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Guo CH, Chu MJ, Liu T, Wang J, Zou M, Liu BT. High prevalence and transmission of bla NDM-positive Escherichia coli between farmed ducks and slaughtered meats: An increasing threat to food safety. Int J Food Microbiol 2024; 424:110850. [PMID: 39094468 DOI: 10.1016/j.ijfoodmicro.2024.110850] [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: 02/14/2024] [Revised: 06/18/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
The emergence of carbapenem-resistant bacteria especially carbapenem-resistant Escherichia coli (CREC) in food animals poses a serious threat to food safety and public health. Reports about the dissemination of carbapenem-resistant bacteria along the food animal production chain are scattered and mainly focus on swine and chicken. Abuse of antibiotics in duck farms is common especially in China which has the largest duck production industry, however, the CREC transmission between farmed ducks and slaughtered meats remains unclear and the role of slaughterhouse in disseminating CREC among duck meats remains largely unknown. Herein, we collected 251 fecal samples from five typical duck farms along with 125 slaughtered meat samples (25 from each farm) in the corresponding slaughterhouse in Anhui Province, China, in December 2018. All samples were screened for CREC isolates which were analyzed for the presence of carbapenemase genes and colistin resistance gene mcr. The resistance profiles, transferability, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing and phylogenetic analysis of the CREC isolates from both ducks and meats were further characterized. This is the first report presenting the high prevalence of blaNDM-positive CREC isolates in ducks from duck farms (57.8 %) and slaughtered meats (33.6 %) in the corresponding slaughterhouse. Among the 203 blaNDM-positive CREC isolates obtained in this study, 19.2 % harbored mcr-1 and all CREC isolates showed resistance to nearly all currently available antibiotics (except tigecycline). Of note, mcr-1 was found in 17.8 % of the meat-derived CREC carrying blaNDM. Based on the PFGE analysis, clonal spread of blaNDM-positive CREC including some also carrying mcr-1 was found between farmed ducks and slaughtered duck meats even from different farms. Special attention should be paid to the clonal dissemination of meat-derived CREC within the slaughterhouse, which contributed to the high prevalence of blaNDM in slaughtered meats. Additionally, horizontal transmission mainly mediated by transferable blaNDM-5-bearing IncX3 plasmids, untypable blaNDM-1-bearing plasmids and mcr-1-bearing IncHI2 plasmids further facilitated the rapid spread of such multidrug-resistant strains. Notably, the blaNDM-bearing plasmids and mcr-1-bearing plasmids in CREC from meats were highly similar to those from animals and humans. More worryingly, the phylogenomic analysis showed that CREC isolates from both ducks and corresponding meats clustered with previously reported human CREC isolates carrying mcr-1 in different geographical areas including China. These findings further prove that the CREC and resistance plasmids in farmed ducks could transmit to meats even from different farms via the slaughterhouse and then trigger infections in humans. The high prevalence and clonal transmission of CREC isolates including those also carrying mcr-1 between ducks and meats are alarming, and urgent control measures are required to reduce the dissemination of such organisms.
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Affiliation(s)
- Cai-Hong Guo
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Mei-Jun Chu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Tiantian Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Junjie Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Ming Zou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Bao-Tao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.
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Sabino YNV, de Melo MD, da Silva GC, Mantovani HC. Unraveling the diversity and dissemination dynamics of antimicrobial resistance genes in Enterobacteriaceae plasmids across diverse ecosystems. J Appl Microbiol 2024; 135:lxae028. [PMID: 38323496 DOI: 10.1093/jambio/lxae028] [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: 10/08/2023] [Revised: 01/08/2024] [Accepted: 02/05/2024] [Indexed: 02/08/2024]
Abstract
AIM The objective of this study was to investigate the antimicrobial resistance genes (ARGs) in plasmids of Enterobacteriaceae from soil, sewage, and feces of food-producing animals and humans. METHODS AND RESULTS The plasmid sequences were obtained from the NCBI database. For the identification of ARG, comprehensive antibiotic resistance database (CARD), and ResFinder were used. Gene conservation and evolution were investigated using DnaSP v.6. The transfer potential of the plasmids was evaluated using oriTfinder and a MOB-based phylogenetic tree was reconstructed using Fastree. We identified a total of 1064 ARGs in all plasmids analyzed, conferring resistance to 15 groups of antibiotics, mostly aminoglycosides, beta-lactams, and sulfonamides. The greatest number of ARGs per plasmid was found in enterobacteria from chicken feces. Plasmids from Escherichia coli carrying multiple ARGs were found in all ecosystems. Some of the most abundant genes were shared among all ecosystems, including aph(6)-Id, aph(3'')-Ib, tet(A), and sul2. A high level of sequence conservation was found among these genes, and tet(A) and sul2 are under positive selective pressure. Approximately 62% of the plasmids carrying at least one ARG were potentially transferable. Phylogenetic analysis indicated a potential co-evolution of Enterobacteriaceae plasmids in nature. CONCLUSION The high abundance of Enterobacteriaceae plasmids from diverse ecosystems carrying ARGs reveals their widespread distribution and importance.
