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Wu J, Liu L, Wang J, Wang Y, Li X, Wang X, Jiang S, Li W, Zhang J, Zhang X. Transcriptomic analysis of induced resistance to polymyxin in carbapenem-resistant Enterobacter cloacae complex isolate carrying mcr-9. J Glob Antimicrob Resist 2024; 37:225-232. [PMID: 38750896 DOI: 10.1016/j.jgar.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 03/17/2024] [Accepted: 04/15/2024] [Indexed: 06/06/2024] Open
Abstract
OBJECTIVES Polymyxins are currently the last-resort treatment against multi-drug resistant Gram-negative bacterial infections, but plasmid-mediated mobile polymyxin resistance genes (mcr) threaten its efficacy, especially in carbapenem-resistant Enterobacter cloacae complex (CRECC). The objective of this study was to provide insights into the mechanism of polymyxin-induced bacterial resistance and the effect of overexpression of mcr-9. METHODS The clinical strain CRECC414 carrying the mcr-9 gene was treated with a gradient concentration of polymyxin. Subsequently, the broth microdilution was used to determine the minimum inhibitory concentration (MIC) and RT-qPCR was utilized to assess mcr-9 expression. Transcriptome sequencing and whole genome sequencing (WGS) was utilized to identify alterations in strains resulting from increased polymyxin resistance, and significant transcriptomic differences were analysed alongside a comprehensive examination of metabolic networks at the genomic level. RESULTS Polymyxin treatment induced the upregulation of mcr-9 expression and significantly elevated the MIC of the strain. Furthermore, the WGS and transcriptomic results revealed a remarkable up-regulation of arnBCADTEF gene cassette, indicating that the Arn/PhoPQ system-mediated L-Ara4N modification is the preferred mechanism for achieving high levels of resistance. Additionally, significant alterations in bacterial gene expression were observed with regards to multidrug efflux pumps, oxidative stress and repair mechanisms, cell membrane biosynthesis, as well as carbohydrate metabolic pathways. CONCLUSION Polymyxin greatly disrupts the transcription of vital cellular pathways. A complete PhoPQ two-component system is a prerequisite for polymyxin resistance of Enterobacter cloacae, even though mcr-9 is highly expressed. These findings provide novel and important information for further investigation of polymyxin resistance of CRECC.
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Affiliation(s)
- Jiming Wu
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Longjin Liu
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jianmin Wang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Ying Wang
- Department of Microbiology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Xinhui Li
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoyu Wang
- Department of Microbiology, The First Affiliated Hospital of Jiamusi University, Jiamusi, China
| | - Shan Jiang
- Department of Pathogenic Biology, Basic Medicine of Jiamusi University, Jiamusi, China
| | - Wengang Li
- Department of Pathogenic Biology, Basic Medicine of Jiamusi University, Jiamusi, China
| | - Jisheng Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.
| | - Xiaoli Zhang
- Department of Microbiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
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Wang Q, Han YY, Zhang TJ, Chen X, Lin H, Wang HN, Lei CW. Whole-genome sequencing of Escherichia coli from retail meat in China reveals the dissemination of clinically important antimicrobial resistance genes. Int J Food Microbiol 2024; 415:110634. [PMID: 38401379 DOI: 10.1016/j.ijfoodmicro.2024.110634] [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: 12/29/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Escherichia coli is one of the important reservoirs of antimicrobial resistance genes (ARG), which often causes food-borne diseases and clinical infections. Contamination with E. coli carrying clinically important antimicrobial resistance genes in retail meat products can be transmitted to humans through the food chain, posing a serious threat to public health. In this study, a total of 330 E. coli strains were isolated from 464 fresh meat samples from 17 food markets in China, two of which were identified as enterotoxigenic and enteropathogenic E. coli. Whole genome sequencing revealed the presence of 146 different sequence types (STs) including 20 new STs, and 315 different clones based on the phylogenetic analysis, indicating the high genetic diversity of E. coli from retail meat products. Antimicrobial resistance profiles showed that 82.42 % E. coli were multidrug-resistant strains. A total of 89 antimicrobial resistance genes were detected and 12 E. coli strains carried clinically important antimicrobial resistance genes blaNDM-1, blaNDM-5, mcr-1, mcr-10 and tet(X4), respectively. Nanopore sequencing revealed that these resistance genes are located on different plasmids with the ability of horizontal transfer, and their genetic structure and environment are closely related to plasmids isolated from humans. Importantly, we reported for the first time the presence of plasmid-mediated mcr-10 in E. coli from retail meat. This study revealed the high genetic diversity of food-borne E. coli in retail meat and emphasized their risk of spreading clinically important antimicrobial resistance genes.
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Affiliation(s)
- Qin Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Ying-Yue Han
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Tie-Jun Zhang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Xuan Chen
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Heng Lin
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Hong-Ning Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.
| | - Chang-Wei Lei
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.
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Mondal AH, Khare K, Saxena P, Debnath P, Mukhopadhyay K, Yadav D. A Review on Colistin Resistance: An Antibiotic of Last Resort. Microorganisms 2024; 12:772. [PMID: 38674716 PMCID: PMC11051878 DOI: 10.3390/microorganisms12040772] [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: 03/17/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Antibiotic resistance has emerged as a significant global public health issue, driven by the rapid adaptation of microorganisms to commonly prescribed antibiotics. Colistin, previously regarded as a last-resort antibiotic for treating infections caused by Gram-negative bacteria, is increasingly becoming resistant due to chromosomal mutations and the acquisition of resistance genes carried by plasmids, particularly the mcr genes. The mobile colistin resistance gene (mcr-1) was first discovered in E. coli from China in 2016. Since that time, studies have reported different variants of mcr genes ranging from mcr-1 to mcr-10, mainly in Enterobacteriaceae from various parts of the world, which is a major concern for public health. The co-presence of colistin-resistant genes with other antibiotic resistance determinants further complicates treatment strategies and underscores the urgent need for enhanced surveillance and antimicrobial stewardship efforts. Therefore, understanding the mechanisms driving colistin resistance and monitoring its global prevalence are essential steps in addressing the growing threat of antimicrobial resistance and preserving the efficacy of existing antibiotics. This review underscores the critical role of colistin as a last-choice antibiotic, elucidates the mechanisms of colistin resistance and the dissemination of resistant genes, explores the global prevalence of mcr genes, and evaluates the current detection methods for colistin-resistant bacteria. The objective is to shed light on these key aspects with strategies for combating the growing threat of resistance to antibiotics.
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Affiliation(s)
- Aftab Hossain Mondal
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kriti Khare
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Prachika Saxena
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Parbati Debnath
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kasturi Mukhopadhyay
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 712-749, Republic of Korea
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Gharaibeh MH, Al Sheyab SY, Malkawi IM, Al Qudsi FR. Phenotypic and genotypic characterization of Escherichia coli isolated from the chicken liver in relation to slaughterhouse conditions. Heliyon 2024; 10:e27759. [PMID: 38515697 PMCID: PMC10955320 DOI: 10.1016/j.heliyon.2024.e27759] [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: 10/17/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Avian pathogenic Escherichia coli (APEC) has been identified as a sub-group of extraintestinal pathogenic E. coli (ExPEC). Recent studies indicate APEC as a potential foodborne zoonotic pathogen and a source or reservoir of human extraintestinal infections. The slaughtering and processing of poultry in low-income countries such as Jordan occurs in two distinct ways: in informal facilities known as Natafat and in formal slaughterhouses. This study compared E. coli phenotypes and genotypes according to slaughtering conditions (formal slaughterhouses vs. informal slaughter facilities). Therefore, liver samples (n = 242) were collected from formal (n = 121) and informal slaughter facilities (n = 121). Results revealed a high prevalence (94.2%) of E. coli among all isolates, with 59 (17 formal and 42 informal) isolates considered avian pathogenic E. coli (APEC) based on the virulence-associated genes. The prevalence of resistance among isolates was relatively high, reaching up to 99% against penicillin and 97% against nalidixic acid. However, the prevalence of resistance was the lowest (1.3%) against both meropenem and imipenem. Based on the MIC test findings, colistin resistance was 46.9% (107/228). The mcr -1 gene prevalence was 51.4% (55/107), of which 17.1 % were from formal plants (6/36) and 68.1% from informal facilities (49/72). Interestingly, only one isolate (0.9%) expressed mcr-10. Escherichia coli O157:H7 and associated virulence genes were found more in informal (n = 15 genes) than in formal slaughterhouses (n = 8). Phylogroups B1, C, and A were the most frequent in 228 E. coli isolates, while G, B2, and clade were the least frequent. In conclusion, these findings highlight the importance of implementing biosecurity measures in slaughterhouses to reduce antibiotic-resistant E. coli spread. Furthermore, this study provides valuable insights into the effects of wet market (Natafat) slaughter conditions on increasing bacterial resistance and virulence.
