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Huang J, Lv C, Li M, Rahman T, Chang YF, Guo X, Song Z, Zhao Y, Li Q, Ni P, Zhu Y. Carbapenem-resistant Escherichia coli exhibit diverse spatiotemporal epidemiological characteristics across the globe. Commun Biol 2024; 7:51. [PMID: 38184739 PMCID: PMC10771496 DOI: 10.1038/s42003-023-05745-7] [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: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
Carbapenem-resistant Escherichia coli (CREC) poses a severe global public health risk. This study reveals the worldwide geographic spreading patterns and spatiotemporal distribution characteristics of resistance genes in 7918 CREC isolates belonging to 497 sequence types (ST) and originating from 75 countries. In the last decade, there has been a transition in the prevailing STs from highly virulent ST131 and ST38 to higher antibiotic-resistant ST410 and ST167. The rise of multi-drug resistant strains of CREC carrying plasmids with extended-spectrum beta-lactamase (ESBL) resistance genes could be attributed to three important instances of host-switching events. The spread of CREC was associated with the changing trends in blaNDM-5, blaKPC-2, and blaOXA-48, as well as the plasmids IncFI, IncFII, and IncI. There were intercontinental geographic transfers of major CREC strains. Various crucial transmission hubs and patterns have been identified for ST131 in the United Kingdom, Italy, the United States, and China, ST167 in India, France, Egypt, and the United States, and ST410 in Thailand, Israel, the United Kingdom, France, and the United States. This work is valuable in managing CREC infections and preventing CREC occurrence and transmission inside healthcare settings and among diverse hosts.
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Affiliation(s)
- Jiewen Huang
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Lv
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Li
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Xiaokui Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Song
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanan Zhao
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Peihua Ni
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yongzhang Zhu
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Biswas U, Das S, Barik M, Mallick A. Situation Report on mcr-Carrying Colistin-Resistant Clones of Enterobacterales: A Global Update Through Human-Animal-Environment Interfaces. Curr Microbiol 2023; 81:12. [PMID: 37989899 DOI: 10.1007/s00284-023-03521-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 11/23/2023]
Abstract
In the twenty-first century, antibiotic resistance (ABR) is one of the acute medical emergencies around the globe, overwhelming human-animal-environmental interfaces. Hit-or-mis use of antibiotics exacerbates the crisis of ABR, dispersing transferable resistance traits and challenging treatment regimens based on life-saving drugs such as colistin. Colistin is the highest priority critically important antimicrobials for human medicine, but its long use as a growth promoter in animal husbandry reduces clinical efficacy. Since 2015, the emergence and spread of mobile colistin resistance (mcr)-carrying colistin-resistant clones of Enterobacterales have been markedly sustained in both humans and animals, especially in developing countries. Hospital and community transmissions of mcr clones pose a high risk for infection prevention and outbreaks at the national and international levels. Several public health and limited one health studies have highlighted the genomic insights of mcr clones, clarifying the chromosomal sequence types (STs) and plasmid incompatibility (Inc) types. But this information is segregated into humans and animals, and rarely are environmental sectors complicating the understanding of possibly intercontinental and sectoral transmission of these clones. India is the hotspot for superbugs, including mcr-carrying colistin-resistant isolates that threaten cross-border transmission. The current review provided an up-to-date worldwide scenario of mcr-carrying STs and plasmid Inc types among the Gram-negative bacilli of Enterobacterales across human-animal-environmental interfaces and correlated with the available information from India.
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Affiliation(s)
- Urmy Biswas
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Surojit Das
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Mili Barik
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Abhi Mallick
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
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Bhusal B, Yadav B, Dawadi P, Rijal KR, Ghimire P, Banjara MR. Multi-drug Resistance, β-Lactamases Production, and Coexistence of bla NDM-1 and mcr-1 in Escherichia coli Clinical Isolates From a Referral Hospital in Kathmandu, Nepal. Microbiol Insights 2023; 16:11786361231152220. [PMID: 36741474 PMCID: PMC9893399 DOI: 10.1177/11786361231152220] [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: 12/07/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023] Open
Abstract
The ability of pathogenic Escherichia coli to produce carbapenemase enzymes is a characteristic that allows them to resist various antibiotics, including last-resort antibiotics like colistin and carbapenem. Our objectives were to identify rapidly developing antibiotic resistance (AR), assess β-lactamases production, and detect mcr-1 and bla NDM-1 genes in the isolates. A prospective cross-sectional study was carried out in a referral hospital located in Kathmandu from November 2019 to December 2020 using standard laboratory and molecular protocols. Among 77 total E. coli isolates, 64 (83.1%) of them were categorized as MDR. Phenotypically 13 (20.3%) colistin-resistant, 30 (46.9%) ESBL and 8 (12.5%) AmpC producers, and 5 (7.8%) ESBL/AmpC co-producers were distributed among MDR-E. coli. Minimum inhibitory concentrations (MIC) against the majority of MDR isolates were exhibited at 1 g/L. Of these 77 E. coli isolates, 24 (31.2%) were carbapenem-resistant. Among these carbapenem-resistant bacteria, 11 (45.9%) isolates were reported to be colistin-resistant, while 15 (62.5%) and 2 (8.3%) were MBL and KPC producers, respectively. Out of 15 MBL producers, 6 (40%) harbored bla NDM-1, and 8 (61.5%) out of 13 colistin-resistant pathogens possessed mcr-1. The resistance by colistin- and carbapenem were statistically associated (P < .001). However, only 2 (18.2%) of the co-resistant bacteria were found to have both genes. Our study revealed the highly prevalent MDR and the carbapenem-resistant E. coli and emphasized that the pathogens possess a wide range of capabilities to synthesize β-lactamases. These findings could assist to expand the understanding of AR in terms of enzyme production.