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Affiliation(s)
| | - Mariana Dias de Melo
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Giarlã Cunha da Silva
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Hilario Cuquetto Mantovani
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 53706, Madison, WI, USA
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Ma L, Qu Y, Wang W, Wang D. Characterization of Klebsiella pneumoniae carrying the blaNDM-1 gene in IncX3 plasmids and the rare In1765 in an IncFIB-IncHI1B plasmid. Front Cell Infect Microbiol 2024; 13:1324846. [PMID: 38274736 PMCID: PMC10808583 DOI: 10.3389/fcimb.2023.1324846] [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: 10/20/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Background Today, the blaNDM gene is widely distributed on several plasmids from a variety of Gram-negative bacteria, primarily in transposons and gene cassettes within their multidrug-resistant (MDR) regions. This has led to the global dissemination of the blaNDM gene. Methods The determination of class A beta-lactamase, class B and D carbapenemases was performed according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI). Antimicrobial susceptibility testing was performed using both the BioMerieux VITEK2 system and antibiotic paper diffusion methods. Plasmid transfer was then evaluated by conjugation experiments and plasmid electroporation assays. To comprehensively analyze the complete genome of K. pneumoniae strain F11 and to investigate the presence of mobile genetic elements associated with antibiotic resistance and virulence genes, Nanopore and Illumina sequencing platforms were used, and bioinformatics methods were applied to analyze the obtained data. Results Our findings revealed that K. pneumoniae strain F11 carried class A beta-lactamase and classes B+D carbapenemases, and exhibited resistance to commonly used antibiotics, particularly tigecycline and ceftazidime/avibactam, due to the presence of relevant resistance genes. Plasmid transfer assays demonstrated successful recovery of plasmids pA_F11 and pB_F11, with average conjugation frequencies of 2.91×10-4 and 1.56×10-4, respectively. However, plasmids pC_F11 and pD_F11 failed in both conjugation and electroporation experiments. The MDR region of plasmid pA_F11 contained rare In1765, TnAs2, and TnAs3 elements. The MDR2 region of plasmid pB_F11 functioned as a mobile genetic "island" and lacked the blaNDM-1 gene, serving as a "bridge" connecting the early composite structure of bleMBL and blaNDM-1 to the recent composite structure. Additionally, the MDR1 region of plasmid pB_F11 comprised In27, TnAs1, TnAs3, and Tn2; and plasmid pC_F11 harbored the recent composite structure of bleMBL and blaNDM-1 within Tn3000 which partially contained partial Tn125. Conclusion This study demonstrated that complex combinations of transposons and integron overlaps, along with the synergistic effects of different drug resistance and virulence genes, led to a lack of effective therapeutic agents for strain F11, therefore its dissemination and prevalence should be strictly controlled.
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Affiliation(s)
- Liman Ma
- School of Medicine, Taizhou University, Taizhou, Zhejiang, China
- Department of Central Laboratory, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Ying Qu
- Department of Clinical Medicine Laboratory, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Wenji Wang
- Department of Central Laboratory, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, Zhejiang, China
- School of Life Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Dongguo Wang
- School of Medicine, Taizhou University, Taizhou, Zhejiang, China
- Department of Central Laboratory, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, Zhejiang, China
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Yamaguchi T, Yokota M, Jinnai M, Minh DTN, Hoang ON, Le Thi H, Thanh PN, Hoang Hoai P, Nguyen Do P, Van CD, Motooka D, Nakamura S, Kawahara R, Kumeda Y, Hase A, Nakayama T. Detection of chromosome-mediated bla NDM-1-carrying Aeromonas spp. in the intestinal contents of fresh water river fish in Ho Chi Minh City, Vietnam. MARINE POLLUTION BULLETIN 2024; 198:115812. [PMID: 38043208 DOI: 10.1016/j.marpolbul.2023.115812] [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: 04/26/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023]
Abstract
The spread of antibiotic-resistant bacteria is a global problem that should be addressed through the perspective of the "one health" concept. The purpose of this study was to determine the contamination rate of antibiotic-resistant Aeromonas spp. in fresh water river fish purchased from a fish market in Vietnam. We then defined the pattern of antibiotic resistance to assess antibiotic-resistant contamination. Antibiotic-resistant Aeromonas spp. were detected in the intestinal contents of 32 of 80 fish. blaNDM-1 was detected in seven strains. Extended-spectrum β-lactamase and AmpC β-lactamase-related genes were detected in 28 strains, including blaCTX-M-55, blaCTX-M-15, blaCTX-M-1, and blaDHA,blaFOX, and blaMOX. The blaNDM-1 detected in the seven Aeromonas spp. strains were found chromosomally. This finding suggests that the blaNDM gene is stable in the natural environment and may spread widely into animals and humans via Aeromonas spp. with a transposon. Our results suggest the importance of continuing to monitor carbapenemase genes in Aeromonas spp. to evaluate the possibility that they may spread in other Enterobacterales, and to elucidate the mechanism of spread.
