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Song K, Jin L, Cai M, Wang Q, Wu X, Wang S, Sun S, Wang R, Chen F, Wang H. Decoding the origins, spread, and global risks of mcr-9 gene. EBioMedicine 2024; 108:105326. [PMID: 39260038 DOI: 10.1016/j.ebiom.2024.105326] [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: 04/10/2024] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND The global spread of the plasmid-mediated mcr (mobilized colistin resistance) gene family presents a significant threat to the efficacy of colistin, a last-line defense against numerous Gram-negative pathogens. The mcr-9 is the second most prevalent variant after mcr-1. METHODS A dataset of 698 mcr-9-positive isolates from 44 countries is compiled. The historical trajectory of the mcr-9 gene is reconstructed using Bayesian analysis. The effective reproduction number is used innovatively to study the transmission dynamics of this mobile-drug-resistant gene. FINDINGS Our investigation traces the origins of mcr-9 back to the 1960s, revealing a subsequent expansion from Western Europe to the America and East Asia in the late 20th century. Currently, its transmissibility remains high in Western Europe. Intriguingly, mcr-9 likely emerged from human-associated Salmonella and exhibits a unique propensity for transmission within the Enterobacter. Our research provides a new perspective that this host preference may be driven by codon usage biases in plasmids. Specifically, mcr-9-carrying plasmids prefer the nucleotide C over T compared to mcr-1-carrying plasmids among synonymous codons. The same bias is seen in Enterobacter compared to Escherichia (respectively as their most dominant genus). Furthermore, we uncovered fascinating patterns of coexistence between different mcr-9 subtypes and other resistance genes. Characterized by its low colistin resistance, mcr-9 has used this seemingly benign feature to silently circumnavigate the globe, evading conventional detection methods. However, colistin-resistant Enterobacter strains with high mcr-9 expression have emerged clinically, implying a strong risk of mcr-9 evolving into a global "true-resistance-gene". INTERPRETATION This study explores the mcr-9 gene, emphasizing its origin, adaptability, and dissemination potential. Given the high mcr-9 expression colistin-resistant strains was observed in clinically the prevalence of mcr-9 poses a significant challenge to drug resistance prevention and control within the One Health framework. FUNDING This work was partially supported by the National Natural Science Foundation of China (Grant No. 32141001 and 81991533).
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Affiliation(s)
- Kaiwen Song
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Longyang Jin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Meng Cai
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Xingyu Wu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Fengning Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
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Li Y, Sun Z. Phenotypic and genomic insights into the pathogenicity and antimicrobial resistance of an Enterobacter roggenkampii strain isolated from diseased silver arowana (Osteoglossum bicirrhosum). JOURNAL OF FISH DISEASES 2024; 47:e13898. [PMID: 38014710 DOI: 10.1111/jfd.13898] [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: 08/30/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Enterobacter roggenkampii is an opportunistic pathogen that causes infections in a wide range of hosts. A bacterial strain named EOBSR_19 was isolated from diseased silver arowana, Osteoglossum bicirrhosum. This bacterium was identified as E. roggenkampii based on the phenotypic characteristics and sequence analysis of the16S rDNA and gyrB genes. Average nucleotide identity and phylogenetic analysis based on the whole genome sequence further confirmed the bacterial taxonomy of EOBSR_19. Artificial experimental infection indicated that EOBSR_19 was pathogenic to fish. Antimicrobial susceptibility test showed it was multi-drug resistant. The EOBSR_19 was found to be resistant to 18 antibiotics belonging to quinolones, macrolides, sulfonamides, aminoglycosides, and β-lactams classes. The whole genome sequencing analysis showed that EOBSR_19 carried 730 virulence genes that were annotated for different functional modules, such as adhesion and invasion, secretion system, siderophore transport system and bacterial toxin. Among them, the virulence genes related to adhesion and invasion were the most abundant. In addition, drug resistance genes involved in multiple mechanisms of antimicrobial resistance were identified in its genomics, including multidrug resistance efflux pumps, antibiotic inactivating enzymes, and antibiotic binding site mutations. Its genomic analysis via whole-genome sequencing provided insights into the pathogenicity and antimicrobial resistance.
