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Liu K, Wang M, Zhang Y, Fang C, Zhang R, Fang L, Sun J, Liu Y, Liao X. Distribution of antibiotic resistance genes and their pathogen hosts in duck farm environments in south-east coastal China. Appl Microbiol Biotechnol 2024; 108:136. [PMID: 38229327 PMCID: PMC10789667 DOI: 10.1007/s00253-023-12842-4] [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] [Revised: 08/18/2023] [Accepted: 10/13/2023] [Indexed: 01/18/2024]
Abstract
Livestock farms are major reservoirs of antibiotic resistance genes (ARGs) that are discharged into the environment. However, the abundance, diversity, and transmission of ARGs in duck farms and its impact on surrounding environments remain to be further explored. Therefore, the characteristics of ARGs and their bacterial hosts from duck farms and surrounding environment were investigated by using metagenomic sequencing. Eighteen ARG types which consist of 823 subtypes were identified and the majority conferred resistance to multidrug, tetracyclines, aminoglycosides, chloramphenicols, MLS, and sulfonamides. The floR gene was the most abundant subtype, followed by sul1, tetM, sul2, and tetL. ARG abundance in fecal sample was significantly higher than soil and water sample. Our results also lead to a hypothesis that Shandong province have been the most contaminated by ARGs from duck farm compared with other four provinces. PcoA results showed that the composition of ARG subtypes in water and soil samples was similar, but there were significant differences between water and feces samples. However, the composition of ARG subtypes were similar between samples from five provinces. Bacterial hosts of ARG subtypes were taxonomically assigned to eight phyla that were dominated by the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. In addition, some human bacterial pathogens could be enriched in duck feces, including Enterococcus faecium, Acinetobacter baumannii, and Staphylococcus aureus, and even serve as the carrier of ARGs. The combined results indicate that a comprehensive overview of the diversity and abundance of ARGs, and strong association between ARGs and bacterial community shift proposed, and benefit effective measures to improve safety of antibiotics use in livestock and poultry farming. KEY POINTS: • ARG distribution was widespread in the duck farms and surroundings environment • ARG abundance on the duck farms was significantly higher than in soil and water • Human bacterial pathogens may serve as the vectors for ARGs.
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Affiliation(s)
- Kaidi Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, People's Republic of China
- School of Agricultural Science and Engineering, Liaocheng University, No.1 Hunan Road, Liaocheng, 252000, Shandong, China
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Minge Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, People's Republic of China
- School of Agricultural Science and Engineering, Liaocheng University, No.1 Hunan Road, Liaocheng, 252000, Shandong, China
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Yin Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, People's Republic of China
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Chang Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, People's Republic of China
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Rongmin Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, People's Republic of China
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Liangxing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, People's Republic of China
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, People's Republic of China
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Yahong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, People's Republic of China
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Xiaoping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, People's Republic of China.
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China.
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Yang Y, Xie S, He F, Xu Y, Wang Z, Ihsan A, Wang X. Recent development and fighting strategies for lincosamide antibiotic resistance. Clin Microbiol Rev 2024; 37:e0016123. [PMID: 38634634 DOI: 10.1128/cmr.00161-23] [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] [Indexed: 04/19/2024] Open
Abstract
SUMMARYLincosamides constitute an important class of antibiotics used against a wide range of pathogens, including methicillin-resistant Staphylococcus aureus. However, due to the misuse of lincosamide and co-selection pressure, the resistance to lincosamide has become a serious concern. It is urgently needed to carefully understand the phenomenon and mechanism of lincosamide resistance to effectively prevent and control lincosamide resistance. To date, six mobile lincosamide resistance classes, including lnu, cfr, erm, vga, lsa, and sal, have been identified. These lincosamide resistance genes are frequently found on mobile genetic elements (MGEs), such as plasmids, transposons, integrative and conjugative elements, genomic islands, and prophages. Additionally, MGEs harbor the genes that confer resistance not only to antimicrobial agents of other classes but also to metals and biocides. The ultimate purpose of discovering and summarizing bacterial resistance is to prevent, control, and combat resistance effectively. This review highlights four promising strategies, including chemical modification of antibiotics, the development of antimicrobial peptides, the initiation of bacterial self-destruct program, and antimicrobial stewardship, to fight against resistance and safeguard global health.