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Affiliation(s)
- Mohammad H. Gharaibeh
- Department of Basic Veterinary Medical Science, Faculty of Veterinary Medicine, Jordan University of Science and Technology, P. O. Box 3030, Irbid, 22110, Jordan
| | - Sahba Y. Al Sheyab
- Department of Basic Veterinary Medical Science, Faculty of Veterinary Medicine, Jordan University of Science and Technology, P. O. Box 3030, Irbid, 22110, Jordan
| | - Ismail M. Malkawi
- Department of Basic Veterinary Medical Science, Faculty of Veterinary Medicine, Jordan University of Science and Technology, P. O. Box 3030, Irbid, 22110, Jordan
| | - Farah R. Al Qudsi
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid, 21121, Jordan
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Sourenian T, Palkovicova J, Papagiannitsis CC, Dolejska M, Hrabak J, Bitar I. A novel F type plasmid encoding mcr-10 in a clinical Enterobacter ludwigii strain from a tertiary hospital in the Czech Republic. J Glob Antimicrob Resist 2024; 37:195-198. [PMID: 38555080 DOI: 10.1016/j.jgar.2024.03.015] [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: 11/21/2023] [Revised: 03/16/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024] Open
Abstract
OBJECTIVE Here we describe a novel IncFIA plasmid harbouring mcr-10 gene in a clinical Enterobacter ludwigii strain isolated at the University Hospital in Pilsen in the Czech Republic. METHODS The strain was subjected to antibiotic susceptibility testing. Whole genome sequencing was performed using Illumina for short-read sequencing and Oxford Nanopore Technologies for long-read sequencing followed by hybrid assembly. The resulting genome was used to detect species using average nucleotide identity, resistance genes, plasmid replicon and MLST (using centre for genomic epidemiology databases; ResFinder, PlasmidFinder and MLST, respectively) and virulence genes using VFDB. RESULTS Τhe strain showed susceptibility against tetracycline, cefuroxime and chloramphenicol, and it was susceptible to the second and third generation of cephalosporins, carbapenems and colistin. Genome analysis identified the strain as E. ludwigii sequence type ST20 and located the mcr-10 gene on an IncFIA (HI1)/IncFII (Yp) plasmid (pI9455333_MCR10; 129 863 bp). Upon blasting the nucleotide sequence of pI9455333_MCR10 against the NCBI database, no similar plasmid sequence was detected, implying a novel plasmid structure. Nevertheless, it showed a partial similarity with pRHBSTW-00123_3 and FDAARGOS 1432, which were detected in Enterobacter cloacae complex (ECC) strains in wastewater samples in 2017 in UK and in 2021 in the United States, respectively, and pEC81-mcr, which was detected in a clinical Escherichia coli strain in 2020 in China. Moreover, I9455333cz genome carried virulence genes coding for curli fibers, fimbrial adherence determinants, siderophore aerobactin, iron uptake proteins and regulators of sigma factor. CONCLUSION In conclusion, we identified a novel IncF plasmid harbouring mcr-10 gene in a clinical Enterobacter ludwigii strain. To our knowledge, this is the first clinical report of mcr-10 in the Czech Republic.
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Affiliation(s)
- Tsolaire Sourenian
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Jana Palkovicova
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia; Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | | | - Monika Dolejska
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia; Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, 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, Czech Republic
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.
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Portal EAR, Sands K, Farley C, Boostrom I, Jones E, Barrell M, Carvalho MJ, Milton R, Iregbu K, Modibbo F, Uwaezuoke S, Akpulu C, Audu L, Edwin C, Yusuf AH, Adeleye A, Mukkadas AS, Maduekwe D, Gambo S, Sani J, Walsh TR, Spiller OB. Characterisation of colistin resistance in Gram-negative microbiota of pregnant women and neonates in Nigeria. Nat Commun 2024; 15:2302. [PMID: 38485761 PMCID: PMC10940312 DOI: 10.1038/s41467-024-45673-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/30/2024] [Indexed: 03/18/2024] Open
Abstract
A mobile colistin resistance gene mcr was first reported in 2016 in China and has since been found with increasing prevalence across South-East Asia. Here we survey the presence of mcr genes in 4907 rectal swabs from mothers and neonates from three hospital sites across Nigeria; a country with limited availability or history of colistin use clinically. Forty mother and seven neonatal swabs carried mcr genes in a range of bacterial species: 46 Enterobacter spp. and single isolates of; Shigella, E. coli and Klebsiella quasipneumoniae. Ninety percent of the genes were mcr-10 (n = 45) we also found mcr-1 (n = 3) and mcr-9 (n = 1). While the prevalence during this collection (2015-2016) was low, the widespread diversity of mcr-gene type and range of bacterial species in this sentinel population sampling is concerning. It suggests that agricultural colistin use was likely encouraging sustainment of mcr-positive isolates in the community and implementation of medical colistin use will rapidly select and expand resistant isolates.
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Affiliation(s)
- E A R Portal
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - K Sands
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK.