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Affiliation(s)
- Yuerui Li
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Zhongshi Sun
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
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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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Piña-Iturbe A, Hoppe-Elsholz G, Suazo ID, Kalergis AM, Bueno SM. Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258. Microb Genom 2023; 9:001138. [PMID: 38079200 PMCID: PMC10763509 DOI: 10.1099/mgen.0.001138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
The ICEKp258.2 genomic island (GI) has been proposed as an important factor for the emergence and success of the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type (ST) 258. However, a characterization of this horizontally acquired element is lacking. Using bioinformatic and experimental approaches, we found that ICEKp258.2 is not confined to ST258 and ST512, but also carried by ST3795 strains and emergent invasive multidrug-resistant pathogens from ST1519. We also identified several ICEKp258.2-like GIs spread among different K. pneumoniae STs, other Klebsiella species and even other pathogen genera, uncovering horizontal gene transfer events between different STs and bacterial genera. Also, the comparative and phylogenetic analyses of the ICEKp258.2-like GIs revealed that the most closely related ICEKp258.2-like GIs were harboured by ST11 strains. Importantly, we found that subinhibitory concentrations of antibiotics used in treating K. pneumoniae infections can induce the excision of this GI and modulate its gene expression. Our findings provide the basis for the study of ICEKp258.2 and its role in the success of K. pneumoniae ST258. They also highlight the potential role of antibiotics in the spread of ICEKp258.2-like GIs among bacterial pathogens.
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Affiliation(s)
- Alejandro Piña-Iturbe
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Present address: Escuela de Medicina Veterinaria, Facultad de Agronomía y Sistemas Naturales, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Guillermo Hoppe-Elsholz
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Isidora D. Suazo
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330023, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
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Ota Y, Prah I, Mahazu S, Gu Y, Nukui Y, Koike R, Saito R. Novel insights into genetic characteristics of blaGES-encoding plasmids from hospital sewage. Front Microbiol 2023; 14:1209195. [PMID: 37664110 PMCID: PMC10469963 DOI: 10.3389/fmicb.2023.1209195] [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: 04/20/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction The prevalence of Guiana extended-spectrum (GES)-type carbapenemase producers is increasing worldwide, and hospital water environments are considered as potential reservoirs. However, the genetic features underlying this resistance are not yet fully understood. This study aimed to characterize blaGES-encoding plasmids from a single-hospital sewage sample in Japan. Methods Carbapenemase producers were screened using carbapenemase-selective agar and polymerase chain reaction. Whole-genome sequencing analyzes were performed on the carbapenemase-producing isolates. Results Eleven gram-negative bacteria (four Enterobacter spp., three Klebsiella spp., three Aeromonas spp., and one Serratia spp.) with blaGES-24 (n = 6), blaGES-6 (n = 4), and blaGES-5 (n = 1) were isolated from the sewage sample. Five blaGES-24 and a blaGES-5 were localized in IncP-6 plasmids, whereas three blaGES-6 plasmids were localized in IncC plasmids with IncF-like regions. The remaining blaGES-6 and blaGES-24 were, respectively, localized on IncFIB-containing plasmids with IncF-like regions and a plasmid with an IncW-like replication protein. The IncP-6 and IncW-like plasmids had a close genetic relationship with plasmids from Japan, whereas the IncC/IncF-like and IncFIB/IncF-like plasmids were closely related to those from the United States and Europe. All blaGES genes were located on the class 1 integron cassette of the Tn3 transposon-related region, and the IncC/IncF-like plasmid carried two copies of the integron cassette. Eight of the eleven blaGES-encoding plasmids contained toxin-antitoxin system genes. Discussion The findings on the plasmids and the novel genetic content from a single wastewater sample extend our understanding regarding the diversity of resistance and the associated spread of blaGES, suggesting their high adaptability to hospital effluents. These findings highlight the need for the continuous monitoring of environmental GES-type carbapenemase producers to control their dissemination.
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Affiliation(s)
- Yusuke Ota
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Samiratu Mahazu
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiaki Gu
- Department of Infectious Diseases, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoko Nukui
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuji Koike
- Clinical Research Center, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
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El Zowalaty ME, Falgenhauer L, Forsythe S, Helmy YA. Draft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa. J Glob Antimicrob Resist 2023; 33:231-237. [PMID: 36948496 DOI: 10.1016/j.jgar.2023.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/23/2023] [Accepted: 03/07/2023] [Indexed: 03/24/2023] Open
Abstract
OBJECTIVES Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa. METHODS The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees. RESULTS Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (blaACT-9), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes. The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin. CONCLUSION The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance.
