from a CRBSI patient. Antimicrobial susceptibility of central venous catheters (CVCs) and hemoculture (HC) isolates was evaluated, including whole genome sequencing (WGS) resistome analysis and evaluation of gene expression to obtain insight into their AMR determinants. Crystal violet assay was used to assess dual biofilm biomass and microscopy was used to elucidate a microorganism’s distribution within biofilms assembled on different materials. Bacteria were multidrug-resistant including resistance to colistin and beta-lactams, likely linked to the mcr-9-like phosphoethanolamine transferase and to an ACT family cephalosporin-hydrolyzing class C beta-lactamase, respectively. The R398I and Y132F mutations in the ERG11 gene and its differential expression might account for C. parapsilosis resistance to fluconazole. The phenotype of dual biofilms assembled on glass, polystyrene and polyurethane depends on the material and how biofilms were initiated by one or both pathogens. Biofilms assembled on polyurethane were denser and richer in the extracellular polymeric matrix, and microorganisms were differently distributed on the inner/outer surface of the CVC.
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Affiliation(s)
- Matúš Štefánek
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
| | | | - Vítor Borges
- Genomics and Bioinformatic Unit, Department of Infectious Diseases (DDI), National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatic Unit, Department of Infectious Diseases (DDI), National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatic Unit, Department of Infectious Diseases (DDI), National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - João Rodrigues
- Unidade Laboratorial Integrada de Microbiologia, Department of Infectious Diseases (DDI), National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisboa, Portugal
| | - Isabel Faria
- Laboratório de Microbiologia e Biologia Molecular do Serviço de Patologia Clínica, Centro Hospitalar de lisboa Ocidental (CHLO), 1349-019 Lisboa, Portugal
| | - Maria Ana Pessanha
- Laboratório de Microbiologia e Biologia Molecular do Serviço de Patologia Clínica, Centro Hospitalar de lisboa Ocidental (CHLO), 1349-019 Lisboa, Portugal
| | - Filomena Martins
- Direção do Programa de Prevenção e Controlo de Infeção e Resistência aos Antimicrobianos, Centro Hospitalar de lisboa Ocidental (CHLO), 1349-019 Lisboa, Portugal
| | - Raquel Sabino
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisboa, Portugal
- Institute of Environmental Health, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
| | - Cristina Veríssimo
- Reference Unit for Parasitic and Fungal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge (INSA), 1649-016 Lisboa, Portugal
| | | | | | - Helena Bujdáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia
| | - Luisa Jordao
- Unidade de Investigação & Desenvolvimento, Departamento de Saúde Ambiental, Instituto Nacional de Saude Dr. Ricardo Jorge (INSA),1649-016 Lisboa, Portugal
- Correspondence:
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Laidoudi Y, Ngaiganam EP, Marié JL, Pagnier I, Rolain JM, Mouhamadou Diene S, Davoust B. Colistin Resistance Mechanism in Enterobacter hormaechei subsp. steigerwaltii Isolated from Wild Boar (Sus scrofa) in France. Pathogens 2022; 11:pathogens11091022. [PMID: 36145454 PMCID: PMC9504195 DOI: 10.3390/pathogens11091022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Wild animals may act as efficient antimicrobial-resistance reservoirs and epidemiological links between humans, livestock, and natural environments. By using phenotypic and genotypic characterization, the present study highlighted the occurrence of an antimicrobial-resistant (i.e., amoxicillin, amoxicillin–clavulanic acid, cephalothin, and colistin) Enterobacter hormaechei subsp. steigerwaltii strain in wild boar (Sus scrofa) from France. The molecular analysis conducted showed non-synonymous mutations in the pmrA/pmrB and phoQ/phoP operons and the phoP/Q regulator mgrB gene, leading to colistin resistance. The present data highlight the need for continuous monitoring of multidrug-resistant bacteria in wild animals to limit the spread of these threatening pathogens.
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Affiliation(s)
- Younes Laidoudi
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Edgarthe Priscilla Ngaiganam
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Jean-Lou Marié
- Animal Epidemiology Expert Group, French Military Health Service, 37076 Tours, France
| | - Isabelle Pagnier
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Seydina Mouhamadou Diene
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Bernard Davoust
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
- Animal Epidemiology Expert Group, French Military Health Service, 37076 Tours, France
- Correspondence:
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Mmatli M, Mbelle NM, Osei Sekyere J. Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update. Front Cell Infect Microbiol 2022; 12:941358. [PMID: 36093193 PMCID: PMC9462459 DOI: 10.3389/fcimb.2022.941358] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/01/2022] [Indexed: 12/28/2022] Open
Abstract
Background Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane. Results and discussion Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI2 conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins. Conclusion The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, United States
- Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
- *Correspondence: John Osei Sekyere, ;
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Li S, Jiang X, Li C, Ju Y, Yue L, Chen F, Hu L, Wang J, Hu X, Tuohetaerbaike B, Wen H, Zhang W, Zhou D, Yin Z, Chen F. A blaSIM-1 and mcr-9.2 harboring Klebsiella michiganensis strain reported and genomic characteristics of Klebsiella michiganensis. Front Cell Infect Microbiol 2022; 12:973901. [PMID: 36093205 PMCID: PMC9448873 DOI: 10.3389/fcimb.2022.973901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
As a newly emerging Klebsiella pathogen, more and more Klebsiella michiganensis drug resistant strains have been reported in recent years, which posed serious threats to public health. Here we first reported a multidrug-resistant K. michiganensis strain 12084 with two blaSIM-1 and one mcr-9.2 genes isolated from the sputum specimen of a patient in the Second Affiliated Hospital of Zhejiang University School of Medicine and analyzed its genetic basis and drug-resistance phenotypes. Genetic analysis showed that this strain harbored three different incompatibility groups (IncHI2, IncHI5, and IncFIIpKPHS2:IncFIB-4.1) of plasmids (p12084-HI2, p12084-HI5, and p12084-FII). A total of 26 drug-resistance genes belonging to 12 classes of antibiotics were identified, most of which (24) were located on two plasmids (p12084-HI2 and p12084-HI5). Interestingly, two blaSIM-1 genes were identified to locate on p12084-HI2 and p12084-HI5, respectively, both of which were embedded in In630, indicating their genetic homogeny. It was noting that one blaSIM-1 gene was situated in a novel unit transposon (referred to as Tn6733) on the p12084-HI5 plasmid. We also discovered an mcr-9.2 gene on the p12084-HI2 plasmid. To the best of our knowledge, this is the first report of a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain. We then investigated the population structure/classification, and antibiotic resistance for all 275 availably global K. michiganensis genomes. Population structure revealed that K. michiganensis could be divided into two main clades (Clade 1 and Clade 2); the most popular ST29 was located in Clade 1, while other common STs (such as ST50, ST27, and ST43) were located in Clade 2. Drug-resistance analysis showed 25.5% of the K. michiganensis strains (70/275) harboring at least one carbapenemase gene, indicating severe drug resistance of K. michiganensis beyond our imagination; this is a dangerous trend and should be closely monitored, especially for ST27 K. michiganensis with the most drug-resistant genes among all the STs. Overall, we reported a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain, and further revealed the population structure/classification, and drug-resistance of K. michiganensis, which provided an important framework, reference, and improved understanding of K. michiganensis.