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - C Farley
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - I Boostrom
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - E Jones
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - M Barrell
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - M J Carvalho
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - R Milton
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Centre for Trials Research, Cardiff University, Cardiff, UK
| | - K Iregbu
- National Hospital Abuja, Abuja, Nigeria
| | - F Modibbo
- Murtala Muhammad Specialist Hospital, Kano, Nigeria
| | - S Uwaezuoke
- Federal Medical Centre -Jabi, Abuja, Nigeria
| | - C Akpulu
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
- National Hospital Abuja, Abuja, Nigeria
- Interdisciplinary Biosciences DTP, University of Oxford, Oxford, UK
| | - L Audu
- National Hospital Abuja, Abuja, Nigeria
| | - C Edwin
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A H Yusuf
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A Adeleye
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - A S Mukkadas
- Department of Medical Microbiology Aminu Kano Teaching Hospital, Kano, Nigeria
| | - D Maduekwe
- Wuse General Hospital Abuja, Abuja, Nigeria
| | - S Gambo
- Department of Paediatrics, Murtala Muhammed Specialist Hospital, Kano, Nigeria
| | - J Sani
- Department of Paediatrics Abdullahi Wase Teaching Hospital, Kano, Nigeria
| | - T R Walsh
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - O B Spiller
- Department of Medical Microbiology, Division of Infection and Immunity, Cardiff University, Cardiff, UK
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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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Puljko A, Barišić I, Dekić Rozman S, Križanović S, Babić I, Jelić M, Maravić A, Udiković-Kolić N. Molecular epidemiology and mechanisms of carbapenem and colistin resistance in Klebsiella and other Enterobacterales from treated wastewater in Croatia. ENVIRONMENT INTERNATIONAL 2024; 185:108554. [PMID: 38479059 DOI: 10.1016/j.envint.2024.108554] [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: 12/19/2023] [Revised: 01/30/2024] [Accepted: 03/02/2024] [Indexed: 03/26/2024]
Abstract
Among the most problematic bacteria with clinical relevance are the carbapenem-resistant Enterobacterales (CRE), as there are very limited options for their treatment. Treated wastewater can be a route for the release of these bacteria into the environment and the population. The aim of this study was to isolate CRE from treated wastewater from the Zagreb wastewater treatment plant and to determine their phenotypic and genomic characteristics. A total of 200 suspected CRE were isolated, 148 of which were confirmed as Enterobacterales by MALDI-TOF MS. The predominant species was Klebsiella spp. (n = 47), followed by Citrobacter spp. (n = 40) and Enterobacter cloacae complex (cplx.) (n = 35). All 148 isolates were carbapenemase producers with a multidrug-resistant phenotype. Using multi-locus sequence typing and whole-genome sequencing (WGS), 18 different sequence types were identified among these isolates, 14 of which were associated with human-associated clones. The virulence gene analysis of the sequenced Klebsiella isolates (n = 7) revealed their potential pathogenicity. PCR and WGS showed that the most frequent carbapenemase genes in K. pneumoniae were blaOXA-48 and blaNDM-1, which frequently occurred together, while blaKPC-2 together with blaNDM-1 was mainly detected in K. oxytoca, E. cloacae cplx. and Citrobacter spp. Colistin resistance was observed in 40% of Klebsiella and 57% of Enterobacter isolates. Underlying mechanisms identified by WGS include known and potentially novel intrinsic mechanisms (point mutations in the pmrA/B, phoP/Q, mgrB and crrB genes) and acquired mechanisms (mcr-4.3 gene). The mcr-4.3 gene was identified for the first time in K. pneumoniae and is probably located on the conjugative IncHI1B plasmid. In addition, WGS analysis of 13 isolates revealed various virulence genes and resistance genes to other clinically relevant antibiotics as well as different plasmids possibly associated with carbapenemase genes. Our study demonstrates the important role that treated municipal wastewater plays in harboring and spreading enterobacterial pathogens that are resistant to last-resort antibiotics.
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Affiliation(s)
- Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, Austrian Institute of Technology, Giefinggasse 4, 1210 Vienna, Austria
| | - Svjetlana Dekić Rozman
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivana Babić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Marko Jelić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21 000 Split, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
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9
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Kigen C, Muraya A, Wachira J, Musila L. The first report of the mobile colistin resistance gene, mcr-10.1, in Kenya and a novel mutation in the phoQ gene (S244T) in a colistin-resistant Enterobacter cloacae clinical isolate. Microbiol Spectr 2024; 12:e0185523. [PMID: 38230935 PMCID: PMC10846102 DOI: 10.1128/spectrum.01855-23] [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: 05/03/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
This study describes the identification of the mcr-10.1 gene in a clinical isolate of an ST1 Enterobacter cloacae isolate cultured in 2015 in Kenya. The isolate was multidrug resistant, phenotypically non-susceptible to various antibiotics, including colistin. Whole genome sequence analyses indicated carriage of chromosomally encoded antimicrobial resistance genes and the colistin-resistant gene mcr-10.1 located on a 72-kb plasmid designated pECC011b with an IncFIA(HI1) replicon directly adjacent to tyrosine recombinase gene, xerC, and downstream of an ISKPn26 insertion sequence. Studies have shown that expression of mcr-10.1 may not be sufficient to confer colistin resistance, but a novel non-synonymous mutation (S244T) was identified in the phoQ gene known to influence colistin resistance within lipid modification pathways, which could have complemented the mcr-10.1 resistance mechanism. In silico analysis of the mutant phoQ protein shows the location of the mutation to be at the Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases (HAMP) region, which plays a crucial role in the protein's activity. This study and our previous report of mcr-8 in Klebsiella pneumoniae indicate the presence of mobile mcr genes in the Enterobacterales order of bacteria in Kenya. The study points to the importance of regulation of colistin in the animal industry and enhancing surveillance in both human and animal health to curb the spread of mcr genes and accurately assess the risks posed by these mobile genetic elements in both sectors.IMPORTANCEThis paper reports the detection of new colistin resistance mechanisms in Kenya in a clinical isolate of Enterobacter cloacae in a patient with a healthcare-associated infection. The plasmid-mediated resistance gene, mcr-10.1, and a novel amino acid mutation S244T in the phoQ gene, located in a region of the protein involved in membrane cationic stability contributing to colistin resistance, were detected. Colistin is a critical last-line drug for multidrug-resistant (MDR) gram-negative human infections and is used for treatment and growth promotion in the animal industry. The emergence of the resistance mechanisms points to the potential overuse of colistin in the animal sector in Kenya, which enhances resistance, threatens the utility of colistin, and limits treatment options for MDR infections. This study highlights the need to enhance surveillance of colistin resistance across sectors and strengthen One Health policies that ensure antimicrobial stewardship and implementation of strategies to mitigate the spread of antibiotic resistance.
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Affiliation(s)
- Collins Kigen
- Department of Emerging Infectious Diseases, USAMRD—Africa, Kenya, Nairobi, Kenya
- Department of Emerging Infectious Diseases, Kenya Medical Research Institute, Nairobi, Kenya
| | - Angela Muraya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - James Wachira
- Department of Emerging Infectious Diseases, USAMRD—Africa, Kenya, Nairobi, Kenya
- Department of Emerging Infectious Diseases, Kenya Medical Research Institute, Nairobi, Kenya
| | - Lillian Musila
- Department of Emerging Infectious Diseases, USAMRD—Africa, Kenya, Nairobi, Kenya
- Department of Emerging Infectious Diseases, Kenya Medical Research Institute, Nairobi, Kenya
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10
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Ahmadi Y, Savini F, Mutter N, Barišić I. Application of Antimicrobial Peptides as Diagnostic Biosensors. Anal Chem 2024; 96:256-264. [PMID: 38115687 PMCID: PMC10783173 DOI: 10.1021/acs.analchem.3c03854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
The COVID-19 pandemic has shown how emerging infectious diseases could quickly affect the global health and economy. New pathogens with pandemic potential are also expected to appear soon. Moreover, the large use of antibiotics has led to the development of different so-called "superbugs" capable of escaping all of the current antibiotics. In this context, the early and cost-effective detection of pathogens is crucial to avoid the spreading of new pathogens. Here, we present molecular sensors for the recognition of a broad panel of different bacterial species. The detection is based on the use of bacteria-binding peptides (BBPs) in combination with horseradish peroxidase (HRP). We developed a reliable ELISA-like assay that permits us to study the affinity of different BBPs toward some of the most important bacterial pathogens.
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Affiliation(s)
- Yasaman Ahmadi
- Molecular
Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Filippo Savini
- Molecular
Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Natalie Mutter
- Molecular
Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Ivan Barišić
- Molecular
Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
- Eko
Refugium, Crno Vrelo
2, 47240 Slunj, Croatia
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11
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Seethalakshmi PS, RU VPN, Prabhakaran A, Prathiviraj R, Pamanji R, Kiran GS, Selvin J. Genomic investigation unveils high-risk ESBL producing Enterobacteriaceae within a rural environmental water body. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 6:100216. [PMID: 38274946 PMCID: PMC10809108 DOI: 10.1016/j.crmicr.2023.100216] [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] [Indexed: 01/27/2024] Open
Abstract
Antimicrobial resistance is regarded as a global threat to public health, animals, and the environment, emerging in response to extensive utilization of antimicrobials. The determinants of antimicrobial resistance are transported to susceptible bacterial populations through genetic recombination or through gene transfer, mediated by bacteriophages, plasmids, transposons, and insertion sequences. To determine the penetration of antimicrobial resistance into the bacterial population of the Thiruvandarkoil Lake, a water body located in the rural settings of Puducherry, India, culture-based microbiological and genomic approaches were used. Resistant bacterial isolates obtained from microbiological screening were subjected to whole genome sequencing and the genetic determinants of antimicrobial resistance were identified using in silico genomic tools. Cephalosporin-resistant isolates were found to produce extended spectrum beta lactamases, encoded by blaVEB-6 (in Proteus mirabilis PS01), blaSHV-12 and ompK36 mutation (in Klebsiella quasipneumoniae PS02) and blaSHV-12, blaACT-16, blaCTX-M and blaNDM-1 in (Enterobacter hormaechei PS03). Genes encoding heavy metal resistance, virulence and resistance to detergents were also detected in these resistant isolates. Among ESBL-producing organisms, one mcr-9-positive Enterobacter hormaechei was also identified in this study. To our knowledge, this is the first report of mcr-9 carrying bacterium in the environment in India. This study seeks the immediate attention of policy makers, researchers, government officials and environmental activists in India, to develop surveillance programs to monitor the dissemination of antimicrobial resistance in the environment.