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Affiliation(s)
| | - Masaharu Yokota
- Division of Microbiology Osaka Institute of Public Health, Osaka, Japan
| | - Michio Jinnai
- Kanagawa Prefectural Institute of Public Health, Kanagawa, Japan
| | | | | | - Hien Le Thi
- Institute of Public Health, Ho Chi Minh City, Viet Nam
| | | | | | | | | | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Ryuji Kawahara
- Division of Microbiology Osaka Institute of Public Health, Osaka, Japan
| | | | | | - Tatsuya Nakayama
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.
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Zhu DM, Ding Q, Li PH, Wang YL, Li YZ, Yu Li X, Li GM, Ma HX, Kong LC. Antimicrobial resistance in E. Coli of animal origin and discovery of a novel ICE mobile element in Northeast China. BMC Vet Res 2023; 19:255. [PMID: 38053138 DOI: 10.1186/s12917-023-03828-5] [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: 08/24/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Multidrug resistance in Enterobacteriaceae including resistance to quinolones is rising worldwide. The development of resistance may lead to the emergence of new transmission mechanisms. In this study, the collection of different E. coli was performed from animals and subjected to subsequent procedures including pulsed-field gel electrophoresis, micro-broth dilution method, polymerase chain reaction. Whole genome sequencing of E. coli C3 was performed to detect the affinity, antimicrobial resistance and major carriers of the isolates. RESULTS A total of 66 E. coli were isolated and their antibiotic resistance genes, frequency of horizontal transfer and genetic environment of E. coli C3 were determined. The results showed there were both different and same types in PFGE typing, indicating clonal transmission of E. coli among different animals. The detection of antimicrobial resistance and major antibiotic resistance genes and the plasmid transfer results showed that strains from different sources had high levels of resistance to commonly used clinical antibiotics and could be spread horizontally. Whole-genome sequencing discovered a novel ICE mobile element. CONCLUSION In summary, the antimicrobial resistance of E. coli in northeast China is a serious issue and there is a risk of antimicrobial resistance transmission. Meanwhile, a novel ICE mobile element appeared in the process of antimicrobial resistance formation.
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Affiliation(s)
- Dao Mi Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Qiang Ding
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Peng Hui Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Yong Liang Wang
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Ya Zhuo Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Xuan Yu Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Gong Mei Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
| | - Hong Xia Ma
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China.
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China.
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China.
| | - Ling Cong Kong
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China.
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China.
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Gao Y, Du P, Zhang P, Wang J, Liu Z, Fanning S, Wang Z, Li R, Bai L. Dynamic evolution and transmission of a bla NDM-1-bearing fusion plasmid in a clinical Escherichia coli. Microbiol Res 2023; 275:127450. [PMID: 37454426 DOI: 10.1016/j.micres.2023.127450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Plasmids are the main driving forces for the rapid dissemination of blaNDM-1. In recent years, blaNDM-1-carrying fusion plasmids have been frequently reported. However, the evolutionary patterns of blaNDM-1-carrying fusion plasmids remain largely unknown. Herein, we reported a blaNDM-1-bearing fusion plasmid pZX35-269k possessing IncFII and IncA/C2 replicons from clinical ST349 E. coli 13ZX35. The backbone of pZX35-269k was structurally unstable, which was manifested in different types of structural dissociation during conjugation and passage, thereby forming various daughter plasmids. Moreover, the same events were observed in the clinical setting as well. We found that pZX35-269k exhibited highly identical to two plasmids (pZX30-70k and pZX30-192k) in 13ZX30, both of which were isolated from the same hospital. Sequence analysis highlighted that two plasmids in 13ZX30 evolved from pZX35-269k through homologous recombination of a 4856-bp fragment. Collectively, this study confirmed the transmission and structural evolution of a blaNDM-1-bearing fusion plasmid in both laboratory and clinical settings, and provided clear evidence of plasmid spread and evolution in clinical settings. Such versatile plasmids may represent a potential risk for the public health.
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Affiliation(s)
- Yanyun Gao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China
| | - Pengcheng Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, People's Republic of China
| | - Pei Zhang
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, 22, Yangling 712100 Shaanxi, People's Republic of China
| | - Ziyi Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China
| | - Séamus Fanning
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China; UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China.
| | - Li Bai
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.