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Affiliation(s)
- Shuangshuang Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyuan Jiang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Cuidan Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Yingjiao Ju
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liya Yue
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Xin Hu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Bahetibieke Tuohetaerbaike
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Hao Wen
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- *Correspondence: Zhe Yin, ; Fei Chen,
| | - Fei Chen
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Respiratory Medicine, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Zhe Yin, ; Fei Chen,
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Hu K, Zhang J, Zou J, Zeng L, Li J, Wang J, Long W, Zhang X. Molecular characterization of NDM-1-producing carbapenem-resistant E. cloacae complex from a tertiary hospital in Chongqing, China. Front Cell Infect Microbiol 2022; 12:935165. [PMID: 36004335 PMCID: PMC9393607 DOI: 10.3389/fcimb.2022.935165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe aim of this study was to clarify the molecular characterization of NDM-1-producing carbapenem-resistant Enterobacter cloacae complex (CREL) at a teaching hospital in Chongqing, China.MethodsAntimicrobial susceptibility and resistance genes were analyzed. Epidemiological relationship was analyzed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Conjugation experiments were performed to determine the transferability of plasmids. Whole-genome sequencing (WGS) of strains was implemented, and the genetic environment of the blaNDM-1- and mcr-9-carrying plasmids was analyzed.ResultsA total of 10 blaNDM-1-positive CREL isolates were identified. All isolates harbored multiple resistance genes. ECL68 and ECL78 co-produce blaNDM-1 and mcr-9. Among the four different sequence types (STs) detected, ST1466 was assigned as a novel ST. Six isolates exhibited highly similar PFGE patterns. Conjugation assay proved that all plasmids containing blaNDM-1 or mcr-9 could be transferred to the recipient Escherichia coli. WGS indicated that blaNDM-1 genes were carried by diverse plasmids, including IncHI2/IncN, IncX3, and one unclassified plasmid type. The backbone structure of these plasmids is involved in replication initiation (repAB), partitioning (parABM), and conjugation/type IV secretion (tra/virB). Analysis of the genetic environment showed that blaNDM-1 in three plasmids exhibited a highly similar structure to protype Tn125. Co-existence of blaNDM-1 and the colistin resistance gene mcr-9 was detected in the two isolates, ECL68 and ECL78. In ECL68, blaNDM-1 and mcr-9 were present on the same plasmid while located in two separate plasmids in ECL78. The genetic environment of mcr-9 was organized as IS26-wbuC-mcr-9-IS903-pcoS-pcoE-rcnA-rcnR, and the two-component system encoding genes qseC and qseB was not found in two plasmids, which could explain mcr-9-harboring strains’ colistin susceptibility.ConclusionsWe first report a nosocomial outbreak of NDM-1-producing E. cloacae complex ST177 in China. Conjugative plasmids contributed to the horizontal transfer of antibiotic resistance genes. The prevalence and even coexistence of blaNDM-1 and mcr-9 may further threaten public health. Our results highlight further surveillance for blaNDM-1, and mcr-9 is essential to prevent its dissemination.
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Affiliation(s)
- Kewang Hu
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Microbiology, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jisheng Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jingbo Zou
- Department of Microbiology, Yongchuan District Center for Disease Control and Prevention of Chongqing, Chongqing, China
| | - Lingyi Zeng
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Molecular biology, Jiaxing Maternal and Child Health Hospital, Jiaxing, China
| | - Jie Li
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jianmin Wang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Wenzhang Long
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoli Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Xiaoli Zhang,
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Zhou H, Wang S, Wu Y, Dong N, Ju X, Cai C, Li R, Li Y, Liu C, Lu J, Chan EWC, Chen S, Zhang R, Shen Z. Carriage of the mcr-9 and mcr-10 genes in clinical strains of the Enterobacter cloacae complex in China: a prevalence and molecular epidemiology study. Int J Antimicrob Agents 2022; 60:106645. [PMID: 35907595 DOI: 10.1016/j.ijantimicag.2022.106645] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/02/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Enterobacter cloacae complex (ECC) is among the most common carbapenem-resistant Enterobacteriaceae in China. The emergence of the mcr renders CRE strains resistant to the last-line antibiotic colistin. We investigated the prevalence of mcr-9 and mcr-10 in carbapenem-resistant ECC (CRECC) and carbapenem-susceptible ECC (CSECC) in China. METHODS We collected CRECC and CSECC strains from different regions of China. The antimicrobial susceptibility tests, conjugation experiments, whole genome sequencing, bioinformatic analysis, and quantitative RT-PCR were performed to understand the mechanisms of resistance and transmission of mcr in ECC. RESULTS A total of 534 ECC were collected, among which 57 (10.7%) and 23 (4.3%) were positive for mcr-9 and mcr-10, respectively. The prevalence of mcr-9 in CRECC was significantly higher than that in CSECC (31.8% vs 3.7%, p < 0.001), while the prevalence of mcr-10 in CRECC was significantly lower (0.8% vs 5.5%, p < 0.05). Most mcr-9-positive strains (n=45, 78.9%) exhibited multidrug-resistant phenotype, and four (17.4%) of the mcr-10-positive strains exhibited multi-drug resistance. Coexistence of mcr and carbapenemase genes was commonly observed, including 41 (71.9%) mcr-9-positive strains and one (4.3%) mcr-10-positive strain, and the possibility of co-transfer was confirmed by conjugation experiments. The mcr-positive ECC were highly diverse, while most mcr genes were plasmid-encoded indicating the important role of plasmids on the transmission of mcr in ECC. Furthermore, the expression of mcr-9 was increased after induction by colistin. CONCLUSIONS The widespread of mcr genes, as well as its co-transfer with carbapenemase genes among ECC strains, posed an urgent threat to public health.