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Affiliation(s)
- P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Puducherry 605014, India
| | | | | | | | - Rajesh Pamanji
- Department of Microbiology, Pondicherry University, Puducherry 605014, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry 605014, India
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12
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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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Donà V, Nordmann P, Kittl S, Schuller S, Bouvier M, Poirel L, Endimiani A, Perreten V. Emergence of OXA-48-producing Enterobacter hormaechei in a Swiss companion animal clinic and their genetic relationship to clinical human isolates. J Antimicrob Chemother 2023; 78:2950-2960. [PMID: 37923369 DOI: 10.1093/jac/dkad337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Enterobacter hormaechei producing the carbapenemase OXA-48 was identified repeatedly in infections in companion animals hospitalized at a Swiss veterinary clinic where OXA-48-producing Klebsiella pneumoniae was previously reported. OBJECTIVES To determine the genetic relatedness of animal and human E. hormaechei strains collected in Switzerland during 2017-22 and their mobile genetic elements. METHODS Hybrid assemblies for phylogenetic and comparative analysis of animal (n = 9) and human (n = 25) isolates were obtained by sequencing with Illumina, PacBio and Oxford Nanopore Technologies. Antimicrobial susceptibility was tested by broth microdilution. RESULTS The animal strains were identified as E. hormaechei subsp. xiangfangensis ST114 (n = 6) and ST418 (n = 2), and E. hormaechei subsp. hoffmannii ST78 (n = 1). Human E. hormaechei belonged to subspecies steigerwaltii (n = 10), xiangfangensis (n = 13), hoffmannii (n = 1) and hormaechei (n = 1), with a heterogeneous ST distribution differing from the animal strains, except for two ST114. Core-gene SNP analysis confirmed the clonality of the animal ST114 and ST418 isolates (0 to 10 SNPs), and close relatedness of animal and human ST114 strains (80-120 SNPs). The strains harboured the blaOXA-48 gene on ca. 63 kb IncL-type plasmids (n = 27); on ca. 72 kb IncL plasmids co-harbouring blaCTX-M-14 (n = 2); and on ca. 150-180 kb IncFIB (n = 4) or hybrid IncFIB/IncL (n = 1) plasmids. The blaOXA-48-harbouring plasmids and the blaDHA-1-carrying ISCR1 element in one animal ST114 and both ST418 clones were likely acquired from previously spreading K. pneumoniae strains. CONCLUSIONS Common ecological niches favour the spread of plasmid-borne carbapenemases among Enterobacterales and the emergence of MDR E. hormaechei clones.
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Affiliation(s)
- Valentina Donà
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland
| | - Patrice Nordmann
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Sonja Kittl
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland
| | - Simone Schuller
- Department of Clinical Veterinary Medicine, University of Bern, Bern, Switzerland
| | - Maxime Bouvier
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Laurent Poirel
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Längassstrasse 122, CH-3012 Bern, Switzerland
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14
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Liang L, Zhong LL, Wang L, Zhou D, Li Y, Li J, Chen Y, Liang W, Wei W, Zhang C, Zhao H, Lyu L, Stoesser N, Doi Y, Bai F, Feng S, Tian GB. A new variant of the colistin resistance gene MCR-1 with co-resistance to β-lactam antibiotics reveals a potential novel antimicrobial peptide. PLoS Biol 2023; 21:e3002433. [PMID: 38091366 PMCID: PMC10786390 DOI: 10.1371/journal.pbio.3002433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 01/12/2024] [Accepted: 11/14/2023] [Indexed: 01/13/2024] Open
Abstract
The emerging and global spread of a novel plasmid-mediated colistin resistance gene, mcr-1, threatens human health. Expression of the MCR-1 protein affects bacterial fitness and this cost correlates with lipid A perturbation. However, the exact molecular mechanism remains unclear. Here, we identified the MCR-1 M6 variant carrying two-point mutations that conferred co-resistance to β-lactam antibiotics. Compared to wild-type (WT) MCR-1, this variant caused severe disturbance in lipid A, resulting in up-regulation of L, D-transpeptidases (LDTs) pathway, which explains co-resistance to β-lactams. Moreover, we show that a lipid A loading pocket is localized at the linker domain of MCR-1 where these 2 mutations are located. This pocket governs colistin resistance and bacterial membrane permeability, and the mutated pocket in M6 enhances the binding affinity towards lipid A. Based on this new information, we also designed synthetic peptides derived from M6 that exhibit broad-spectrum antimicrobial activity, exposing a potential vulnerability that could be exploited for future antimicrobial drug design.
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Affiliation(s)
- Lujie Liang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Lan-Lan Zhong
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Dianrong Zhou
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Yaxin Li
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jiachen Li
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Yong Chen
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Wanfei Liang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Wenjing Wei
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Chenchen Zhang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Hui Zhao
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lingxuan Lyu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Nicole Stoesser
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Yohei Doi
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Siyuan Feng
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Guo-Bao Tian
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
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15
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Luo Q, Wu Y, Bao D, Xu L, Chen H, Yue M, Draz MS, Kong Y, Ruan Z. Genomic epidemiology of mcr carrying multidrug-resistant ST34 Salmonella enterica serovar Typhimurium in a one health context: The evolution of a global menace. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165203. [PMID: 37406695 DOI: 10.1016/j.scitotenv.2023.165203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
The rapid global dissemination of Salmonella enterica sequence type 34 (ST34) has sparked significant concern due to its resistance to critical antimicrobials and its ability to spread across various sectors. In order to investigate the evolution and transmission dynamics of this epidemic clonal lineage, as well as the horizontal transfer of mcr-carrying plasmids within the One Health framework, we conducted a comprehensive genomic epidemiological study. This study focused on the 11 mcr-carrying S. enterica isolates obtained from clinical settings in China, while also considering 2337 publicly available genomes of mcr-carrying S. enterica collected from 20 countries and diverse sources spanning over a 22-year period. Among the mcr-positive Salmonella isolates, ST34 was found to be the predominant lineage, comprising 30.12 % (704/2337) of the total collection. These isolates were identified as either serovar Typhimurium or its monophasic variant, which were obtained from both clinical and non-clinical sources. Phylogeographic analyses traced the global spread of the mcr-carrying ST34 lineage, which was divided into three distinct clusters, with 83.10 % of them carrying mcr-1 or/and mcr-9 genes. Notably, the mcr-1 positive ST34 isolates were primarily found in China (190/298, 63.76 %), with only four from the United States. Conversely, mcr-9 positive ST34 isolates were predominantly identified in the United States (261/293, 89.08 %), while none were observed in China. The mcr-1 positive ST34 isolates was predicted to have originated from clinical sources in United Kingdom, whereas mcr-9 positive ST34 isolates was likely derived from environmental sources in Germany. The most recent common ancestor for mcr-1 and mcr-9 carrying ST34 S. enterica was estimated to have emerged around 1983 and 1951. These findings provided thorough and intuitive insights into the intercontinental spread of mcr-carrying S. enterica ST34 lineage in a One Health context. Ongoing surveillance is crucial for effectively monitoring the worldwide dissemination of this multidrug-resistant high-risk clone.