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Affiliation(s)
- Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi 41012, UAE.
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany; German Center for Infection Research, Site Giessen-Marburg-Langen, Giessen, Germany; Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
| | | | - Yosra A Helmy
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, Kentucky, USA.
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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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Fukuda A, Nakano H, Suzuki Y, Nakajima C, Usui M. Conjugative IncHI2/HI2A plasmids harbouring mcr-9 in colistin-susceptible Escherichia coli isolated from diseased pigs in Japan. Access Microbiol 2022; 4:acmi000454. [PMID: 36644431 PMCID: PMC9833416 DOI: 10.1099/acmi.0.000454] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022] Open
Abstract
Colistin is a last resort antimicrobial used for the treatment of gram-negative bacterial infections. Plasmid-mediated colistin resistance (mcr) genes are a cause of global concern, and, thus far, mcr-1-10 have been identified. In a previous study, we screened mcr-1-5 in Escherichia coli derived from diseased pigs in Japan and reported a high prevalence of mcr-1, -3 and -5. However, the previous report on the prevalence of mcr genes was inaccurate. In the present study, we aimed to clarify the prevalence of all reported variants of mcr in E. coli derived from the diseased pigs, which were previously screened for mcr-1-5. Additionally, we also characterized the mcr-9-positive E. coli , which was detected in this study. We screened mcr in 120 E. coli strains from diseased pigs and mcr-positive E. coli and an mcr-carrying plasmid were also characterized. One mcr-9-positive colistin-susceptible E. coli strain was detected (0.8 %). Plasmid-mediated mcr-9 was transferred to E. coli ML4909 as the recipient strain, and it was located on IncHI2/HI2A plasmid p387_L with other antimicrobial resistance genes (ARGs). The region harbouring ARGs including mcr-9, was similar to that on the Klebsiella pneumoniae chromosome harbouring mcr-9 isolated in Japan. mcr-3, -5 and -9 were detected (4.2 %) in colistin-susceptible strains. mcr-9 was found to be disseminated via the plasmid IncHI2/HI2A p387_L and transferred and inserted into chromosomes via a transposon. Our results suggest that mcr genes should be monitored regularly, regardless of their susceptibility to colistin.
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Affiliation(s)
- Akira Fukuda
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Hitomi Nakano
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Yasuhiko Suzuki
- Hokkaido University International Institute for Zoonosis Control, Division of Bioresources, Sapporo, Hokkaido, Japan
| | - Chie Nakajima
- Hokkaido University International Institute for Zoonosis Control, Division of Bioresources, Sapporo, Hokkaido, Japan
| | - Masaru Usui
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan,*Correspondence: Masaru Usui,
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Jiang S, Wang X, Yu H, Zhang J, Wang J, Li J, Li X, Hu K, Gong X, Gou X, Yang Y, Li C, Zhang X. Molecular antibiotic resistance mechanisms and co-transmission of the mcr-9 and metallo-β-lactamase genes in carbapenem-resistant Enterobacter cloacae complex. Front Microbiol 2022; 13:1032833. [PMID: 36386624 PMCID: PMC9659896 DOI: 10.3389/fmicb.2022.1032833] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/28/2022] [Indexed: 11/25/2023] Open
Abstract
Carbapenem-resistant Enterobacter cloacae complex (CRECC) has increasingly emerged as a major cause of healthcare-associated infections, with colistin being one of the last-resort antibiotics of treatment. Mobile colistin resistance (mcr)-9 is a member of a growing family of mcr genes and has been reported to be an inducible gene encoding an acquired phosphoethanolamine transferase. Here, we collected 24 ECC strains from Chongqing, China from 2018 to 2021. Subsequently, antibiotic resistance genes and the transmission dynamics of the strains were determined by PCR, whole-genome sequencing, and bioinformatic analysis. The mcr-9 was identified in IncHI2/2A or IncHI2/2A + IncN plasmids from six CRECC strains and was co-located with bla NDM-1 or bla IMP-4 in 2/6 plasmids. The genetic environment of mcr-9.1 was composed of IS903B-mcr-9.1-wbuC-IS26 in the five mcr-9.1-harboring-plasmid, but IS1B was located downstream of mcr-9.2 in the pECL414-1 sequence. We also found that the pNDM-068001 plasmid carrying mcr-9.1 could be a hybrid plasmid, formed by a Tn6360-like bla NDM-1 region inserted into an mcr-9.1-positive IncHI2/2A plasmid. A conjugation assay showed that plasmids mediated the co-dissemination of mcr-9 and metallo-β-lactamase (MBL) genes. In addition, we performed induction assays with sub-inhibitory concentrations of colistin and found an increase in the relative expression levels of the mcr-9.2, qseC, and qseB genes, as well as an increase in the minimum inhibitory concentration values of colistin in the CRECC414 strain. These findings provide a basis for studying the regulatory mechanisms of mcr-9 expression and highlight the importance of effective monitoring to assess the prevalence of MBL and mcr-9 co-existing plasmids.