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Affiliation(s)
- Hongwei Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Siheng Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Yuchen Wu
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Ning Dong
- Department of Medical Microbiology, School of Biology and Basic Medical Science, Medical College of Soochow University, Suzhou, China
| | - Xiaoyang Ju
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Chang Cai
- China Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Ruichao Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, P. R. China
| | - Yan Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, P. R. China
| | - Congcong Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Jiayue Lu
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong Special Administrative Region, China.
| | - Rong Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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Xu T, Xue CX, Huang J, Wu J, Chen R, Zhou K. Emergence of an epidemic hypervirulent clone of Enterobacter hormaechei coproducing mcr-9 and carbapenemases. THE LANCET MICROBE 2022; 3:e474-e475. [DOI: 10.1016/s2666-5247(22)00122-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 10/18/2022] Open
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Elbaradei A, Sayedahmed MS, El-Sawaf G, Shawky SM. Screening of mcr-1 among Gram-Negative Bacteria from Different Clinical Samples from ICU Patients in Alexandria, Egypt: One-Year Study. Pol J Microbiol 2022; 71:83-90. [PMID: 35635164 PMCID: PMC9152917 DOI: 10.33073/pjm-2022-011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/12/2022] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial resistance represents a global dilemma. Our present study aimed to investigate the presence of mcr-1 among different Gram-negative bacteria including Enterobacteriaceae (except intrinsically resistant to colistin) and Pseudomonas aeruginosa. Gram-negative bacterial isolates were collected from different ICUs in several Alexandria hospitals from June 2019 to June 2020. The identification of these Gram-negative isolates was made using the VITEK-2® system (BioMérieux, France). SYBR Green-based PCR was used to screen for the presence of mcr-1 using a positive control that we amplified and sequenced earlier in our pilot study. All isolates were screened for the presence of mcr-1 regardless of their colistin susceptibility. Isolates that harbored mcr-1 were tested for colistin susceptibility and for the presence of some beta-lactamase genes. Klebsiella pneumoniae isolates harboring mcr-1 were capsule typed using the wzi sequence analysis. Four hundred eighty isolates were included in this study. Only six isolates harbored mcr-1.1. Of these, four were resistant to colistin, while two (K. pneumoniae and P. aeruginosa) were susceptible to colistin. Five of the six isolates were resistant to carbapenems. They harbored blaOXA-48, and three of them co-harbored blaNDM-1. K-58 was the most often found among our K. pneumoniae harboring mcr-1.1. To our knowledge, this is the first time to report colistin susceptible P. aeruginosa and K. pneumoniae harboring the mcr-1.1 gene in Egypt. Further studies are needed to investigate the presence of the mcr genes among colistin susceptible isolates to shed more light on its significance as a potential threat. ![]()
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Affiliation(s)
- Amira Elbaradei
- Department of Microbiology and Immunology, Faculty of Pharmacy , Pharos University in Alexandria , Alexandria , Egypt
- Alexandria University Hospital , Alexandria University , Alexandria , Egypt
| | - Mahrous S. Sayedahmed
- Department of Microbiology, Medical Research Institute , Alexandria University , Alexandria , Egypt
| | - Gamal El-Sawaf
- Department of Microbiology, Medical Research Institute , Alexandria University , Alexandria , Egypt
| | - Sherine M. Shawky
- Department of Microbiology, Medical Research Institute , Alexandria University , Alexandria , Egypt
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Fan J, Cai H, Fang Y, He J, Zhang L, Xu Q, Yang Y, Leptihn S, Yu Y, Zhao D, Hua X. Molecular Genetic Characteristics of Plasmid-Borne mcr-9 in Salmonella enterica Serotype Typhimurium and Thompson in Zhejiang, China. Front Microbiol 2022; 13:852434. [PMID: 35369459 PMCID: PMC8969412 DOI: 10.3389/fmicb.2022.852434] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/28/2022] [Indexed: 11/25/2022] Open
Abstract
Salmonella enterica is a zoonotic food-borne pathogen threatening public health around the world. As is the case with many other pathogens, the spread of mobilized colistin resistance (mcr) alleles is of grave concern. In this study, totally 689 clinical Salmonella isolates were collected from a local hospital in Hangzhou, Zhejiang Province, China between 2009 and 2018. Resistance genes were screen by PCR. Two mcr-9-positive Salmonella strains S15 and S639 were identified which belong to serotype Typhimurium and Thompson, respectively. We observed that both mcr-9 genes were located on conjugative IncHI2 plasmids which encoded numerous resistance genes, likely facilitating the dissemination of mcr-9 by co-resistance mechanisms. The mcr-9 cassettes encoded on the two plasmids were not identical: downstream of the mcr-9 genes, we found IS1 on one plasmid (pS15), while the other had a WbuC-IS26 (pS639). Despite the presence of mcr-9 cassettes, the strains were not rendered colistin resistant. Yet, it is of epidemiological importance to implement surveillance to be able to observe and possibly control the spread of mcr-9 due to its potential to mediate resistance to the last-resort antibiotic colistin.