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Affiliation(s)
- Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Danni Bao
- Department of Clinical Laboratory, Sanmen People's Hospital, Taizhou, China
| | - Linna Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; School of Laboratory Medicine and Biotechnology, Hangzhou Medical College, Hangzhou, China
| | - Hangfei Chen
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meina Yue
- Department of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou, China
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH, USA
| | - Yingying Kong
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 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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16
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Smelikova E, Drevinek P, Nyc O, Brajerova M, Tkadlec J, Krutova M. To screen or not to screen medical students for carriage of multidrug-resistant pathogens? J Hosp Infect 2023; 140:15-23. [PMID: 37478913 DOI: 10.1016/j.jhin.2023.06.028] [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: 02/09/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND The carriage of multidrug-resistant (MDR) pathogens in medical students has not been studied extensively, despite the fact that they are in contact with patients and exposed to a hospital environment. AIM To investigate the intestinal and nasal carriage of MDR pathogens among medical students and its association with their lifestyle and demographic data. METHODS In 2021, first- and final-year medical students were invited to the study. Two rectal swabs were used for detection of extended-spectrum β-lactamase (ESBL)-producing, colistin-, tigecycline- or carbapenem-resistant Gram-negative bacteria and vancomycin-resistant enterococci. Nasal swab was used for Staphylococcus aureus culture. S. aureus isolates were characterized by spa typing; Gram-negative resistant isolates and meticillin-resistant S. aureus (MRSA) were subjected to whole-genome short and/or long sequencing. FINDINGS From 178 students, 80 (44.9%) showed nasal carriage of S. aureus; two isolates were MRSA. In rectal swabs, seven ESBL-producing strains were detected. Sixteen students were colonized by colistin-resistant bacteria, three isolates carried the mcr-1 gene (1.7%). The mcr-9 (10.7%, 19/178) and mcr-10 (2.2%, 4/178) genes were detected by quantitative polymerase chain reaction, but only two colistin-susceptible mcr-10-positive isolates were cultured. The S. aureus nasal carriage was negatively associated with antibiotic and probiotic consumption. S. aureus and colistin-resistant bacteria were detected more frequently among students in contact with livestock. CONCLUSION Medical students can be colonized by (multi)drug-resistant bacteria with no difference between first- and final-year students. The participation of students in self-screening increases their awareness of possible colonization by resistant strains and their potential transmission due to poor hand hygiene.
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Affiliation(s)
- E Smelikova
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - P Drevinek
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - O Nyc
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - M Brajerova
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - J Tkadlec
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - M Krutova
- Department of Medical Microbiology, 2(nd) Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic.
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17
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Zagui GS, Moreira NC, Santos DV, Paschoalato CFPR, Sierra J, Nadal M, Domingo JL, Darini ALC, Andrade LN, Segura-Muñoz SI. Multidrug-resistant Enterobacter spp. in wastewater and surface water: Molecular characterization of β-lactam resistance and metal tolerance genes. ENVIRONMENTAL RESEARCH 2023; 233:116443. [PMID: 37356524 DOI: 10.1016/j.envres.2023.116443] [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: 05/08/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023]
Abstract
Among the ESKAPE group pathogens, Enterobacter spp. is an opportunistic Gram-negative bacillus, widely dispersed in the environment, that causes infections. In the present study, samples of hospital wastewater, raw and treated urban wastewater, as well as surface receiving water, were collected to assess the occurrence of multidrug-resistant (MDR) Enterobacter spp. A molecular characterization of β-lactam antibiotic resistance and metal tolerance genes was performed. According to identification by MALDI-TOF MS, 14 isolates were obtained: 7 E. bugandensis, 5 E. kobei, and 2 E. cloacae. The isolates showed resistance mainly to β-lactam antibiotics, including those used to treat infections caused by MDR bacteria. Multiple antibiotic resistance index was calculated for all isolates. It allowed verify whether sampling points showed a high risk due to antibiotic resistant Enterobacter spp., as well as to determine if the isolates have been in environments with a frequent antibiotic use. Twelve isolates showed β-lactam antibiotic resistance gene, being the blaKPC widely detected. Regarding metal tolerance, 13 isolates showed at least two genes that encode metal tolerance mechanisms. Overall, metal tolerance mechanisms to silver, copper, mercury, arsenic and tellurium were found. New data on metal tolerance mechanisms dispersion and antibiotic-resistance characterization of the E. bugandensis and E. kobei species were here provided. The occurrence of MDR Enterobacter spp. in analyzed samples draws attention to an urgent need to put control measures into practice. It also evidences waterborne spread of clinically important antibiotic-resistant bacteria recognized as critical priority pathogens.
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Affiliation(s)
- Guilherme Sgobbi Zagui
- Water Resources Research Group, Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Brazil; Laboratory of Ecotoxicology and Environmental Parasitology, Ribeirão Preto College of Nursing, University of São Paulo, Brazil.
| | - Natália Columbaro Moreira
- Special Laboratory of Bacteriology and Molecular Epidemiology, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil
| | - Danilo Vitorino Santos
- Chemical Residue Center, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil
| | | | - Jordi Sierra
- Faculty of Pharmacy, Universitat de Barcelona, Joan XXIII s/n Avenue, 08028, Barcelona, Catalonia, Spain; Laboratory of Toxicology and Environmental Health, School of Medicine, IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201, Reus, Catalonia, Spain
| | - Martí Nadal
- Laboratory of Toxicology and Environmental Health, School of Medicine, IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201, Reus, Catalonia, Spain
| | - José L Domingo
- Laboratory of Toxicology and Environmental Health, School of Medicine, IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201, Reus, Catalonia, Spain
| | - Ana Lúcia Costa Darini
- Special Laboratory of Bacteriology and Molecular Epidemiology, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil
| | - Leonardo Neves Andrade
- Research Laboratory in Bacterial Resistance and Virulence, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Brazil
| | - Susana Inés Segura-Muñoz
- Laboratory of Ecotoxicology and Environmental Parasitology, Ribeirão Preto College of Nursing, University of São Paulo, Brazil.
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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: 0] [Impact Index Per Article: 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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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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20
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Fukuzawa S, Sato T, Aoki K, Yamamoto S, Ogasawara N, Nakajima C, Suzuki Y, Horiuchi M, Takahashi S, Yokota SI. High prevalence of colistin heteroresistance in specific species and lineages of Enterobacter cloacae complex derived from human clinical specimens. Ann Clin Microbiol Antimicrob 2023; 22:60. [PMID: 37454128 DOI: 10.1186/s12941-023-00610-1] [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: 04/14/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Colistin (CST) is a last-line drug for multidrug-resistant Gram-negative bacterial infections. CST-heteroresistant Enterobacter cloacae complex (ECC) has been isolated. However, integrated analysis of epidemiology and resistance mechanisms based on the complete ECC species identification has not been performed. METHODS Clinical isolates identified as "E. cloacae complex" by MALDI-TOF MS Biotyper Compass in a university hospital in Japan were analyzed. Minimum inhibitory concentrations of CST were determined by the broth microdilution method. The population analysis profiling (PAP) was performed for detecting the heteroresistant phenotype. The heat shock protein 60 (hsp60) cluster was determined from its partial nucleotide sequence. From the data of whole-genome sequencing, average nucleotide identity (ANI) for determining ECC species, multilocus sequence type, core genome single-nucleotide-polymorphism-based phylogenetic analysis were performed. phoPQ-, eptA-, and arnT-deleted mutants were established to evaluate the mechanism underlying colistin heteroresistance. The arnT mRNA expression levels were determined by reverse transcription quantitative PCR. RESULTS Thirty-eight CST-resistant isolates, all of which exhibited the heteroresistant phenotype by PAP, were found from 138 ECC clinical isolates (27.5%). The prevalence of CST-resistant isolates did not significantly differ among the origin of specimens (29.0%, 27.8%, and 20.2% for respiratory, urine, and blood specimens, respectively). hsp60 clusters, core genome phylogeny, and ANI revealed that the CST-heteroresistant isolates were found in all or most of Enterobacter roggenkampii (hsp60 cluster IV), Enterobacter kobei (cluster II), Enterobacter chuandaensis (clusters III and IX), and Enterobacter cloacae subspecies (clusters XI and XII). No heteroresistant isolates were found in Enterobacter hormaechei subspecies (clusters VIII, VI, and III) and Enterobacter ludwigii (cluster V). CST-induced mRNA upregulation of arnT, which encodes 4-amino-4-deoxy-L-arabinose transferase, was observed in the CST-heteroresistant isolates, and it is mediated by phoPQ pathway. Isolates possessing mcr-9 and mcr-10 (3.6% and 5.6% of total ECC isolates, respectively) exhibited similar CST susceptibility and PAP compared with mcr-negative isolates. CONCLUSIONS Significant prevalence (approximately 28%) of CST heteroresistance is observed in ECC clinical isolates, and they are accumulated in specific species and lineages. Heteroresistance is occurred by upregulation of arnT mRNA induced by CST. Acquisition of mcr genes contributes less to CST resistance in ECC.