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Affiliation(s)
- Yingying Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shiyu Xie
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fangjing He
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yindi Xu
- Institute of Animal Husbandry Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Zhifang Wang
- Institute of Animal Husbandry Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Awais Ihsan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal campus, Islamabad, Pakistan
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
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Ly YT, Leuko S, Moeller R. An overview of the bacterial microbiome of public transportation systems-risks, detection, and countermeasures. Front Public Health 2024; 12:1367324. [PMID: 38528857 PMCID: PMC10961368 DOI: 10.3389/fpubh.2024.1367324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
When we humans travel, our microorganisms come along. These can be harmless but also pathogenic, and are spread by touching surfaces or breathing aerosols in the passenger cabins. As the pandemic with SARS-CoV-2 has shown, those environments display a risk for infection transmission. For a risk reduction, countermeasures such as wearing face masks and distancing were applied in many places, yet had a significant social impact. Nevertheless, the next pandemic will come and additional countermeasures that contribute to the risk reduction are needed to keep commuters safe and reduce the spread of microorganisms and pathogens, but also have as little impact as possible on the daily lives of commuters. This review describes the bacterial microbiome of subways around the world, which is mainly characterized by human-associated genera. We emphasize on healthcare-associated ESKAPE pathogens within public transport, introduce state-of-the art methods to detect common microbes and potential pathogens such as LAMP and next-generation sequencing. Further, we describe and discuss possible countermeasures that could be deployed in public transportation systems, as antimicrobial surfaces or air sterilization using plasma. Commuting in public transport can harbor risks of infection. Improving the safety of travelers can be achieved by effective detection methods, microbial reduction systems, but importantly by hand hygiene and common-sense hygiene guidelines.
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Affiliation(s)
| | | | - Ralf Moeller
- Department of Radiation Biology, Institute for Aerospace Medicine, German Aerospace Center, Cologne, Germany
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Xiu L, Liu H, Xie Y, Hu Q, Li H, Chen F, Wang C, Zhang Y, Hou L, Yin K. Alternations of antibiotic resistance genes and microbial community dynamics on shared bicycles before and after pandemic lockdown. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169625. [PMID: 38157892 DOI: 10.1016/j.scitotenv.2023.169625] [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: 10/17/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
The prevalence of shared bicycles has raised concerns over their potential to transmit pathogens and microbes harboring antibiotic resistance genes (ARGs), which pose significant human health risks. This study investigated the impact of anthropogenic activities on the composition of ARGs and microbial communities on shared bicycles during the COVID-19 pandemic and subsequent lockdown when shared bicycle usage was altered. A total of 600 swab samples from shared bicycle surfaces were collected in Shanghai before and during COVID-19 lockdown periods. Even during lockdown, 12 out of 14 initially detected ARG subtypes persisted, indicating their tenacity in the face of reduced anthropogenic activities. These ARGs displayed significantly higher absolute and relative abundance levels before the lockdown. In addition, the percentage of potential pathogens in the total microbial abundance remained at 0.029 % during the lockdown, which was lower than the pre-lockdown percentage of 0.035 % and suggested that these risks persist within shared bicycle systems. Interestingly, although microbial abundance decreased without the consecutive use of shared bicycles during lockdown, the microbial diversity increased under the impact of restricted anthropogenic activities (p < 0.001). This emphasizes the need for continuous monitoring and research to comprehend microbial community behaviors in various environments. This study uncovered the underlying impacts of the COVID-19 lockdown on the microbial and ARG communities of shared bicycles, providing comprehensive insights into the health management of shared transportation. Although lockdown can decrease the abundance of ARGs and potential pathogens, additional interventions are needed to prevent their continued spread.
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Affiliation(s)
- Leshan Xiu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai Academy of Environment Sciences, Shanghai, China.
| | - Haodong Liu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Yi Xie
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Huimin Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Fumin Chen
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Chenxi Wang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| | - Yuqian Zhang
- Department of Surgery, Division of Surgery Research, Mayo Clinic, Rochester, MN 55905, USA; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Liyuan Hou
- Department of Civil and Environmental Engineering, Utah State University, UT 84322, USA; Utah Water Research Laboratory, 1600 Canyon Road, Logan, UT 84321, USA.
| | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China.