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Affiliation(s)
- Jianzhong Fan
- Department of Laboratory Medicine, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Youhong Fang
- Department of Gastroenterology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Linghong Zhang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qingye Xu
- Department of Laboratory Medicine, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunxing Yang
- Department of Laboratory Medicine, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sebastian Leptihn
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Zhejiang University, Haining, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Dongdong Zhao,
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Xiaoting Hua,
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Wareth G, Linde J, Hammer P, Pletz MW, Neubauer H, Sprague LD. WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in Klebsiella pneumoniae Isolates from Powdered Milk Produced in Germany. Microorganisms 2022; 10:microorganisms10030564. [PMID: 35336140 PMCID: PMC8956024 DOI: 10.3390/microorganisms10030564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
The emergence of Klebsiella pneumoniae (K. pneumoniae) in German healthcare is worrying. It is not well-investigated in the veterinary world and food chains. In the current study, antibiotic susceptibility profiles of 24 K. pneumoniae strains isolated from powdered milk samples produced in Germany were investigated by a microdilution test. Next-generation sequencing (NGS) was applied to identify genomic determinants for antimicrobial resistance (AMR), virulence-associated genes and plasmids replicons. All isolates were susceptible to the majority (14/18) of tested antibiotics. Resistance to colistin, fosfomycin, chloramphenicol and piperacillin was found. The ambler class A ß-lactamase, blaSHV variants were identified in all isolates, of which blaSHV-187 was most prevalent and found in 50% of isolates. Single-nucleotide-variants of oqxA and oqxB conferring resistance to phenicol/quinolone were found in all isolates, and the oqxB17 was the most prevalent found in 46% of isolates. 67% of isolates harbored fosA genes; however, only one was fosfomycin-resistant. Two isolates harbored genes conferring resistance to colistin, despite being susceptible. The majority of identified virulome genes were iron uptake siderophores. Two enterobactins (entB, fepC), six adherence-related genes belonging to E. coli common pilus (ECP) and one secretion system (ompA gene) were found in all isolates. In contrast, yersiniabactin was found in two isolates. One ST23 strain was susceptible to all tested antibiotics, and harbored determinants discriminatory for hypervirulent strains, e.g., aerobactin, salmochelin, yersiniabactin, enterobactin and regulator of mucoid phenotype A genes that are highly associated with hypervirulent K. pneumoniae. The IncF plasmid family was found in all strains, while almost half of the isolates harbored Col440I-type plasmids and nine isolates harbored various Inc-type plasmids. The presence of K. pneumoniae carrying different resistomes and major virulent specific virulomes in powdered milk samples is alarming. This could threaten public health, particularly of neonates and infants consuming dried milk.
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Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena University, 07743 Jena, Germany;
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
- Correspondence:
| | - Jörg Linde
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
| | - Philipp Hammer
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany;
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena University, 07743 Jena, Germany;
- Research Campus Infectognostics, Philosophenweg 7, 07743 Jena, Germany
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
| | - Lisa D. Sprague
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
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Polyclonal emergence of MDR Enterobacter cloacae complex isolates producing multiple extended spectrum beta-lactamases at Maputo Central Hospital, Mozambique. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2022. [DOI: 10.1007/s12210-021-01039-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AbstractEnterobacter spp. are important nosocomial pathogens responsible of a wide variety of infections, mainly due to Extended Spectrum β-Lactamase (ESBL) producing isolates, constituting a global public health issue in terms of clinical treatment and infection control, especially in low-income countries, where last-line treatment is often unavailable and there is weak nosocomial surveillance. In this study, we conducted a phenotypic and molecular characterization of 8 clinical Enterobacter spp. strains, isolated from patient’s blood in three hospitals in Mozambique. Isolates were identified by MALDI-TOF and antimicrobial Susceptibility Testing was performed by VITEK 2 system. Half of isolates were analyzed by PCR for β-lactamases genes, other isolates by Whole Genome Sequencing. We identified all isolates as Enterobacter cloacae complex (ECC), those from Maputo Central Hospital were polyclonal, multidrug resistant (5/8), and ESBL producers (50%), carrying blaCTX-M-15 and different assortment of blaSHV-12, blaTEM-1B and blaOXA-1, and AmpCs blaCMH-3, blaACT-7 and blaACT-9 genes. Resistance determinants linked to fluoroquinolone (aac(6')Ib-cr and qnrB1) and others antimicrobials were also found. Notably, one isolate showed phenotypically resistance to colistin, while another colistin susceptible isolate carried a silent mcr-9 gene. ECC nosocomial surveillance is urgently needed to contain and prevent the dissemination of ESBLs producing clones, and mcr-9 spread to other Enterobacteriaceae.
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Kawamoto Y, Kaku N, Akamatsu N, Sakamoto K, Kosai K, Morinaga Y, Ohmagari N, Izumikawa K, Yamamoto Y, Mikamo H, Kaku M, Oishi K, Yanagihara K. The surveillance of colistin resistance and mobilized colistin resistance genes in multidrug-resistant Enterobacteriaceae isolated in Japan. Int J Antimicrob Agents 2021; 59:106480. [PMID: 34801675 DOI: 10.1016/j.ijantimicag.2021.106480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/03/2021] [Accepted: 11/12/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND The plasmid-mediated bacterial colistin-resistant gene, mcr, is of global concern in clinical healthcare. However, there are few reports of surveillance for mcr in Japan. The aim of this study was to assess the prevalence of colistin resistance by identifying nine mcr genes in extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae and carbapenem-resistant Enterobacteriaceae (CRE) isolates in Japan. METHODS A total of 273 ESBL and CRE clinical isolates were collected from patients in five tertiary hospitals from August 2016 to March 2017. Minimum inhibitory concentration (MIC) of colistin was measured using the microdilution method. Polymerase chain reaction (PCR) was performed to detect mcr-1 to mcr-9 genes in all strains. Whole-genome sequencing (WGS) analysis was conducted for any mcr-genes identified that had not been previously reported in patients from Japan. RESULTS The rate of colistin resistance was 7.7% in all strains, with a higher rate in the CRE strains than in the ESBL-producing strains (20.4% versus 1.1%). The mcr-5 and mcr-9 gene were detected in one ESBL-producing Escherichia coli strain (1/273, 0.37%) and three CRE strains (3/273, 1.1%), respectively. As the ESBL-producing E. coli strain was the first clinical strain with mcr-5 in Japan, WGS analysis was performed for the strain. The sequence type of the mcr-5-positive strain was ST1642 and it carried two distinct plasmids, ESBL gene-carrying pN-ES-6-1, and mcr-5.1-carrying pN-ES-6-2. CONCLUSIONS The results of this study showed that the frequency of colistin resistance and mcr-positive strains is not high in Japan. As the MIC for colistin was low in the mcr-5.1 and mcr-9 gene-positive strain, continuous monitoring of mcr genes is necessary.