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Affiliation(s)
- Shan Jiang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Pathogenic Biology, Jiamusi University School of Basic Medicine, Jiamusi, China
| | - Xiaoyu Wang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Department of Microbiology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Haidong Yu
- Department of Microbiology, Shenzhen University General Hospital, Shenzhen, China
| | - Jisheng Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jianmin Wang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Li
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Xinhui Li
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - 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
| | - Xue Gong
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Gou
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Yang Yang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Chunjiang Li
- Department of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Xiaoli Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
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Cañada-García JE, Grippo N, de Arellano ER, Bautista V, Lara N, Navarro AM, Cabezas T, Martínez-Ramírez NM, García-Cobos S, Calvo J, Cercenado E, Aracil B, Pérez-Vázquez M, Oteo-Iglesias J. Phenotypic and molecular characterization of IMP-producing Enterobacterales in Spain: Predominance of IMP-8 in Klebsiella pneumoniae and IMP-22 in Enterobacter roggenkampii. Front Microbiol 2022; 13:1000787. [PMID: 36246266 PMCID: PMC9554532 DOI: 10.3389/fmicb.2022.1000787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Little is known about IMP-producing Enterobacterales (IMP-Ent) in Europe. We analyzed at genomic and phenotypic level IMP-Ent isolates circulating in Spain in a 9-year period. Materials and methods IMP-Ent isolates submitted to our reference laboratory were included. Antibiotic susceptibility was performed using microdilution method (EUCAST), and IMP-carbapenemase activity was measured with carbapenemase inhibitors, the β-CARBA method, the modified Hodge test (MHT), and the modified carbapenemase inhibition method (mCIM). All isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis. Results Fifty IMP-Ent isolates, collected from 19 hospitals in 13 Spanish provinces, were detected: Klebsiella pneumoniae (IMP-Kpn) (24; 48%), Enterobacter roggenkampii (13; 26%), Enterobacter hormaechei (8, 16%), Klebsiella oxytoca (two; 4%), Enterobacter asburiae (one, 2%), Serratia marcescens (one; 2%) and Escherichia coli (one; 2%). All isolates were positive by the MHT and β-CARBA tests; 48 (96%) were mCIM positive; 12 (24%) and 26 (52%) displayed positive inhibition with dipicolinic (meropenem) and EDTA (ertapenem), respectively. Five IMP-carbapenemase types were identified: IMP-8 (22; 44%), IMP-22 (17; 34%), IMP-13 (7; 14%), IMP-28 (two; 4%), and IMP-15 (two; 4%), predominating IMP-8 in K. pneumoniae and IMP-22 in E. roggenkampii. IMP-28 was exclusively identified in K. oxytoca and IMP-15 in E. hormaechei. Predominant STs were ST405 (29.2%), ST15 (25%) and ST464 (20.8%) in IMP-Kpn; ST96 (100%) in E. roggenkampii and ST182 (62.5%) in E. hormachei. Colistin and amikacin were the most active non-carbapenem antibiotics against IMP-Ent. Conclusion IMP-Ent isolates remain infrequent in Spain, although in recent years have been circulating causing nosocomial outbreaks, being IMP-8-producing K. pneumoniae and IMP-22-producing E. roggenkampii the most frequently detected in this study. Inhibition with EDTA or dipicolinic acid presented false negative results in some IMP-producing strains. Active microbiological and molecular surveillance is essential for a better comprehension and control of IMP-Ent dissemination.