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Cerbino GN, Traglia GM, Ayala Nuñez T, Parmeciano Di Noto G, Ramírez MS, Centrón D, Iriarte A, Quiroga C. Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages. Front Microbiol 2023; 14:1124225. [PMID: 36925471 PMCID: PMC10011109 DOI: 10.3389/fmicb.2023.1124225] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.
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Affiliation(s)
- Gabriela N Cerbino
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - German M Traglia
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Teolincacihuatl Ayala Nuñez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Gisela Parmeciano Di Noto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - María Soledad Ramírez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, Fullerton, CA, United States
| | - Daniela Centrón
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
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Epidemiology, molecular characterization, and drug resistance of IncHI5 plasmids from Enterobacteriaceae. Int Microbiol 2022; 26:371-378. [PMID: 36383268 DOI: 10.1007/s10123-022-00299-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/06/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022]
Abstract
The increasingly frequent occurence of IncHI5 plasmids has attracted worldwide attention. The aim of this study was to perform an in-depth bioinformatics analysis to determine the genetic characteristics and global distribution of all IncHI5 plasmids. The geographic distribution and epidemiology of all IncHI5 plasmids from GenBank were analyzed based on relevant literature reports and background information from the National Center for Biotechnology Information (NCBI). Detailed annotation of antibiotic resistance genes was performed. A total of 65 IncHI5 plasmid genomes were collected in GenBank. All IncHI5 plasmids were carried by Enterobacteriaceae, of which Klebsiella pneumoniae accounted for the largest proportion (50%, 33/65). The host bacterium of IncHI5 plasmids was mainly isolated from Homo Sapiens (81%, 53/65). All strains carrying IncHI5 plasmids were mainly distributed in China (83%, 54/65). Evolutionary analysis can divide IncHI5 plasmids into two groups, namely Groups I/II, of which Group II was more widely distributed worldwide. This study showed that Enterobacteriaceae, especially Klebsiella, was the main host for IncHI5 plasmid. Almost all IncHI5 plasmids carried multiple types of antibiotic resistance genes, related to Tn1696 or Tn6535. The IncHI5 plasmids should be of continuing interest as good repositories for antibiotic resistance genes.
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Li A, Yu R, Zhao W, Schwarz S, Li C, Yao H, Du XD. Characterization of a genomic Island carrying the tet(X4) gene in porcine Acinetobacter towneri co-harboring plasmid-borne blaNDM−1 and blaOXA−58 genes. Front Vet Sci 2022; 9:1002149. [PMID: 36246313 PMCID: PMC9557058 DOI: 10.3389/fvets.2022.1002149] [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: 07/24/2022] [Accepted: 09/12/2022] [Indexed: 12/03/2022] Open
Abstract
Tigecycline and carbapenems are last-resort antimicrobial agents to treat serious infections caused by multi-drug resistant bacterial pathogens. However, the co-occurrence of tigecycline and carbapenem resistance determinants challenges the clinical efficacy of these antimicrobial agents. In this study, we report the co-existence of tet(X4), blaNDM−1 and blaOXA−58 genes in the porcine Acinetobacter towneri isolate 19110F47. Sequence analysis revealed that tet(X4) gene, along with the florfenicol resistance gene floR, was flanked by three copies of IS91-like elements, which can form three different translocatable units (TUs), and were located in a 41,098-bp multidrug resistance region (MDRR) within a novel 100,354-bp genomic island (GI) region. TUs comprising floR-virD2-ISVsa3, hp-abh-tet(X4)-ISVsa3 and virD2-floR-ISVsa3-hp-abh-tet(X4)-ISVsa3 can be looped out from the chromosomal DNA and facilitate the transfer of the TU-based resistance genes into other plasmidic or chromosomal sites. In addition, the carbapenemase genes blaNDM−1 and blaOXA−58 were found on different non-conjugative multiresistance plasmids in this isolate, with the genetic contexts ISAba125-blaNDM−1-bleMBL-tnpR and ΔISAba3-blaOXA−58-ISAba3, respectively. The simultaneous occurrence of tet(X4), blaNDM−1 and blaOXA−58 in the same porcine A. towneri isolate emphasizes the importance of antimicrobial resistance surveillance in food-producing animals.