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Affiliation(s)
- Yasuhide Kawamoto
- Department of Laboratory Medicine, Nagasaki University Hospital, Japan
| | - Norihito Kaku
- Department of Laboratory Medicine, Nagasaki University Hospital, Japan; Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, USA.
| | - Norihiko Akamatsu
- Department of Laboratory Medicine, Nagasaki University Hospital, Japan
| | - Kei Sakamoto
- Department of Laboratory Medicine, Nagasaki University Hospital, Japan; Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Kosuke Kosai
- Department of Laboratory Medicine, Nagasaki University Hospital, Japan; Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Yoshitomo Morinaga
- Department of Laboratory Medicine, Nagasaki University Hospital, Japan; Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan; Department of Microbiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Koichi Izumikawa
- Department of Infectious Diseases, Nagasaki University Graduate School of Biomedical Sciences, Japan
| | - Yoshihiro Yamamoto
- Department of Clinical Infectious Diseases, Graduate School of Medicine and Pharmaceutical Sciences for Research, University of Toyama, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine, Japan
| | - Mitsuo Kaku
- Department of Infection Control and Laboratory Diagnostics, Tohoku University Graduate School of Medicine, Japan
| | - Kazunori Oishi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases Correspondence, Japan; Toyama Institute of Health, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Hospital, Japan; Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Japan
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Nakamura A, Nakamura T, Niki M, Kuchibiro T, Nishi I, Komatsu M. Genomic Characterization of ESBL- and Carbapenemase-Positive Enterobacteriaceae Co-harboring mcr-9 in Japan. Front Microbiol 2021; 12:665432. [PMID: 34504474 PMCID: PMC8421803 DOI: 10.3389/fmicb.2021.665432] [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: 02/08/2021] [Accepted: 07/16/2021] [Indexed: 12/30/2022] Open
Abstract
Worldwide spread of Enterobacteriaceae resistant to colistin, a polypeptide antibacterial drug for last-resort treatment of carbapenemase-producing Enterobacteriaceae (CPE) infections, is concerning. This study aimed to elucidate colistin MICs and molecular characteristics of mcr-1 to mcr-9 of ESBL-producing Escherichia coli (ESBL-Ec) and CPE in Japan and clarify the genomic structure of strains harboring mcr genes (especially mcr-9). This study included 168 ESBL-Ec and 126 CPE strains isolated at Japanese medical facilities. Colistin susceptibility testing and multiplex PCR targeting mcr-1 to mcr-9 were performed for all strains with S1-nuclease pulsed-field gel electrophoresis, Southern blot hybridization, and whole-genome sequencing (WGS) with hybrid assembly performed for mcr gene-carrying strains. Two CPE strains showed a MIC ≥ 4 μg/ml in colistin susceptibility testing, with no known resistance mechanism detected. However, PCR conducted on all target strains detected three mcr-9-carrying strains showing colistin susceptibility. The blaCTX–M–62-positive E. coli THUN648 strain simultaneously carried blaCTX–M–62 and mcr-9 on a 275-kbp plasmid. Besides, blaIMP–6 + blaCTX–M–2-positive Klebsiella pneumoniae THUN262 and blaGES–24-positive Enterobacter kobei THUN627 had mcr-9 encoded on the chromosome. Only THUN627 encoded qseB/C, which is suggested to be a regulatory gene for mcr-9, downstream of mcr-9. However, this strain showed no increased expression of these genes in mRNA quantitative analysis under colistin exposure. Colistin MICs of ESBL-Ec and CPE in Japan were all below 2 μg/ml, which is below the epidemiological cutoff (ECOFF) value (https://eucast.org/) or clinical breakpoint (CB) (CLSI M100-S30) reported for colistin, indicating neither “microbiological” nor “clinical” resistance. Several colistin-susceptible Enterobacteriaceae carrying silent mcr-9 encoded on plasmids and chromosomes have already spread worldwide along with other antimicrobial resistance genes. However, the mechanism of colistin resistance by mcr-9 remains unclear.
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Affiliation(s)
- Akihiro Nakamura
- Department of Clinical Laboratory Science, Faculty of Health Care, Tenri Health Care University, Tenri, Japan
| | - Tatsuya Nakamura
- Faculty of Health Sciences, Kyoto Tachibana University, Kyoto, Japan
| | - Makoto Niki
- Department of Infection Control and Prevention, Osaka City University Hospital, Osaka, Japan
| | - Tomokazu Kuchibiro
- Department of Clinical Laboratory, Naga Municipal Hospital, Wakayama, Japan
| | - Isao Nishi
- Laboratory for Clinical Investigation, Osaka University Hospital, Osaka, Japan
| | - Masaru Komatsu
- Department of Clinical Laboratory Science, Faculty of Health Care, Tenri Health Care University, Tenri, Japan
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Diaconu EL, Alba P, Feltrin F, Di Matteo P, Iurescia M, Chelli E, Donati V, Marani I, Giacomi A, Franco A, Carfora V. Emergence of IncHI2 Plasmids With Mobilized Colistin Resistance ( mcr)- 9 Gene in ESBL-Producing, Multidrug-Resistant Salmonella Typhimurium and Its Monophasic Variant ST34 From Food-Producing Animals in Italy. Front Microbiol 2021; 12:705230. [PMID: 34335538 PMCID: PMC8322855 DOI: 10.3389/fmicb.2021.705230] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/14/2021] [Indexed: 12/18/2022] Open
Abstract
A collection of 177 genomes of Salmonella Typhimurium and its monophasic variant isolated in 2014-2019 from Italian poultry/livestock (n = 165) and foodstuff (n = 12), previously screened for antimicrobial susceptibility and assigned to ST34 and single-locus variants, were studied in-depth to check the presence of the novel mcr-9 gene and to investigate their genetic relatedness by whole genome sequencing (WGS). The study of accessory resistance genes revealed the presence of mcr-9.1 in 11 ST34 isolates, displaying elevated colistin minimum inhibitory concentration values up to 2 mg/L and also a multidrug-resistant (MDR) profile toward up to seven antimicrobial classes. Five of them were also extended-spectrum beta-lactamases producers (bla SHV - 12 type), mediated by the corresponding antimicrobial resistance (AMR) accessory genes. All mcr-9-positive isolates harbored IncHI2-ST1 plasmids. From the results of the Mash analysis performed on all 177 genomes, the 11 mcr-9-positive isolates fell together in the same subcluster and were all closely related. This subcluster included also two mcr-9-negative isolates, and other eight mcr-9-negative ST34 isolates were present within the same parental branch. All the 21 isolates within this branch presented an IncHI2/2A plasmid and a similar MDR gene pattern. In three representative mcr-9-positive isolates, mcr-9 was demonstrated to be located on different IncHI2/IncHI2A large-size (∼277-297 kb) plasmids, using a combined Illumina-Oxford Nanopore WGS approach. These plasmids were also compared by BLAST analysis with publicly available IncHI2 plasmid sequences harboring mcr-9. In our plasmids, mcr-9 was located in a ∼30-kb region lacking different genetic elements of the typical core structure of mcr-9 cassettes. In this region were also identified different genes involved in heavy metal metabolism. Our results underline how genomics and WGS-based surveillance are increasingly indispensable to achieve better insights into the genetic environment and features of plasmid-mediated AMR, as in the case of such IncHI2 plasmids harboring other MDR genes beside mcr-9, that can be transferred horizontally also to other major Salmonella serovars spreading along the food chain.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Virginia Carfora