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Affiliation(s)
- Javier E. Cañada-García
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Natalin Grippo
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Educación Médica e Investigaciones Clínicas “Norberto Quirno”, Buenos Aires, Argentina
| | - Eva Ramírez de Arellano
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Verónica Bautista
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Noelia Lara
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana María Navarro
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Teresa Cabezas
- Servicio de Microbiología, Hospital de Poniente, Almería, Spain
| | | | - Silvia García-Cobos
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Calvo
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Emilia Cercenado
- Servicio de Microbiología, Hospital Universitario Gregorio Marañón, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Belén Aracil
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: María Pérez-Vázquez,
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Spanish Network for Research in Infectious Diseases (REIPI), Instituto de Salud Carlos III, Madrid, Spain
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11
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Isolation, Whole-Genome Sequencing, and Annotation of Two Antibiotic-Producing and -Resistant Bacteria, Enterobacter roggenkampii RIT 834 and Acinetobacter pittii RIT 835, from Disposable Masks Collected from the Environment. Microbiol Resour Announc 2022; 11:e0075722. [PMID: 36094212 PMCID: PMC9583802 DOI: 10.1128/mra.00757-22] [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] [Indexed: 11/20/2022] Open
Abstract
We report the whole-genome sequence and annotation of two antibiotic-resistant bacteria, Enterobacter roggenkampii RIT 834 and Acinetobacter pittii RIT 835, isolated from disposed masks. We found that these strains are resistant to five of seven commonly used antibiotics and that they produce bactericidal compounds against Escherichia coli.
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12
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Anyanwu MU, Jaja IF, Nwobi OC, Mgbeahuruike AC, Ikpendu CN, Okafor NA, Oguttu JW. Epidemiology and Traits of Mobile Colistin Resistance ( mcr) Gene-Bearing Organisms from Horses. Microorganisms 2022; 10:microorganisms10081499. [PMID: 35893557 PMCID: PMC9394310 DOI: 10.3390/microorganisms10081499] [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: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) threaten the efficacy of colistin (COL), a polymyxin antibiotic that is used as a last-line agent for the treatment of deadly infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. COL has been used for more than 60 years for the prophylactic control and treatment of infections in livestock husbandry but not in horses. Polymyxin B is used for the prophylactic control and empirical treatment of infections in horses without conducting sensitivity tests. The lack of sensitivity testing exerts selection pressure for the acquisition of the mcr gene. By horizontal transfer, mcr-1, mcr-5, and mcr-9 have disseminated among horse populations globally and are harbored by Escherichia coli, Klebsiella, Enterobacter, Citrobacter, and Salmonella species. Conjugative plasmids, insertion sequences, and transposons are the backbone of mcr genes in the isolates, which co-express genes conferring multi- to extensive-drug resistance, including genes encoding extended-spectrum β-lactamase, ampicillinase C, fosfomycin, and fluoroquinolone resistance, and virulence genes. The transmission of mcr genes to/among bacterial strains of equine origin is non-clonal. Contact with horses, horse manure, feed/drinking water, farmers, farmers’ clothing/farm equipment, the consumption of contaminated horse meat and its associated products, and the trading of horses, horse meat, and their associated products are routes for the transmission of mcr-gene-bearing bacteria in, to, and from the equine industry.
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Affiliation(s)
- Madubuike Umunna Anyanwu
- Microbiology Unit, Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka 400001, Nigeria;
- Correspondence: (M.U.A.); (I.F.J.); Tel.: +27-78-549-2098 (I.F.J.); Fax: +27-86-770-6869 (I.F.J.)
| | - Ishmael Festus Jaja
- Department of Agriculture and Animal Health, Florida Campus, University of South Africa, Johannesburg 1709, South Africa;
- Correspondence: (M.U.A.); (I.F.J.); Tel.: +27-78-549-2098 (I.F.J.); Fax: +27-86-770-6869 (I.F.J.)