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Affiliation(s)
- Aijuan Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Runhao Yu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Wenbo Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Stefan Schwarz
- Department of Veterinary Medicine, Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre of Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Chenglong Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Hong Yao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Hong Yao
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Xiang-Dang Du
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10
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Dong H, Li Y, Cheng J, Xia Z, Liu W, Yan T, Chen F, Wang Z, Li R, Shi J, Qin S. Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on blaNDM Transmission. Microbiol Spectr 2022; 10:e0215621. [PMID: 35225688 PMCID: PMC9049954 DOI: 10.1128/spectrum.02156-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/30/2022] [Indexed: 12/14/2022] Open
Abstract
Incidences of nosocomial infections mediated by New Delhi metallo-β-lactamase (NDM) enzyme-producing Enterobacterales are increasing globally, resulting in a great burden to public health. The carbapenem-resistant Enterobacterales (CRE) were collected from Henan, China during 2013-2016. The blaNDM-positive strains were characterized using PCR, antimicrobial susceptibility testing, conjugation assay, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blot, whole-genome sequencing (WGS), and bioinformatics analysis. Eighty-one NDM-producing strains were identified among 391 nonduplicate CRE strains. Among them, four strains cocarried mcr and blaNDM genes, and two carried blaIMP-4 and blaNDM genes. The coexistence of blaNDM-5 and mcr-9 in Enterobacter hormaechei was found for the first time. In total, four blaNDM subtypes were identified. Among them, blaNDM-1 and blaNDM-5 were predominant. There was an obvious increasing trend in blaNDM-5 from 2013 to 2016. Thirteen different bacterial species were found among the 81 strains, and Escherichia coli was the dominant strain. blaNDM genes were located on nine different Inc-type plasmids, most of them on the IncX3 plasmids, except for the Pr-15-2-50 strain, which was located on the chromosome. We characterized two novel plasmids: the IncHI5-like plasmid carrying blaNDM-9 found in K. pneumonia, and the IncI1 blaNDM-5-positive plasmid. These findings provide the genomic basis for the widespread transmission of blaNDM and pave the way for the formulation of more effective monitoring and control methods. IMPORTANCE To control the emergence and transmission of CRE, it is important to perform retrospective genomic investigations. It is important to evaluate the plasmid diversity, genetic environment, and evolutionary relationships of the blaNDM-positive clinical strains in the early transmission stages. This study conducted an in-depth analysis of blaNDM-positive pathogens during a 4-year period using different methods for observing the high prevalence and active transmission of blaNDM-positive CRE. Moreover, we also explored the coexistence of the blaNDM and mcr, a clinically important mobile colistin resistance gene. This study shows that the prevalence of blaNDM-positive pathogens in Henan is high and the isolation rates increase each year. Moreover, plasmid-mediated horizontal transfer plays an important role in blaNDM dissemination. The co-occurrence of multiple resistance genes highlighted a long-lasting evolutionary pathway. Therefore, we have suggested the long-term continuous surveillance of clinical pathogens carrying blaNDM to learn the future transmission trend and curb the public health risk caused by CRE.
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Affiliation(s)
- Huiyue Dong
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jing Cheng
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Ziwei Xia
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Wentian Liu
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Tingting Yan
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Fangfang Chen
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China
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11
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Wei H, Kong L, Wang Y, Huang Z, Yang X, Zhou C, Li C, Ma B, Li C, Lei C, Wang H. Characterization and Public Health Insights of the New Delhi Metallo-β-Lactamase-Producing Enterobacterales from Laying Hens in China. Microorganisms 2022; 10:microorganisms10040800. [PMID: 35456850 PMCID: PMC9029685 DOI: 10.3390/microorganisms10040800] [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: 02/24/2022] [Revised: 03/26/2022] [Accepted: 04/09/2022] [Indexed: 02/04/2023] Open
Abstract
The New Delhi metallo-β-lactamase (NDM) is a major element for the rapid expansion of the carbapenem-resistant Enterobacterales, which poses a great challenge to public health security. NDM-producing Enterobacterales strains (50 Escherichia coli, 40 Klebsiella pneumoniae, and 5 Enterobacter cloacae) were isolated from laying hens in China for the surveillance of antibiotic-resistant pathogens, and all were found to be multi-drug resistant bacteria. The genomic analysis of these NDM-positive bacteria revealed the ST167, ST617, and ST410 of the fifteen ST-type E. coli clones and ST37 of the four ST-type K. pneumoniae clones to be the same types as the human-derived strains. Among them, some new clone types were also found. Most of the blaNDM genes (blaNDM-1 or blaNDM-5) were on the IncX3 plasmids (n = 80) and were distributed in E. coli, K. pneumoniae, and E. cloacae, while the remaining blaNDM-5 genes were harbored in the E. coli ST167 with IncFII plasmids (n = 15). The typeⅠ1 of the eight IncX3 plasmid subtypes was consistent with the human-derived pNDM5_020001 plasmid (accession no. CP032424). In addition, these two plasmids did not affect the growth of the host bacteria and could be reproduced stably without antibiotics. Our study revealed the high genetic propensity of the NDM-positive Enterobacterales from the laying hens and human commensal Enterobacterales, suggesting the potentially enormous risk of its transmission to humans.
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Affiliation(s)
- Hongcheng Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Linghan Kong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Yulong Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Zheren Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Xue Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Changyu Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Chao Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Boheng Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Cui Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (H.W.); (L.K.); (Y.W.); (Z.H.); (X.Y.); (C.Z.); (C.L.); (B.M.); (C.L.); (C.L.)