- National Reference Laboratory for Antimicrobial Resistance, General Diagnostics Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,”Rome, Italy
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Sarangi J, Matsuo N, Nonogaki R, Hayashi M, Kawamura K, Suzuki M, Jin W, Tamai K, Ogawa M, Wachino JI, Kimura K, Yagi T, Arakawa Y. Molecular epidemiology of Enterobacter cloacae complex isolates with reduced carbapenem susceptibility recovered by blood culture. Jpn J Infect Dis 2021; 75:41-48. [PMID: 34193664 DOI: 10.7883/yoken.jjid.2021.141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Enterobacter cloacae complex (ECC) is one of the most common causes of bacteremia and leads to poor clinical outcomes. The aim of this study was to clarify the antimicrobial susceptibility profiles and genetic backgrounds of non-carbapenemase-producing reduced-carbapenem-susceptible (RCS) ECC blood isolates in Japan using agar dilution antimicrobial susceptibility testing, whole-genome sequencing, and quantitative polymerase chain reaction for assays of ampC, ompC and ompF transcripts. Forty-two ECC blood isolates were categorized into RCS and carbapenem-susceptible groups based on imipenem minimum inhibitory concentration. RCS ECC blood isolates belonged to distinct species and sequence types and produced varying class C β-lactamases. The E. roggenkampii, E. asburiae, and E. bugandensis isolates belonged only to the RCS group. Some E. hormaecheii ssp. steigerwaltii isolates of the RCS group exhibited AmpC overexpression caused by amino acid substitutions in AmpD and AmpR along with ompF gene downregulation. These findings suggest that non-carbapenemase-producing RCS ECC blood isolates are genetically diverse.
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Affiliation(s)
- Jayathilake Sarangi
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Japan
| | - Nao Matsuo
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Japan
| | - Rina Nonogaki
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Japan
| | - Michiko Hayashi
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Japan
| | - Kumiko Kawamura
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Japan
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University, School of Medicine, Japan
| | - Wanchun Jin
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Japan
| | | | | | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Japan
| | - Kouji Kimura
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Japan.,Department of Medical Technology, Faculty of Medical Sciences, Shubun University, Japan
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Macesic N, Blakeway LV, Stewart JD, Hawkey J, Wyres KL, Judd LM, Wick RR, Jenney AW, Holt KE, Peleg AY. Silent spread of mobile colistin resistance gene mcr-9.1 on IncHI2 'superplasmids' in clinical carbapenem-resistant Enterobacterales. Clin Microbiol Infect 2021; 27:1856.e7-1856.e13. [PMID: 33915285 DOI: 10.1016/j.cmi.2021.04.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVES mcr-9.1 is a newly described mobile colistin resistance gene. We have noted its presence in multiple species of carbapenem-resistant Enterobacterales (CRE) from our institution. We aimed to determine the clinical features, genomic context and phenotypic impact of mcr-9.1 carriage in a series of patients between 2010 and 2019. METHODS We identified 32 patients with mcr-9.1-carrying CRE isolates (mCRE) and collected demographic, antimicrobial exposure and infection data. Whole-genome sequencing (including short and long reads) was performed on 32 isolates. We assessed sequence similarity of mcr-9.1-harbouring plasmids, then compared our findings with plasmids for which sequence data were publicly available. RESULTS There was no colistin exposure in patients prior to isolation of mCRE. mcr-9.1 was identified on IncHI2 plasmids across four different bacterial species and was co-located with blaIMP-4 in 23/30 plasmids studied. mCRE isolates did not demonstrate phenotypic colistin resistance, either at baseline or following sublethal colistin exposure, thus showing that mcr-9.1 alone is not sufficient for resistance. Publicly available sequence data indicated the presence of carbapenemase genes in 236/619 mcr-9.1-carrying genomes (38%). IncHI2 plasmids carrying mcr-9.1 and carbapenemase genes were detected in genomes from North America, Europe, North Africa, Asia and Oceania. CONCLUSIONS Spread of mcr-9.1 in CRE from our institution was driven by IncHI2 'superplasmids', so termed because of their large size and their prolific carriage of resistance determinants. These were also detected in global CRE genomes. Phenotypic colistin resistance was not detected in our isolates but remains to be determined from global mCRE.
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Affiliation(s)
- Nenad Macesic
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia; Department of Infectious Diseases, Alfred Health, Melbourne, Australia.
| | - Luke V Blakeway
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia; Department of Infectious Diseases, Alfred Health, Melbourne, Australia
| | - James D Stewart
- Department of Infectious Diseases, Cairns Hospital, Cairns, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Adam W Jenney
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia; Department of Infectious Diseases, Alfred Health, Melbourne, Australia; Microbiology Unit, Alfred Pathology Service, Alfred Health, Melbourne, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia; The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Anton Y Peleg
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia; Department of Infectious Diseases, Alfred Health, Melbourne, Australia; Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Australia
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Wang X, Ling Z, Sun N, Liu Y, Huang J, Wang L. Molecular genetic characteristics of mcr-9-harbouring Salmonella enterica serotype Typhimurium isolated from raw milk. Int J Antimicrob Agents 2021; 57:106332. [PMID: 33798705 DOI: 10.1016/j.ijantimicag.2021.106332] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 11/28/2022]
Abstract
Among the 10 reported mcr genes, mcr-9 was first identified in Salmonella enterica serotype Typhimurium, which is a leading cause of foodborne illness worldwide. However, information about the prevalence and genetic features of mcr-9 is still lacking, especially among food samples. This study reports the presence of mcr-9 in raw milk samples from China; the prevalence rate was low (0.83%, 1/120). mcr-9 was located on a transferable plasmid, and was stable in wild-type S. enterica. However, it had a biological fitness cost when transferred to an Escherichia coli recipient. Whole-genome sequencing revealed that mcr-9 was located on the IncHI2A-type plasmid, and was surrounded by IS903B and IS26 in its flanking regions. The mcr-9-carrying S. enterica 19SE belonged to ST26 and had a multi-drug-resistant phenotype. It was confirmed that mcr-9 did not mediate colistin resistance in this study, indicating that its transfer may not facilitate the dissemination of colistin resistance.