| | - Obichukwu Chisom Nwobi
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka 400001, Nigeria;
| | | | - Chinaza Nnenna Ikpendu
- Department of Veterinary Microbiology, Michael Okpara University of Agriculture, Umudike 440101, Nigeria;
| | | | - James Wabwire Oguttu
- Department of Agriculture and Animal Health, Florida Campus, University of South Africa, Johannesburg 1709, South Africa;
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13
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Urase T, Goto S, Sato M. Monitoring Carbapenem-Resistant Enterobacterales in the Environment to Assess the Spread in the Community. Antibiotics (Basel) 2022; 11:antibiotics11070917. [PMID: 35884172 PMCID: PMC9311640 DOI: 10.3390/antibiotics11070917] [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: 06/06/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 11/20/2022] Open
Abstract
The usefulness of wastewater-based epidemiology (WBE) was proven during the COVID-19 pandemic, and the role of environmental monitoring of emerging infectious diseases has been recognized. In this study, the prevalence of carbapenem-resistant Enterobacterales (CRE) in Japanese environmental samples was measured in the context of applying WBE to CRE. A total of 247 carbapenem-resistant isolates were obtained from wastewater, treated wastewater, and river water. Treated wastewater was shown to be an efficient target for monitoring CRE. The results of the isolate analysis showed that WBE may be applicable to Escherichia coli-carrying New Delhi metallo-β-lactamase (NDM)-type carbapenemase, the Enterobacter cloacae complex and Klebsiella pneumoniae complex-carrying IMP-type carbapenemase. In addition, a certain number of CRE isolated in this study carried Guiana extended spectrum (GES)-type carbapenemase although their clinical importance was unclear. Only a few isolates of Klebsiella aerogenes were obtained from environmental samples in spite of their frequent detection in clinical isolates. Neither the KPC-type, the oxacillinase (OXA)-type nor the VIM-type of carbapenemase was detected in the CRE, which reflected a low regional prevalence. These results indicated the expectation and the limitation of applying WBE to CRE.
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14
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First Report of the Colistin Resistance Gene mcr-10.1 Carried by Inc pA1763-KPC Plasmid pSL12517-mcr10.1 in Enterobacter cloacae in Sierra Leone. Microbiol Spectr 2022; 10:e0112722. [PMID: 35695522 PMCID: PMC9431528 DOI: 10.1128/spectrum.01127-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mobile colistin resistance (mcr) gene mcr-10.1 has been distributed widely since it was initially identified in 2020. The aim of this study was to report the first mcr-10.1 in Africa and the first mcr in Sierra Leone; furthermore, we presented diverse modular structures of mcr-10.1 loci. Here, the complete sequence of one mcr-10.1-carrying plasmid in one clinical Enterobacter cloacae isolate from Sierra Leone was determined. Detailed genetic dissection and comparison were applied to this plasmid, together with a homologous plasmid carrying mcr-10.1 from GenBank. Moreover, a genetic comparison of 19 mcr-10.1 loci was performed. In this study, mcr-10.1 was carried by an IncpA1763-KPC plasmid from one Enterobacter cloacae isolate. A total of 19 mcr-10.1 loci displayed diversification in modular structures through complex transposition and homologous recombination. A site-specific tyrosine recombinase XerC was located upstream of mcr-10.1, and at least one insertion sequence element was inserted adjacent to a conserved xerC-mcr-10.1-orf336-orf177 region. Integration of mcr-10.1 into a different gene context and carried by various Inc plasmids contributed to the wide distribution of mcr-10.1 and enhanced the ability of bacteria to survive under colistin selection pressure. IMPORTANCE Colistin is used as one of the last available choices of antibiotics for patients infected by carbapenem-resistant bacterial strains, but the unrestricted use of colistin aggravated the acquisition and dissemination of mobile colistin resistance (mcr) genes. So far, 10 mcr genes have been reported in four continents around the world. This study presented one mcr-10.1-carrying Enterobacter cloacae isolate from Sierra Leone. The mcr-10.1 gene was identified on an IncpA1763-KPC plasmid. According to the results of genetic comparison of 19 mcr-10.1 loci, the mcr-10.1 gene was found to be located in a conserved xerC-mcr-10.1-orf336-orf177 region, and at least one insertion sequence element was inserted adjacent to this region. To our knowledge, this is the first report of identifying the mcr-10.1 gene in Africa and the mcr gene in Sierra Leone.