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Affiliation(s)
- Bhimarjun Bhusal
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal
| | - Bindeshwar Yadav
- Shahid Gangalal National Heart Center,
Kathmandu, Bagmati, Nepal
| | - Prabin Dawadi
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal
| | - Komal Raj Rijal
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal
| | - Prakash Ghimire
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal
| | - Megha Raj Banjara
- Central Department of Microbiology,
Tribhuvan University, Kathmandu, Bagmati, Nepal,Megha Raj Banjara, Central Department of
Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Bagmati 44618, Nepal.
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Zhao W, Li W, Du XD, Yao H. Hybrid IncFIA/FIB/FIC(FII) plasmid co-carrying bla NDM-5 and fosA3 from an Escherichia coli ST117 strain of retail chicken. Int J Food Microbiol 2022; 382:109914. [PMID: 36088664 DOI: 10.1016/j.ijfoodmicro.2022.109914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
Abstract
Carbapenems and fosfomycin are important antibiotics used to treat Enterobacteriaceae-associated infections. This study aimed to characterize the co-resistance and co-dissemination mechanism of carbapenem and fosfomycin resistance in an Escherichia coli ST117 strain isolated from retail chicken meat. Antimicrobial susceptibility testing showed that an E. coli CS18F strain had a multidrug resistance profile, including carbapenem and fosfomycin resistance. The presence of blaNDM-5 and fosA3 genes was confirmed by PCR and Sanger sequencing. The blaNDM-5 and fosA3 genes were successfully transferred to the recipient strain E. coli J53 via conjugation, and the transconjugants had elevated minimum inhibitory concentrations (MICs) for meropenem and fosfomycin. Whole genome sequencing (WGS) of E. coli CS18F revealed that blaNDM-5 and fosA3 were colocalized on an IncFIA/FIB/FIC(FII) type plasmid of 189,141 bp, which was designated as pCS18F-NDM-Fos. A novel structure with five IS26 sequences flanking the multiple drug resistance region (MDRR) was identified, and three copies of IS26 were found to be flanked blaNDM-5, fosA3, dfrA12, aadA2, and sul1. Three types of translocation units (TUs) were identified by PCR, containing either the resistance gene blaNDM-5 and an IS26 sequence, fosA3, and an IS26 sequence, or both, indicating their potential co-transfer via TUs. Thus, this is an unprecedented report of the presence of a plasmid co-carrying blaNDM-5 and fosA3 and TUs potentially mediating their simultaneous transfer.
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Affiliation(s)
- Wenbo Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Wenjun Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China.
| | - Hong Yao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China.