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Affiliation(s)
- Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhuoren Ling
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Naiyan Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yongshi Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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Umeda K, Nakamura H, Fukuda A, Matsumoto Y, Motooka D, Nakamura S, Yasui Y, Yoshida H, Kawahara R. Genomic characterization of clinical Enterobacter roggenkampii co-harbouring bla IMP-1- and bla GES-5-encoding IncP6 and mcr-9-encoding IncHI2 plasmids isolated in Japan. J Glob Antimicrob Resist 2021; 24:220-227. [PMID: 33385587 DOI: 10.1016/j.jgar.2020.11.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/29/2020] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES The spread of carbapenemase-producing Enterobacterales (CPE) with colistin resistance is a critical public health issue. We genetically characterized the clinical isolate Enterobacter roggenkampii OIPH-N260, which harboured carbapenemase genes blaIMP-1 and blaGES-5 with multiple resistance genes, including mcr-9 and blaCTX-M-9. METHODS This isolate was characterized by whole-genome sequencing, comparative analysis of resistance plasmids, susceptibility tests, bacterial conjugation, S1-nuclease digested pulsed-field-gel electrophoresis, and Southern blot hybridization. RESULTS The OIPH-N260 isolate exhibited resistance to most β-lactams and colistin. It co-harboured two resistance plasmids, the blaIMP-1- and blaGES-5-encoding IncP6 plasmid pN260-3 and mcr-9- and blaCTX-M-9-encoding IncHI2 plasmid pN260-1. The comparative analysis of pN260-3 indicated that a unique blaIMP-1-surrounding region was inserted into the blaGES-5-encoding plasmid with the mobile element IS26, which plays an important role in the spread of resistance genes. pN260-1 did not possess the mcr-9 expression regulative gene qseBC. Both plasmids were transferable into other bacterial species via conjugation. CONCLUSIONS This is the first study to report not only a blaIMP-1 and blaGES-5 co-encoding plasmid, but also the co-harbouring of another plasmid carrying mcr-9 and blaCTX-M-9 in Enterobacter cloacae complex. The development of advanced resistance via IS26-mediated insertion and the co-harbouring of resistance plasmids highlights the need to monitor for resistance genes in CPE.
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Affiliation(s)
- Kaoru Umeda
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka, Japan.
| | - Hiromi Nakamura
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka, Japan
| | - Akira Fukuda
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka, Japan; Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, 582 Bunkyodai Midorimachi, Ebetsu, Hokkaido, Japan
| | - Yuki Matsumoto
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, Japan
| | - Yoshinori Yasui
- Osaka Saiseikai Nakatsu Hospital, 2-10-39 Shibata, Kita-ku, Osaka, Japan
| | - Hideki Yoshida
- Osaka City Public Health Office, 1-2-7-1000 Asahi-cho, Abeno-ku, Osaka, Japan
| | - Ryuji Kawahara
- Division of Microbiology, Osaka Institute of Public Health, 8-34 Tojo-cho, Tennoji-ku, Osaka, Japan
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Mentasti M, David S, Sands K, Khan S, Davies L, Turner L, Wootton M. Rapid detection and differentiation of mobile colistin resistance (mcr-1 to mcr-10) genes by real-time PCR and melt-curve analysis. J Hosp Infect 2021; 110:148-155. [PMID: 33485969 DOI: 10.1016/j.jhin.2021.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND The emergence of multi-drug-resistant (MDR) micro-organisms prompted new interest in older antibiotics, such as colistin, that had been abandoned previously due to limited efficacy or high toxicity. Over the years, several chromosomal-encoded colistin resistance mechanisms have been described; more recently, 10 plasmid-mediated mobile colistin resistance (mcr) genes have been identified. Spread of these genes among MDR Gram-negative bacteria is a matter of serious concern; therefore, reliable and timely mcr detection is paramount. AIM To design and validate a multiplex real-time polymerase chain reaction (PCR) assay for detection and differentiation of mcr genes. METHODS All available mcr alleles were downloaded from the National Center for Biotechnology Information Reference Gene Catalogue, aligned with Clustal Omega and primers designed using Primer-BLAST. Real-time PCR monoplexes were optimized and validated using a panel of 120 characterized Gram-negative strains carrying a wide range of resistance genes, often in combination. Melt-curve analysis was used to confirm positive results. FINDINGS In-silico analysis enabled the design of a 'screening' assay for detection of mcr-1/2/6, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8 and mcr-9/10, paired with an internal control assay to discount inhibition. A 'supplementary' assay was subsequently designed to differentiate mcr-1, mcr-2, mcr-6, mcr-9 and mcr-10. Expected results were obtained for all strains (100% sensitivity and specificity). Melt-curve analysis showed consistent melting temperature results. Inhibition was not observed. CONCLUSIONS The assay is rapid and easy to perform, enabling unequivocal mcr detection and differentiation even when more than one variant is present. Adoption by clinical and veterinary microbiology laboratories would aid the surveillance of mcr genes amongst Gram-negative bacteria.
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Affiliation(s)
- M Mentasti
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK.
| | - S David
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge, UK
| | - K Sands
- School of Medicine, Cardiff University, Cardiff, UK; Department of Zoology, University of Oxford, Oxford, UK
| | - S Khan
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK
| | - L Davies
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK
| | - L Turner
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK
| | - M Wootton
- Specialist Antimicrobial and Chemotherapy Unit, Public Health Wales, University Hospital of Wales, Cardiff, UK
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Paveenkittiporn W, Kamjumphol W, Ungcharoen R, Kerdsin A. Whole-Genome Sequencing of Clinically Isolated Carbapenem-Resistant Enterobacterales Harboring mcr Genes in Thailand, 2016-2019. Front Microbiol 2021; 11:586368. [PMID: 33505364 PMCID: PMC7829498 DOI: 10.3389/fmicb.2020.586368] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/16/2020] [Indexed: 01/26/2023] Open
Abstract
Mobile colistin-resistant genes (mcr) have become an increasing public health concern. Since the first report of mcr-1 in Thailand in 2016, perspective surveillance was conducted to explore the genomic characteristics of clinical carbapenem-resistant Enterobacterales (CRE) isolates harboring mcr in 2016-2019. Thirteen (0.28%) out of 4,516 CRE isolates were found to carry mcr genes, including 69.2% (9/13) of E. coli and 30.8% (4/13) of K. pneumoniae isolates. Individual mcr-1.1 was detected in eight E. coli (61.5%) isolates, whereas the co-occurrence of mcr-1.1 and mcr-3.5 was seen in only one E. coli isolate (7.7%). No CRE were detected carrying mcr-2, mcr-4, or mcr-5 through to mcr-9. Analysis of plasmid replicon types carrying mcr revealed that IncX4 was the most common (61.5%; 8/13), followed by IncI2 (15.4%; 2/13). The minimum inhibitory concentration values for colistin were in the range of 4-16 μg/ml for all CRE isolates harboring mcr, suggesting they have 100% colistin resistance. Clermont phylotyping of nine mcr-harboring carbapenem-resistant E. coli isolates demonstrated phylogroup C was predominant in ST410. In contrast, ST336 belonged to CC17, and the KL type 25 was predominant in carbapenem-resistant K. pneumoniae isolates. This report provides a comprehensive insight into the prevalence of mcr-carrying CRE from patients in Thailand. The information highlights the importance of strengthening official active surveillance efforts to detect, control, and prevent mcr-harboring CRE and the need for rational drug use in all sectors.