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Affiliation(s)
- Shota Fukuzawa
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
- Clinical Laboratory, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan.
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan.
- One Health Research Center, Hokkaido University, Sapporo, Japan.
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Soh Yamamoto
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriko Ogasawara
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University, International Institute for Zoonosis Control, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University, International Institute for Zoonosis Control, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Motohiro Horiuchi
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Satoshi Takahashi
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
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21
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Zeng H, Tan Y, Su J, Gao F, Lei T, Liang B. Co-occurrence of blaNDM-1, rmtC, and mcr-9 in multidrug-resistant Enterobacter kobei strain isolated from an infant with urinary tract infection. J Glob Antimicrob Resist 2023; 33:221-226. [PMID: 37062506 DOI: 10.1016/j.jgar.2023.03.011] [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: 08/23/2022] [Revised: 11/01/2022] [Accepted: 03/27/2023] [Indexed: 04/18/2023] Open
Abstract
OBJECTIVES The co-emergence of mcr and carbapenem resistance genes in Gram-negative bacteria is a serious problem. This study aims to clarify the genetic characteristic of one novel multidrug-resistant Enterobacter kobei EC1382 with mcr-9 causing urinary tract inflammation in an infant. METHODS Antimicrobial drug susceptibility testing was performed for this isolate using the broth microdilution method. Whole-genome sequencing was performed using the Illumina PacBio RS II platform and HiSeq platform, and the antimicrobial resistance genes, mobile elements, and plasmid replicon types were identified. Conjugation analysis was performed using Escherichia coli C600 as recipients. RESULTS Enterobacter kobei EC1382 was resistant to carbapenem, aminoglycoside, and cephalosporin. Twenty-five antimicrobial resistance genes were identified, including genes conferring resistance to carbapenem (blaNDM-1), colistin (mcr-9), and aminoglycosides (rmtC). The blaNDM-1 gene, accompanied by bleMBL and rmtC located downstream of an ISCR14 element, was detected in the IncFII(Yp) type plasmid pEC1382-2. Interestingly, although E. kobei EC1382 was susceptible to colistin, it had three identical mcr-9 genes (two in the chromosome and one in the IncHI2-type plasmid pEC1382-1). The backbone (∼12.2-kb genetic fragment) of these mcr-9 (flanked by IS903B and IS481-IS26) regions were conserved in this strain, and they were found to be present in various bacteria as three types, implying a silent distribution. CONCLUSIONS To the best of our knowledge, this is the first study to demonstrate the coexistence of blaNDM-1, rmtC, and mcr-9 in E. kobei. The silent prevalence of mcr-9 in bacteria may be a threat to public health.
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Affiliation(s)
- Haiyan Zeng
- School of Biomedicine and Pharmaceutical Science, Guangdong Univeristy of Technology, Guangzhou, China
| | - Yujing Tan
- School of Biomedicine and Pharmaceutical Science, Guangdong Univeristy of Technology, Guangzhou, China
| | - Jianhui Su
- School of Biomedicine and Pharmaceutical Science, Guangdong Univeristy of Technology, Guangzhou, China
| | - Fei Gao
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Tao Lei
- School of Public Health, Xiangnan University, Chenzhou, China.
| | - Bingshao Liang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China.
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Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 190] [Impact Index Per Article: 190.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
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Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
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23
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Guarneri F, Bertasio C, Romeo C, Formenti N, Scali F, Parisio G, Canziani S, Boifava C, Guadagno F, Boniotti MB, Alborali GL. First Detection of mcr-9 in a Multidrug-Resistant Escherichia coli of Animal Origin in Italy Is Not Related to Colistin Usage on a Pig Farm. Antibiotics (Basel) 2023; 12:antibiotics12040689. [PMID: 37107051 PMCID: PMC10134971 DOI: 10.3390/antibiotics12040689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
The emergence of colistin resistance raises growing concerns because of its use as a last-resort antimicrobial for the treatment of severe gram-negative bacterial infections in humans. Plasmid-borne mobile colistin resistance genes (mcr) are particularly worrisome due to their high propensity to spread. An mcr-9-positive Escherichia coli was isolated from a piglet in Italy, representing the first isolation of this gene from an E. coli of animal origin in the country. Whole genome sequencing (WGS) revealed that mcr-9 was borne by an IncHI2 plasmid carrying several other resistance genes. The strain was indeed phenotypically resistant to six different antimicrobial classes, including 3rd and 4th generation cephalosporins. Despite the presence of mcr-9, the isolate was susceptible to colistin, probably because of a genetic background unfavourable to mcr-9 expression. The lack of colistin resistance, coupled with the fact that the farm of origin had not used colistin in years, suggests that mcr-9 in such a multidrug-resistant strain can be maintained thanks to the co-selection of neighbouring resistance genes, following usage of different antimicrobials. Our findings highlight how a comprehensive approach, integrating phenotypical testing, targeted PCR, WGS-based techniques, and information on antimicrobial usage is crucial to shed light on antimicrobial resistance.
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Affiliation(s)
- Flavia Guarneri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Cristina Bertasio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Federico Scali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Giovanni Parisio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Sabrina Canziani
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Chiara Boifava
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Federica Guadagno
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna—IZSLER, v. Bianchi 9, 25124 Brescia, Italy
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Phenotypic and Genomic Characterization of ST133 Siderophore-Encoding Extensively Drug-Resistant Enterobacter hormaechei. Antimicrob Agents Chemother 2023; 67:e0173722. [PMID: 36920213 PMCID: PMC10112160 DOI: 10.1128/aac.01737-22] [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: 03/16/2023] Open
Abstract
We identified an ST133 extensively drug-resistant Enterobacter hormaechei, C210017, with increased virulence in the Galleria mellonella infection model. Genomic analysis suggested it carried antibiotic resistance genes blaKPC-2 and mcr-9.1, and genes iutAiucABCD and iroBCDEN encoding the virulence factor, siderophores. Comparative genomics of C210017 and the 178 ST133 E. hormaechei strains in the database suggested they all belonged to serotype O3 and most strains (77.5%) carried the IncHI2 superplasmids associated with the resistance, virulence, and adaptation of the host strain.