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, China
- Correspondence: ; Tel.: +86-28-8547-1599
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12
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Luo X, Zhang J, Yuan M, Mou S, Xu M, Hu D, Ma Q, Sun L, Li P, Song Z, Yu L, Mu K. Epidemiology of Klebsiella michiganensis Carrying Multidrug-Resistant IncHI5 Plasmids in the Southeast Coastal Area of China. Infect Drug Resist 2022; 15:1831-1843. [PMID: 35444429 PMCID: PMC9013925 DOI: 10.2147/idr.s358839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/26/2022] [Indexed: 12/18/2022] Open
Abstract
Purpose This study aimed to explore the genomic characterization of multidrug-resistant IncHI5-carrying Klebsiella michiganensis strains and detailed genomic dissection of the IncHI5 plasmids. Materials and Methods Through whole-genome sequencing, the IncHI5 plasmid pK92-qnrS was obtained from a single clinical K. michiganensis isolate K92. All complete genomes of K. michiganensis strains from the Genome database of NCBI were collected and used to construct a maximum likelihood (ML) phylogenetic tree. The epidemiology and geographic distribution of all the K. michiganensis strains were conducted. An extensive comparison of the seven IncHI5 plasmids of K. michiganensis (one from this study, six from GenBank) was applied. Results This study revealed that all K. michiganensis strains carrying IncHI5 plasmids from different clonal groups were located in the southeast coastal area of China. The backbone regions of IncHI5 plasmids were composed of replicon (repHI5B and repFIB), partition (parABC), and conjugal transfer (tra1/tra2). The main accessory resistant regions of IncHI5 could be divided into two categories, Tn1696-related region and Tn6535-related region. These seven IncHI5 plasmids carried multiple drug-resistance genes which were all mediated by the mobile genetic elements (MGEs). Conclusion Data presented here help to provide an overall in-depth understanding of epidemiology and geographic distribution of IncHI5-carrying K. michiganensis and the structure and evolutionary history of IncHI5 plasmids.
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Affiliation(s)
- Xinhua Luo
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Jin Zhang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Min Yuan
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Sihua Mou
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Mengqiao Xu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Dakang Hu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Qinfei Ma
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Lingfen Sun
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Piaopiao Li
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Zhiwei Song
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
| | - Lianhua Yu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China
- Lianhua Yu, Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, 318000, People’s Republic of China, Email
| | - Kai Mu
- Beijing Institute of Radiation Medicine, Beijing, 100850, People’s Republic of China
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, People’s Republic of China
- Correspondence: Kai Mu, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, People’s Republic of China, Tel +86-010-66874794, Email
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13
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Characterization of NDM-1-Producing Carbapenemase in Proteus mirabilis among Broilers in China. Microorganisms 2021; 9:microorganisms9122443. [PMID: 34946044 PMCID: PMC8707091 DOI: 10.3390/microorganisms9122443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/14/2021] [Accepted: 11/23/2021] [Indexed: 11/28/2022] Open
Abstract
Carbapenem-resistant pathogens mediated by metallo-beta-lactamases (MBLs) have spread worldwide, where NDM-1 is a typical and key MBL. Here, we firstly discussed the distribution characterization of NDM-1, which produces multidrug-resistant Proteus mirabilis among broilers in China. From January to April 2019, 40 (18.1%, 40/221) blaNDM-1-carrying P. mirabilis strains were recovered from commercial broilers in slaughterhouse B in China. All the isolates were resistant to imipenem, meropenem and other β-lactams. These isolates belong to five clusters identified via pulsed field gel electrophoresis (PFGE). Further studies on twenty representative strains revealed that seven blaNDM-1 genes were located on plasmids with sizes of 104.5–138.9 kb. Notably, only three strains (PB72, PB96 and PB109) were successfully transferred to Escherichia coli J53, while the other four isolates were located in nontransferable plasmids. The rest were harbored in chromosomes. Ulteriorly, based on whole genome sequencing (WGS), these twenty isolates showed four typical phylogenetic clades according to single nucleotide polymorphisms (SNPs) of a core genome and presented four main genomic backbone profiles, in which type II/III strains shared a similar genetic context. All of the above is evidence of blaNDM-1 transmission and evolution in P. mirabilis, suggesting that the prevalence may be more diverse in broiler farms. Accordingly, as intestinal and environmental symbiotic pathogens, blaNDM-1-positive P. mirabilis will pose greater threats to the environment and public health.