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Affiliation(s)
- Wantana Paveenkittiporn
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Watcharaporn Kamjumphol
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University, Nakhon, Thailand
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Fuentes-Castillo D, Sellera FP, Goldberg DW, Fontana H, Esposito F, Cardoso B, Ikeda J, Kyllar A, Catão-Dias JL, Lincopan N. Colistin-resistant Enterobacter kobei carrying mcr-9.1 and bla CTX-M-15 infecting a critically endangered franciscana dolphin (Pontoporia blainvillei), Brazil. Transbound Emerg Dis 2021; 68:3048-3054. [PMID: 33411986 PMCID: PMC9290994 DOI: 10.1111/tbed.13980] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/29/2020] [Accepted: 01/03/2021] [Indexed: 12/12/2022]
Abstract
The emergence of mobile mcr genes mediating resistance to colistin is a critical public health issue that has hindered the treatment of serious infections caused by multidrug-resistant pathogens in humans and other animals. We report the emergence of the mcr-9.1 gene in a polymyxin-resistant extended-spectrum β-lactamase (ESBL)-producing Enterobacter kobei infecting a free-living franciscana dolphin (Pontoporia blainvillei), threatened with extinction in South America. Genomic analysis confirmed the presence of genes conferring resistance to clinically relevant β-lactam [blaCTX-M-15 , blaACT-9 , blaOXA-1 and blaTEM-1B ], aminoglycoside [aac(3)-IIa, aadA1, aph(3'')-Ib and aph(6)-Id], trimethoprim [dfrA14], tetracycline [tetA], quinolone [aac(6')-Ib-cr and qnrB1], fosfomycin [fosA], sulphonamide [sul2] and phenicol [catA1 and catB3] antibiotics. The identification of mcr-9.1 in a CTX-M-15-producing pathogen infecting a critically endangered animal is of serious concern, which should be interpreted as a sign of further spread of critical priority pathogens and their resistance genes in threatened ecosystems.
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Affiliation(s)
- Danny Fuentes-Castillo
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Fábio P Sellera
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Daphne W Goldberg
- Econservation/Santos Basin Beach Monitoring Project, Rio de Janeiro, Brazil
| | - Herrison Fontana
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Joana Ikeda
- Laboratory of Aquatic Mammals and Bioindicators: Profa Izabel M. G. do N. Gurgel' (MAQUA), Faculty of Oceanography, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - Anneliese Kyllar
- Laboratory of Aquatic Mammals and Bioindicators: Profa Izabel M. G. do N. Gurgel' (MAQUA), Faculty of Oceanography, Rio de Janeiro State University, Rio de Janeiro, Brazil.,CTA/Santos Basin Beach Monitoring Project, Rio de Janeiro, Brazil
| | - José L Catão-Dias
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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Xu T, Zhang C, Ji Y, Song J, Liu Y, Guo Y, Zhou K. Identification of mcr-10 carried by self-transmissible plasmids and chromosome in Enterobacter roggenkampii strains isolated from hospital sewage water. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115706. [PMID: 33069047 DOI: 10.1016/j.envpol.2020.115706] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
The recent emergence of plasmid-borne mobilized colistin resistance (mcr) genes largely challenges the clinical use of colistin. Monitoring the distribution of mcr genes in environment is important for aiding to develop effective control measures. In this study, we aimed to evaluate the occurrence of a recent reported mcr variant, mcr-10, in hospital sewage water. mcr-10 was identified in three Enterobacter roggenkampii strains with high-level colistin resistance (MIC ≥ 16 mg/L). The three strains were assigned to different sequence types suggesting a sporadic dissemination of mcr-10 in the sewage water. Pairwise comparisons of the predicted protein structures of ten mcr homologues revealed that MCR-10 shares a higher similarity with MCR-3, MCR-4, MCR-7, and MCR-9. Overexpression in Escherichia coli Top10 showed that the activity of mcr-10 against colistin is lower than that of mcr-9. mcr-10 expression can be specifically induced by colistin, and it was co-upregulated with phoPQ to mediate the high-level colistin resistance. The mcr-10 gene was detected on self-transmissible plasmids in two isolates and on the chromosome in the other one. Blasting in Genbank suggested that the two mcr-10-bearing plasmids (pECL981-1 and pECL983-1) were novel plasmids, and replicon typing showed that they belong to IncFIB-FII and IncFIB, respectively. Plasmid-curing assay evidence that pECL981-1 was lack of fitness cost for the host. Three novel types of the genetic context were found for the mcr-10 gene in the three isolates. The structure xerC-mcr10 was dominant in mcr-10-positive genomes (39/42) retrieved in Genbank, suggesting that xerC might be involved in the mobilization of mcr-10. To our knowledge, this is the first report of mcr-10-producing E. roggenkampii detected in hospital sewage water. Our study highlights that continuous monitoring of mcr genes in hospital sewage water is imperative for understanding and tackling the dissemination.
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Affiliation(s)
- Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Chuqiu Zhang
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yang Ji
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Jingjie Song
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yang Liu
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yuqi Guo
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.
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Citrobacter telavivum sp. nov. with chromosomal mcr-9 from hospitalized patients. Eur J Clin Microbiol Infect Dis 2020; 40:123-131. [DOI: 10.1007/s10096-020-04003-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
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