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Molecular Characteristics of Antimicrobial Resistance and Virulence in Klebsiella pneumoniae Strains Isolated from Goose Farms in Hainan, China. Appl Environ Microbiol 2022; 88:e0245721. [PMID: 35389252 DOI: 10.1128/aem.02457-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We retrospectively investigated 326 samples that were collected from goose farms in Hainan Province, China, in 2017. A total of 33 carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates were identified from 326 samples, and the 33 CRKP isolates were characterized based on whole-genome sequencing (WGS) data from the Illumina and Oxford Nanopore Technologies (ONT) platforms. All of these 33 CRKP isolates possessed blaNDM-5, and a single isolate coharbored mcr-1 and blaNDM-5, while 4 isolates carried multiple virulence and metal tolerance gene clusters. One CRKP strain (CMG-35-2) was selected for long sequence reading. A hybrid plasmid carrying the virulence, resistance, and metal resistance gene in the strain was found. It possessed 2 backbones [IncFIB(K)-IncFII(K)] within a single plasmid that were closely related to K. pneumoniae plasmids from a human-associated habitat in the United States and from a human isolate in Hong Kong. A mouse abdominal infection model indicated that that strain was of the moderate virulence phenotype. This study revealed that K. pneumoniae on goose farms is an important reservoir for blaNDM-5 and these bacteria are represented by a diversity of sequence types. The heterozygous multiple drug resistance genes carried on plasmids highlighted the genetic complexity of CRKP and the urgent need for continued active surveillance. IMPORTANCE CRKP is one of the most important pathogens, which can cause infection not only in humans but also in waterfowl. The discovery of blaNDM-5-producing K. pneumoniae in waterfowl farms in recent years suggests that waterfowl are an important reservoir for blaNDM-5-producing Enterobacteriaceae. However, there are few studies on the spread of blaNDM-5-producing bacteria in waterfowl farms. Our study showed that the IncX3 plasmid carrying blaNDM-5 in goose farms is widely present in K. pneumoniae isolates and a large number of resistance genes are accumulated in it. We found a transferable IncFIB-FII hybrid plasmid that combines virulence, resistance, and metal resistance genes, which allow transfer of these traits between bacteria in different regions. The results of this study contribute to a better understanding of the prevalence and transmission of carbapenem-resistant K. pneumoniae in goose farms.
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Dadashi M, Sameni F, Bostanshirin N, Yaslianifard S, Khosravi-Dehaghi N, Nasiri MJ, Goudarzi M, Hashemi A, Hajikhani B. Global Prevalence and Molecular Epidemiology of mcr-Mediated Colistin Resistance in Escherichia coli Clinical Isolates: A Systematic Review. J Glob Antimicrob Resist 2021; 29:444-461. [PMID: 34788692 DOI: 10.1016/j.jgar.2021.10.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/10/2021] [Accepted: 10/25/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND AND AIM The continuing rise in infections caused by multi-drug resistant (MDR) bacteria is one of the most serious public health issues in today's societies. Colistin is a last-resort antimicrobial medication used to treat infections caused by MDR gram-negative bacteria; therefore resistance to this antibiotic is extremely hazardous. The current study aimed to evaluate the global prevalence and distribution of colistin resistance genes among human clinical isolates of Escherichia coli (E. coli) as a systematic review. METHODS PubMed, Embase, and Web of Science databases were systematically searched. For further evaluation, all original English-language articles that demonstrated colistin resistance in E. coli clinical isolates published between 2000 and 2020 were examined. RESULTS Out of 4857 initial articles, after various stages of review and evaluation, 190 related articles were selected. More than 79 % of the publications selected in this research were published from 2014 to 2020. In Asia, Europe, America, Africa, and Oceania, the prevalence of mobilized colistin resistance (mcr) producing colistin-resistant E. coli was 66.72%, 25.48%, 5.19%, 2.27%, and 0.32 %, respectively. CONCLUSION The recent widespread spreading of E. coli strains harboring mcr conferring colistin resistance, especially in Asia and Europe, is concerning and needs more attention.
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Affiliation(s)
- Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran; Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Fatemeh Sameni
- Department of Microbiology, School of Medicine, Shahed University, Tehran, Iran
| | - Nazila Bostanshirin
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Somayeh Yaslianifard
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Nafiseh Khosravi-Dehaghi
- Department of Pharmacognosy, School of Pharmacy, Alborz University of Medical Sciences, Karaj, Iran; Evidence-Based Phytotherapy and Complementary Medicine Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Hashemi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Wang Z, Guo L, Liu L, Kuang H, Xiao J, Xu C. Development and comparison of two nanomaterial label-based lateral flow immunoassays for the detection of five antibacterial synergists. NEW J CHEM 2020. [DOI: 10.1039/d0nj03734f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Label is a significant factor when analyzing the performance of lateral flow immunoassays (LFIAs). Thus, this study developed two nanomaterial label-based LFIA and compared their analytical performance in practical applications.
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Affiliation(s)
- Zhongxing Wang
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- People's Republic of China
- International Joint Research Laboratory for Biointerface and Biodetection, and School of Food Science and Technology
| | - Lingling Guo
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- People's Republic of China
- International Joint Research Laboratory for Biointerface and Biodetection, and School of Food Science and Technology
| | - Liqiang Liu
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- People's Republic of China
- International Joint Research Laboratory for Biointerface and Biodetection, and School of Food Science and Technology
| | - Hua Kuang
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- People's Republic of China
- International Joint Research Laboratory for Biointerface and Biodetection, and School of Food Science and Technology
| | - Jing Xiao
- NHC Key Laboratory of Food Safety Risk Assessment
- China National Center for Food Safety Risk Assessment
- Beijing
- People's Republic of China
| | - Chuanlai Xu
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- People's Republic of China
- International Joint Research Laboratory for Biointerface and Biodetection, and School of Food Science and Technology
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