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14
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Identification of a Novel blaNDM Variant, blaNDM-33, in an Escherichia coli Isolate from Hospital Wastewater in China. mSphere 2021; 6:e0077621. [PMID: 34643418 PMCID: PMC8513677 DOI: 10.1128/msphere.00776-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since the discovery of NDM-1 and the worldwide reporting of different variants have raised alarms concerning global health, the problem of carbapenem-resistant Enterobacterales (CRE) has become increasingly serious. Therefore, research on the hydrolytic activity and molecular structure of NDM variants is beneficial to the development of antibacterial drugs. NDM has been evolving into variants that possess different hydrolysis activities toward β-lactam antibiotics. Here, we characterized a novel blaNDM variant, named blaNDM-33, identified from a multidrug-resistant Escherichia coli strain from hospital sewage. NDM-33 differed from NDM-5 with a single-amino-acid substitution (A72T). blaNDM-5 was located in the Tn125-related blaNDM-33 region from an IncX3-type plasmid, pHD6415-NDM, that can be transferred horizontally. The genetic construct of blaNDM-33 showed higher MICs of carbapenems than a blaNDM-5 construct. Enzyme kinetics showed that NDM-33 had higher enzymatic activity for meropenem and cefazolin than NDM-5. The emergence of this novel NDM variant could pose a threat to public health because of its transferability and enhanced carbapenem activity. IMPORTANCE Our study described a novel NDM-33 variant from an E. coli strain isolated from hospital sewage, where it was associated with human disease and antibiotic exposure. Importantly, hospital sewage was increasingly considered to be related to CRE hosts. Pathogens were transmitted from reservoirs through direct and indirect contact, ingestion, and inhalation of contaminated water or aerosols. In addition, under the selective pressure of antibiotics, NDM variants will become the main strain in the hospital water system and evolve into high virulence and high resistance. The monitoring of NDM mutants is of great significance for preventing and controlling the evolution of superbugs.
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15
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Liu Z, Chen R, Xu P, Wang Z, Li R. Characterization of a bla NDM-1-Bearing IncHI5-Like Plasmid From Klebsiella pneumoniae of Infant Origin. Front Cell Infect Microbiol 2021; 11:738053. [PMID: 34660344 PMCID: PMC8517479 DOI: 10.3389/fcimb.2021.738053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
The spread of plasmid-mediated carbapenem-resistant clinical isolates is a serious threat to global health. In this study, an emerging NDM-encoding IncHI5-like plasmid from Klebsiella pneumoniae of infant patient origin was characterized, and the plasmid was compared to the available IncHI5-like plasmids to better understand the genetic composition and evolution of this emerging plasmid. Clinical isolate C39 was identified as K. pneumoniae and belonged to the ST37 and KL15 serotype. Whole genome sequencing (WGS) and analysis revealed that it harbored two plasmids, one of which was a large IncHI5-like plasmid pC39-334kb encoding a wide variety of antimicrobial resistance genes clustered in a single multidrug resistance (MDR) region. The blaNDM-1 gene was located on a ΔISAba125-blaNDM-1-bleMBL-trpF-dsbC structure. Comparative genomic analysis showed that it shared a similar backbone with four IncHI5-like plasmids and the IncHI5 plasmid pNDM-1-EC12, and these six plasmids differed from typical IncHI5 plasmids. The replication genes of IncHI5-like plasmids shared 97.06% (repHI5B) and 97.99% (repFIB-like) nucleotide identity with those of IncHI5 plasmids. Given that pNDM-1-EC12 and all IncHI5-like plasmids are closely related genetically, the occurrence of IncHI5-like plasmid is likely associated with the mutation of the replication genes of pNDM-1-EC12-like IncHI5 plasmids. All available IncHI5-like plasmids harbored 262 core genes encoding replication and maintenance functions and carried distinct MDR regions. Furthermore, 80% of them (4/5) were found in K. pneumoniae from Chinese nosocomial settings. To conclude, this study expands our knowledge of the evolution history of IncHI5-like plasmids, and more attention should be paid to track the evolution pathway of them among clinical, animal, and environmental settings.