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15
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Chen C, Xu H, Liu R, Hu X, Han J, Wu L, Fu H, Zheng B, Xiao Y. Emergence of Neonatal Sepsis Caused by MCR-9- and NDM-1-Co-Producing Enterobacter hormaechei in China. Front Cell Infect Microbiol 2022; 12:879409. [PMID: 35601097 PMCID: PMC9120612 DOI: 10.3389/fcimb.2022.879409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/05/2022] [Indexed: 01/01/2023] Open
Abstract
Mobile colistin resistance (mcr) genes represent an emerging threat to public health. Reports on the prevalence, antimicrobial profiles, and clonality of MCR-9-producing Enterobacter cloacae complex (ECC) isolates on a national scale in China are limited. We screened 3,373 samples from humans, animals, and the environment and identified eleven MCR-9-positive ECC isolates. We further investigated their susceptibility, epidemiology, plasmid profiles, genetic features, and virulence potential. Ten strains were isolated from severe bloodstream infection cases, especially three of them were recovered from neonatal sepsis. Enterobacter hormaechei was the most predominant species among the MCR-9-producing ECC population. Moreover, the co-existence of MCR-9, CTX-M, and SHV-12 encoding genes in MCR-9-positive isolates was globally observed. Notably, mcr-9 was mainly carried by IncHI2 plasmids, and we found a novel ~187 kb IncFII plasmid harboring mcr-9, with low similarity with known plasmids. In summary, our study presented genomic insights into genetic characteristics of MCR-9-producing ECC isolates retrieved from human, animal, and environment samples with one health perspective. This study is the first to reveal NDM-1- and MCR-9-co-producing ECC from neonatal sepsis in China. Our data highlights the risk for the hidden spread of the mcr-9 colistin resistance gene.
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Affiliation(s)
- Chunlei Chen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Ruishan Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinjun Hu
- Department of Infectious Diseases, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, China
| | - Jianfeng Han
- Sansure Biotech Inc. Medical Affairs Department, National Joint Local Engineering Research Center for Genetic Diagnosis of Infection Diseases and Tumors, Beijing, China
| | - Lingjiao Wu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Fu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Beiwen Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Research Units of Infectious Diseases and Microecology, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Beiwen Zheng, ; Yonghong Xiao,
| | - Yonghong Xiao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Research Units of Infectious Diseases and Microecology, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Beiwen Zheng, ; Yonghong Xiao,
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16
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High prevalence of colistin resistance and mcr-9/10 genes in Enterobacter spp. in a tertiary hospital over a decade. Int J Antimicrob Agents 2022; 59:106573. [DOI: 10.1016/j.ijantimicag.2022.106573] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/28/2022] [Accepted: 03/12/2022] [Indexed: 11/22/2022]
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17
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Ghiglione B, Haim MS, Penzotti P, Brunetti F, D Amico González G, Di Conza J, Figueroa-Espinosa R, Nuñez L, Razzolini MTP, Fuga B, Esposito F, Vander Horden M, Lincopan N, Gutkind G, Power P, Dropa M. Characterization of Emerging Pathogens Carrying bla KPC-2 Gene in IncP-6 Plasmids Isolated From Urban Sewage in Argentina. Front Cell Infect Microbiol 2021; 11:722536. [PMID: 34504809 PMCID: PMC8421773 DOI: 10.3389/fcimb.2021.722536] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022] Open
Abstract
Untreated wastewater is a reservoir for multidrug-resistant bacteria, but its role in the spread of antibiotic resistance in the human population remains poorly investigated. In this study, we isolated a KPC-2-producing ST2787 Klebsiella quasipneumoniae subsp. quasipneumoniae (WW14A), recovered from raw sewage at a wastewater treatment plant in Argentina in 2018 and determined its complete genome sequence. Strain WW14A was resistant to all β-lactams, ciprofloxacin and amikacin. A core genome phylogenetic analysis indicated that WW14A was closely related to a GES-5-producing Taiwanese strain isolated from hospital wastewater in 2015 and it was clearly distinct from strains isolated recently in Argentina and Brazil. Interestingly, blaKPC-2 was harbored by a recently described IncP-6 broad-spectrum plasmid which was sporadically reported worldwide and had never been reported before in Argentina. We investigated the presence of the IncP-6 replicon in isolates obtained from the same sampling and found a novel non-typable/IncP-6 hybrid plasmid in a newly assigned ST1407 Enterobacter asburiae (WW19C) also harboring blaKPC-2. Nanopore sequencing and hybrid assembly of strains