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Carson DV, Patiño M, Elashal HE, Cartagena AJ, Zhang Y, Whitley ME, So L, Kayser-Browne AK, Earl AM, Bhattacharyya RP, Link AJ. Cloacaenodin, an Antimicrobial Lasso Peptide with Activity against Enterobacter. ACS Infect Dis 2023; 9:111-121. [PMID: 36519726 PMCID: PMC10038104 DOI: 10.1021/acsinfecdis.2c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Using genome mining and heterologous expression, we report the discovery and production of a new antimicrobial lasso peptide from species related to the Enterobacter cloacae complex. Using NMR and mass spectrometric analysis, we show that this lasso peptide, named cloacaenodin, employs a threaded lasso fold which imparts proteolytic resistance that its unthreaded counterpart lacks. Cloacaenodin has selective, low micromolar, antimicrobial activity against species related to the E. cloacae complex, including species implicated in nosocomial infections and against clinical isolates of carbapenem-resistant Enterobacterales. We further used site-directed mutagenesis to probe the importance of specific residues to the peptide's biosynthesis, stability, and bioactivity.
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Affiliation(s)
- Drew V. Carson
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Monica Patiño
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Hader E. Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexis Jaramillo Cartagena
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Yi Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Megan E. Whitley
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Larry So
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Angelo K. Kayser-Browne
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Roby P. Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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26
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Modi SK, Gaur S, Sengupta M, Singh MS. Mechanistic insights into nanoparticle surface-bacterial membrane interactions in overcoming antibiotic resistance. Front Microbiol 2023; 14:1135579. [PMID: 37152753 PMCID: PMC10160668 DOI: 10.3389/fmicb.2023.1135579] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/30/2023] [Indexed: 05/09/2023] Open
Abstract
Antimicrobial Resistance (AMR) raises a serious concern as it contributes to the global mortality by 5 million deaths per year. The overall impact pertaining to significant membrane changes, through broad spectrum drugs have rendered the bacteria resistant over the years. The economic expenditure due to increasing drug resistance poses a global burden on healthcare community and must be dealt with immediate effect. Nanoparticles (NP) have demonstrated inherent therapeutic potential or can serve as nanocarriers of antibiotics against multidrug resistant (MDR) pathogens. These carriers can mask the antibiotics and help evade the resistance mechanism of the bacteria. The targeted delivery can be fine-tuned through surface functionalization of Nanocarriers using aptamers, antibodies etc. This review covers various molecular mechanisms acquired by resistant bacteria towards membrane modification. Mechanistic insight on 'NP surface-bacterial membrane' interactions are crucial in deciding the role of NP as therapeutic. Finally, we highlight the potential accessible membrane targets for designing smart surface-functionalized nanocarriers which can act as bacteria-targeted robots over the existing clinically available antibiotics. As the bacterial strains around us continue to evolve into resistant versions, nanomedicine can offer promising and alternative tools in overcoming AMR.
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Affiliation(s)
- Suraj Kumar Modi
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
- Centre of Excellence for Nanosensors and Nanomedicine, Bennett University, Greater Noida, Uttar Pradesh, India
| | - Smriti Gaur
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
| | - Mrittika Sengupta
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
- Centre of Excellence for Nanosensors and Nanomedicine, Bennett University, Greater Noida, Uttar Pradesh, India
- Mrittika Sengupta, ;
| | - Manu Smriti Singh
- Department of Biotechnology, Bennett University, Greater Noida, Uttar Pradesh, India
- Centre of Excellence for Nanosensors and Nanomedicine, Bennett University, Greater Noida, Uttar Pradesh, India
- *Correspondence: Manu Smriti Singh, ;
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Zelendova M, Papagiannitsis CC, Sismova P, Medvecky M, Pomorska K, Palkovicova J, Nesporova K, Jakubu V, Jamborova I, Zemlickova H, Dolejska M. Plasmid-mediated colistin resistance among human clinical Enterobacterales isolates: national surveillance in the Czech Republic. Front Microbiol 2023; 14:1147846. [PMID: 37180238 PMCID: PMC10174314 DOI: 10.3389/fmicb.2023.1147846] [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: 01/19/2023] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
The occurrence of colistin resistance has increased rapidly among Enterobacterales around the world. We performed a national survey of plasmid-mediated colistin resistance in human clinical isolates through a retrospective analysis of samples from 2009 to 2017 and a prospective sampling in 2018-2020. The aim of this study was to identify and characterize isolates with mcr genes from various regions of the Czech Republic using whole genome sequencing (WGS). Of all 1932 colistin-resistant isolates analyzed, 73 (3.8%) were positive for mcr genes. Most isolates carried mcr-1 (48/73) and were identified as Escherichia coli (n = 44) and Klebsiella pneumoniae (n = 4) of various sequence types (ST). Twenty-five isolates, including Enterobacter spp. (n = 24) and Citrobacter freundii (n = 1) carrying the mcr-9 gene were detected; three of them (Enterobacter kobei ST54) co-harbored the mcr-4 and mcr-9 genes. Multi-drug resistance phenotype was a common feature of mcr isolates and 14% (10/73) isolates also co-harbored clinically important beta-lactamases, including two isolates with carbapenemases KPC-2 and OXA-48. Phylogenetic analysis of E. coli ST744, the dominant genotype in this study, with the global collection showed Czech isolates belonged to two major clades, one containing isolates from Europe, while the second composed of isolates from diverse geographical areas. The mcr-1 gene was carried by IncX4 (34/73, 47%), IncHI2/ST4 (6/73, 8%) and IncI2 (8/73, 11%) plasmid groups. Small plasmids belonging to the ColE10 group were associated with mcr-4 in three isolates, while mcr-9 was carried by IncHI2/ST1 plasmids (4/73, 5%) or the chromosome (18/73, 25%). We showed an overall low level of occurrence of mcr genes in colistin-resistant bacteria from human clinical samples in the Czech Republic.
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Affiliation(s)
- Marketa Zelendova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | | | - Petra Sismova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Matej Medvecky
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czechia
| | - Katarina Pomorska
- NRL for ATB, The National Institute of Public Health, Centre for Epidemiology and Microbiology, Prague, Czechia
| | - Jana Palkovicova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | | | - Vladislav Jakubu
- NRL for ATB, The National Institute of Public Health, Centre for Epidemiology and Microbiology, Prague, Czechia
- Department of Microbiology, 3rd Faculty of Medicine, Kralovske Vinohrady University Hospital and National Institute of Public Health, Charles University, Prague, Czechia
| | - Ivana Jamborova
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Helena Zemlickova
- NRL for ATB, The National Institute of Public Health, Centre for Epidemiology and Microbiology, Prague, Czechia
- Department of Microbiology, 3rd Faculty of Medicine, Kralovske Vinohrady University Hospital and National Institute of Public Health, Charles University, Prague, Czechia
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czechia
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Pilsen, Czechia
- *Correspondence: Monika Dolejska,
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28
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Li G, Li X, Wu Y, Xu J, He F. Genomic Insights into the Colistin Resistant mcr-Carrying Escherichia coli Strains in a Tertiary Hospital in China. Antibiotics (Basel) 2022; 11:1522. [PMID: 36358177 PMCID: PMC9686615 DOI: 10.3390/antibiotics11111522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 08/27/2023] Open
Abstract
Colistin is an important antimicrobial agent in the treatment of infections caused by multidrug resistant (MDR) Gram-negative bacteria. The horizontal transfer of mobile colistin resistance gene (mcr) poses a major threat to the public health worldwide. In this study, a total of thirteen mcr-carrying Escherichia coli (MCREC) strains were recovered from a tertiary hospital in Zhejiang, China, between 2016 and 2019. The minimum inhibitory concentration (MIC) of antimicrobial agents, epidemiological characteristics, and transmission dynamics of mcr-carrying isolates were analyzed using antimicrobial susceptibility testing, whole-genome sequencing, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), and southern blotting analysis. All strains were discovered to be resistant to colistin, and the majority displayed MDR phenotype. However, none of the 13 MCREC strains were resistant to carbapenems. The 13 MCREC isolates were divided into 10 different STs, including ST744, ST156, ST453, ST410, ST57, ST131, ST7034, ST2599, ST457, and ST13239, in which ST13239 was discovered for the first time. Based on core genome single nucleotide polymorphism (cgSNP) analysis, no clear epidemiological link was discovered in these strains with the exception of EC2118 and EC3807, which differ by just one SNP. A total of 35 antimicrobial resistance genes which can be divided into 14 classes were identified from the 13 MCREC isolates. According to S1-PFGE and southern blotting analyses, all 13 MCREC strains had plasmid-mediated mcr-1, and nine of them carried conjugative plasmids. In conclusion, our study revealed the emergence and dissemination of colistin-resistant E. coli isolates carrying mcr-1 in a Chinese hospital, which poses a potential risk to anti-infective therapy. More efforts should be taken to monitor the prevalence of mcr-1-carrying bacteria in China.