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Affiliation(s)
- Ziyi Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Ruifei Chen
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Clinical Laboratory of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Poshi Xu
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou, China.,Department of Clinical Laboratory of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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16
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Pot M, Reynaud Y, Couvin D, Ducat C, Ferdinand S, Gravey F, Gruel G, Guérin F, Malpote E, Breurec S, Talarmin A, Guyomard-Rabenirina S. Wide Distribution and Specific Resistance Pattern to Third-Generation Cephalosporins of Enterobacter cloacae Complex Members in Humans and in the Environment in Guadeloupe (French West Indies). Front Microbiol 2021; 12:628058. [PMID: 34248862 PMCID: PMC8268024 DOI: 10.3389/fmicb.2021.628058] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 11/25/2022] Open
Abstract
Species belonging to Enterobacter cloacae complex have been isolated in numerous environments and samples of various origins. They are also involved in opportunistic infections in plants, animals, and humans. Previous prospection in Guadeloupe (French West Indies) indicated a high frequency of E. cloacae complex strains resistant to third-generation cephalosporins (3GCs) in a local lizard population (Anolis marmoratus), but knowledge of the distribution and resistance of these strains in humans and the environment is limited. The aim of this study was to compare the distribution and antibiotic susceptibility pattern of E. cloacae complex members from different sources in a “one health” approach and to find possible explanations for the high level of resistance in non-human samples. E. cloacae complex strains were collected between January 2017 and the end of 2018 from anoles, farm animals, local fresh produce, water, and clinical human samples. Isolates were characterized by the heat-shock protein 60 gene-fragment typing method, and whole-genome sequencing was conducted on the most frequent clusters (i.e., C-VI and C-VIII). The prevalence of resistance to 3GCs was relatively high (56/346, 16.2%) in non-human samples. The associated resistance mechanism was related to an AmpC overproduction; however, in human samples, most of the resistant strains (40/62) produced an extended-spectrum beta-lactamase. No relation was found between resistance in isolates from wild anoles (35/168) and human activities. Specific core-genome phylogenetic analysis highlighted an important diversity in this bacterial population and no wide circulation among the different compartments. In our setting, the mutations responsible for resistance to 3GCs, especially in ampD, were diverse and not compartment specific. In conclusion, high levels of resistance in non-human E. cloacae complex isolates are probably due to environmental factors that favor the selection of these resistant strains, and this will be explored further.
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Affiliation(s)
- Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - Célia Ducat
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - François Gravey
- GRAM 2.0, Normandie University, UNICAEN, UNIROUEN, Caen, France
| | - Gaëlle Gruel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
| | - François Guérin
- GRAM 2.0, Normandie University, UNICAEN, UNIROUEN, Caen, France.,Department of Clinical Microbiology, Caen University Hospital, Caen, France
| | - Edith Malpote
- Laboratory of Clinical Microbiology, University Hospital of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France.,Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France.,Centre for Clinical Investigation 1424, INSERM, Pointe-à-Pitre/Les Abymes, France
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Les Abymes, France
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17
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Dietary Factors of blaNDM Carriage in Health Community Population: A Cross-Sectional Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18115959. [PMID: 34199383 PMCID: PMC8199633 DOI: 10.3390/ijerph18115959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 12/18/2022]
Abstract
AIM There is an ongoing debate as to what extent antimicrobial resistance (AMR) can be transmitted from dietary to humans via the consumption of food products. We investigated this association between dietary and global spreading carbapenem-resistant gene blaNDM Methods: We did a cross-sectional study to assess the risk factors for carrier of blaNDM in health community. Healthy adults were recruited from the residents attending Community Healthcare Service in Shenzhen City (Guangdong Province, China), through 1February 2018 to 31December 2019, and 718 pre-participants were included in this study. Questionnaire were obtained and the qualitative food frequency questionnaire (Q-FFQ) were used to assess dietary intake. qPCR was applied to confirm the carrier of blaNDM in participants'fecal samples. Multivariable logistic regression was used to estimate the odds ratio (OR) and 95% confidence interval (95% CI) of each outcome according to each dietary factor before and after prosperity score matching (PSM). RESULTS we showed that a high intake of coarse grain (OR 1.003; 95% CI 1.001-1.005, p < 0.01) and root and tuber crops (OR 1.003; 95% CI 1.001-1.004, p < 0.05) were independent risk factor for blaNDM carrier in health communities, suggesting a possible transfer of AMRbetweendietary andhumans. Surprisingly, we also showed an association between a higher intake of poultry as a protective, which may be explained by the beneficial effects on the gut microbiota. CONCLUSION Dietary factors such as intake of coarse grain, root and tuber crops and poultry were associated with blaNDM carrier in health communities. The influence of dietary factorson blaNDM carrier in the present study provides insights for the tangible dietary advice with guidelines to the routine of people with the risk of blaNDM carrier. This demonstrates the role of dietary intake in the prevention of blaNDM carrier, since prevention is the best way to control modifiable risk factors. A lower carrier rate of blaNDM is helpful to reduce the possibility of transmission and pathogenicity. Further studies on food, microbiota and antimicrobial resistance are necessary to confirm this possible association and unravel underlying mechanisms.
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Identification of Two Plasmids Coharboring Carbapenemase Genes and tmexCD1-toprJ1 in Clinical Klebsiella pneumoniae ST2667. Antimicrob Agents Chemother 2021; 65:AAC.00625-21. [PMID: 33846130 DOI: 10.1128/aac.00625-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Identification of Tn 6835 and a Novel Genomic Island, MMGI-1, in a Pan-Resistant Morganella morganii Strain. Antimicrob Agents Chemother 2021; 65:AAC.02524-20. [PMID: 33468469 DOI: 10.1128/aac.02524-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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