WW14A and WW19C revealed that both IncP-6 plasmids shared 72% of coverage (~20 kb), with 99.99% of sequence similarity and each one also presented uniquely combined regions that were derived from other plasmids recently reported in different countries of South America, Asia, and Europe. The region harboring the carbapenem resistance gene (~11 kb) in both plasmids contained a Tn3 transposon disrupted by a Tn3-ISApu-flanked element and the core sequence was composed by ΔISKpn6/blaKPC-2/ΔblaTEM-1/ISKpn27. Both strains also carried genes conferring resistance to heavy metals (e.g., arsenic, mercury, lead, cadmium, copper), pesticides (e.g., glyphosate), disinfectants, and several virulence-related genes, posing a potential pathogenic risk in the case of infections. This is the first study documenting blaKPC-2 associated with IncP-6 plasmids in K. quasipneumoniae and Enterobacter cloacae complex from wastewater in Argentina and highlights the circulation of IncP-6 plasmids as potential reservoirs of blaKPC-2 in the environment.
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Affiliation(s)
- Barbara Ghiglione
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Sol Haim
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Pedro Penzotti
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Florencia Brunetti
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gabriela D Amico González
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - José Di Conza
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Roque Figueroa-Espinosa
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Lidia Nuñez
- Facultad de Farmacia y Bioquímica, Cátedra de Salud Pública e Higiene Ambiental, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Tereza Pepe Razzolini
- Departamento de Saúde Ambiental, Laboratório de Microbiologia Ambiental e Resistência Antimicrobiana - MicroRes, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Maximiliano Vander Horden
- Ingeniería - Gerencia Técnica, Dirección de Saneamiento, Agua y Saneamientos Argentinos S.A. (AySA), Buenos Aires, Argentina
| | - Nilton Lincopan
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel Gutkind
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Pablo Power
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Milena Dropa
- Departamento de Saúde Ambiental, Laboratório de Microbiologia Ambiental e Resistência Antimicrobiana - MicroRes, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
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18
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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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Rodríguez-Santiago J, Cornejo-Juárez P, Silva-Sánchez J, Garza-Ramos U. Polymyxin resistance in Enterobacterales: overview and epidemiology in the Americas. Int J Antimicrob Agents 2021; 58:106426. [PMID: 34419579 DOI: 10.1016/j.ijantimicag.2021.106426] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/07/2021] [Accepted: 08/15/2021] [Indexed: 12/30/2022]
Abstract
The worldwide spread of carbapenem- and polymyxin-resistant Enterobacterales represents an urgent public-health threat. However, for most countries in the Americas, the available data are limited, although Latin America has been suggested as a silent spreading reservoir for isolates carrying plasmid-mediated polymyxin resistance mechanisms. This work provides an overall update on polymyxin and polymyxin resistance and focuses on uses, availability and susceptibility testing. Moreover, a comprehensive review of the current polymyxin resistance epidemiology in the Americas is provided. We found that reports in the English and Spanish literature show widespread carbapenemase-producing and colistin-resistant Klebsiella pneumoniae in the Americas determined by the clonal expansion of the pandemic clone ST258 and mgrB-mediated colistin resistance. In addition, widespread IncI2 and IncX4 plasmids carrying mcr-1 in Escherichia coli come mainly from human sources; however, plasmid-mediated colistin resistance in the Americas is underreported in the veterinary sector. These findings demonstrate the urgent need for the implementation of polymyxin resistance surveillance in Enterobacterales as well as appropriate regulatory measures for antimicrobial use in veterinary medicine.
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Affiliation(s)
- J Rodríguez-Santiago
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, México; Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - P Cornejo-Juárez
- Departamento de Infectología, Instituto Nacional de Cancerología (INCan), Ciudad de México, México
| | - J Silva-Sánchez
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, México
| | - U Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, Morelos, México.
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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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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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