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Affiliation(s)
- Guoli Li
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Xinyang Li
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Juan Xu
- School of Public Health, Hangzhou Medical College, Hangzhou 310013, China
| | - Fang He
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou 310014, China
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29
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Emergence and Transmission of Plasmid-Mediated Mobile Colistin Resistance Gene mcr-10 in Humans and Companion Animals. Microbiol Spectr 2022; 10:e0209722. [PMID: 36000890 PMCID: PMC9603504 DOI: 10.1128/spectrum.02097-22] [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] [Indexed: 12/31/2022] Open
Abstract
Mobile colistin resistance (mcr) genes mediated by plasmids have widely disseminated throughout the world. Recently, 10 mcr genes (mcr-1 to mcr-10) and a large number of variants have been identified in more than 60 countries. However, only a few instances of Enterobacter cloacae complex (ECC) bearing mcr-10 from animal origin have been reported globally. The aim of this study was to fill a knowledge gap in mcr-10-positive ECC of animal origin and analyze the potential transmission trend and different characteristics between human and companion animal isolates. The mcr-10 gene was identified on a self-transmissible plasmid in the human isolate and non-transmissible plasmids in other three animal strains. mcr-10 was adjacent to a XerC-type tyrosine recombinase-gene, and various insertion sequences were located on the downstream of core conservative structure xerC-mcr-10, thus indicating this region might be a candidate for insertions of mobile genetic elements and mcr-10 might be mobilized by IS-mediated mechanisms. Moreover, phylogenetic analysis found that mcr-10-positive isolates were mainly distributed in the clade of Enterobacter roggenkampii, exhibiting significant species specificity. These findings indicated that mcr-10 has emerged among Enterobacter spp. within humans and companion animals, highlighting that the importance of taking effective control measures to monitor the dissemination and evolution of mcr genes. IMPORTANCE Colistin was considered as the last-resort drug against severe clinical infections caused by multidrug-resistant Gram-negative pathogens. Mobile colistin resistance (mcr) genes and its variants carried by plasmids have been reported in diverse niches in recent years, and yet few studies reported carriage of mcr-10 in ECC strains of companion animal origin. How plasmid-borne mcr-10 transmitted in opportunistic pathogens and different characteristics of mcr-10-bearing strains isolated from humans and companion animals are not well understood. In this study, we discovered mcr-10-harboring strains in multidrug-resistant ECC isolates of companion animal origin for the first time and conducted a comprehensive analysis of the genetic environment of mcr-10 from multiple countries around the world, providing the potential basis for formulating control measures to slow down the spread of colistin resistance.
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30
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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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31
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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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Xu T, Xue CX, Chen Y, Huang J, Wu W, Lu Y, Huang Q, Chen D, Zhou K. Frequent convergence of mcr-9 and carbapenemase genes in Enterobacter cloacae complex driven by epidemic plasmids and host incompatibility. Emerg Microbes Infect 2022; 11:1959-1972. [PMID: 35848148 PMCID: PMC9359198 DOI: 10.1080/22221751.2022.2103456] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Convergence of mcr and carbapenemase genes has been sporadically detected in Enterobacter cloacae complex (ECC) with an upward trend. However, the state of the epidemic and underlying mechanism of such convergence has been poorly understood. In this study, the co-occurrence of MCR and carbapenemases was systematically analyzed in 230 clinical ECC isolates collected between 2000 and 2018 together with a global dataset consisting of 3,559 ECC genomes compiled from GenBank. We identified 48 mcr-9/mcr-10-positive isolates (MCR-ECC) (20.9%) in our collection, and a comparable ratio of MCR-ECC (720/3559, 20.2%) was detected in the global dataset. A high prevalence of carbapenemase-producing MCR-ECC (MCR-CREC) was further identified in the MCR-ECC of both datasets (16/48, 33.3%; 388/720, 53.9%), demonstrating a frequent convergence of mcr-9/10 and carbapenemase genes in ECC worldwide. An epidemic IncHI2/2A plasmid with a highly conserved backbone was identified and largely contributed to the dissemination of mcr-9 in ECC worldwide. A highly conserved IncX3-type NDM-1-carrying plasmid and IncN-type IMP-4-carrying plasmid were additionally detected in MCR-CREC isolated in China. Our surveillance data showed that MCR-CREC emerged (in 2013) much later than MCR-ECC (in 2000), indicating that MCR-CREC could be derived from MCR-ECC by additional captures of carbapenemase-encoding plasmids. Tests of plasmid stability and incompatibility showed that the mcr-9/mcr-10-encoding plasmids with the NDM-1-encoding plasmids stably remained in ECC but incompatible in Escherichia coli, suggesting that the convergence was host-dependent. The findings extend our concern on the convergence of resistance to the last resort antibiotics and highlight the necessity of continued surveillance in the future.
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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
| | - Chun-Xu Xue
- 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
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, Jiangsu, China
| | - Junxi Huang
- 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
| | - Weiyuan Wu
- Clinical Laboratory, 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
| | - Yuemei Lu
- Clinical Laboratory, 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
| | - Qiuhui Huang
- 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
| | - Dandan Chen
- 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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Zaitsev SS, Khizhnyakova MA, Feodorova VA. First Case Report of Detection of Multidrug-Resistant Enterobacter hormaechei in Clinical Sample from an Aborted Ruminant. Microorganisms 2022; 10:1036. [PMID: 35630478 PMCID: PMC9145581 DOI: 10.3390/microorganisms10051036] [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: 03/26/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/16/2022] Open
Abstract
The emergence of multidrug-resistant (MDR) bacterial strains is one of the significant global challenges with regard to bacterial drug-resistance control. Enterobacter hormaechei organisms belong to the Enterobacter cloacae complex (ECC) and are commonly recognized as causative agents for hospital infections. Recently, a few E. hormaechei MDR strains associated with infection in piglets, calves, and a fox were reported, highlighting the important role of animals and livestock in the emergence and spread of antimicrobial resistance. In this study, the vaginal swab sample from a 5-year-old cow with multiple anamnestic infectious abortions was carefully investigated. The animal was unresponsive to antibiotic therapy recommended by the veterinarian. The MDR bacterial strain isolated from the bovine sample, designated as the Saratov_2019, belonged to Enterobacter hormaechei. The genome-based phylogenetic analysis identified the isolate to be Enterobacter hormaechei subsp. xiangfangensis. The genome of the Saratov_2019 contained a 6364 bp plasmid. Importantly, we revealed the novel sequence type ST1416 and 13 MDR genes correlating with the MDR phenotype in only the chromosome but not the plasmid. These findings indicate that the potential spread of this strain may pose a threat for both animal and human health. The data obtained here support the notion of the important role of livestock in the emergence and spread of antimicrobial resistance, promoting careful investigation of the MDR spectra for livestock-related bacterial isolates. To the best of our knowledge, this is the first report on the association of E. hormaechei subsp. xiangfangensis with the infection of the reproductive system in cattle.
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Affiliation(s)
| | | | - Valentina A. Feodorova
- Federal Research Center for Virology and Microbiology, Branch in Saratov, 410028 Saratov, Russia; (S.S.Z.); (M.A.K.)
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