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Li X, Li G, Huang H, Wan P, Lu Y, Li Z, Xie L, Xiong W, Zeng Z. The occurrence and contamination of optrA-positive methicillin-resistant Staphylococcus aureus from duck farms in Guangdong, China. J Glob Antimicrob Resist 2023; 35:86-92. [PMID: 37689309 DOI: 10.1016/j.jgar.2023.08.015] [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: 12/25/2022] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023] Open
Abstract
OBJECTIVES Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA), is an important zoonotic microorganism that increasingly causes public health concern worldwide. The objective of this study was to determine the prevalence and transmission of S. aureus in duck farms and evaluate its antimicrobial resistance and genetic characteristics. METHODS The samples associated with ducks, feeders, and the environment were collected on 14 duck farms from four areas in Guangdong, China, from 2020 to 2021. All isolates were subjected to antimicrobial susceptibility testing. A comprehensive epidemiological survey of S. aureus was conducted by S. aureus protein A typing and whole-genome sequencing. RESULTS A total of 560 samples were collected. The prevalence rate of MRSA among ducks (8.1%, 11 of 135) was higher compared with that in environmental samples. OptrA-positive ST398-t034 MRSA were first detected from duck farms in China. A total of 79.3% (34 of 46) S. aureus isolates showed multidrug-resistant phenotypes. Notably, some isolates carried multidrug-resistant genes encoding macrolide-lincosamide-streptogramin B, pleuromutilin-pleuromutilin-streptogramin A, and oxazolidinone. Analysis of the virulence genes revealed that the MRSA isolates carried genes encoding gamma-hemolysin, enterotoxin, and leukocidin. ST9-t899 is a primary clonal lineage among duck- and environment-associated MRSA. Single-nucleotide polymorphism analysis showed the potential contamination relationship of optrA-positive ST2308 MRSA isolates carrying the gamma-hemolysin genes and the leukocidin virulence genes between airborne dust and sick ducks. CONCLUSION The contamination of MRSA, especially optrA-positive MRSA, between food animals and the environment is a growing public health concern worldwide. Based on One Health principles, continuous surveillance of MRSA is urgently needed.
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Affiliation(s)
- Xiaoshen Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Guihua Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Honghao Huang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Peng Wan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Yixing Lu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Zhi Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Longfei Xie
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China.
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Chen Q, Zou Z, Cai C, Li H, Wang Y, Lei L, Shao B. Characterization of blaNDM-5-and blaCTX-M-199-Producing ST167 Escherichia coli Isolated from Shared Bikes. Antibiotics (Basel) 2022; 11:antibiotics11081030. [PMID: 36009901 PMCID: PMC9404906 DOI: 10.3390/antibiotics11081030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/17/2022] [Accepted: 07/26/2022] [Indexed: 12/10/2022] Open
Abstract
Shared bikes as a public transport provide convenience for short-distance travel. Whilst they also act as a potential vector for antimicrobial resistant (AR) bacteria and antimicrobial resistance genes (ARGs). However, the understanding of the whole genome sequence of AR strains and ARGs-carrying plasmids collected from shared bikes is still lacking. Here, we used the HiSeq platform to sequence and analyze 24 Escherichia coli isolated from shared bikes around Metro Stations in Beijing. The isolates from shared bikes showed 14 STs and various genotypes. Two blaNDM-5 and blaCTX-M-199-producing ST167 E. coli have 16 resistance genes, four plasmid types and show >95% of similarities in core genomes compared with the ST167 E. coli strains from different origins. The blaNDM-5- or blaCTX-M-199-carrying plasmids sequencing by Nanopore were compared to plasmids with blaNDM-5- or blaCTX-M-199 originated from humans and animals. These two ST167 E. coli show high similarities in core genomes and the plasmid profiles with strains from hospital inpatients and farm animals. Our study indicated that ST167 E. coli is retained in diverse environments and carried with various plasmids. The analysis of strains such as ST167 can provide useful information for preventing or controlling the spread of AR bacteria between animals, humans and environments.
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Affiliation(s)
- Qiyan Chen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (Q.C.); (Z.Z.); (Y.W.)
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China;
| | - Zhiyu Zou
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (Q.C.); (Z.Z.); (Y.W.)
| | - Chang Cai
- College of Arts, Business, Law and Social Sciences, Murdoch University, Perth, WA 6150, Australia;
| | - Hui Li
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China;
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (Q.C.); (Z.Z.); (Y.W.)
| | - Lei Lei
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
- Correspondence: (L.L.); (B.S.)
| | - Bing Shao
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (Q.C.); (Z.Z.); (Y.W.)
- Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing 100013, China;
- Correspondence: (L.L.); (B.S.)
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The Bacterial Urban Resistome: Recent Advances. Antibiotics (Basel) 2022; 11:antibiotics11040512. [PMID: 35453263 PMCID: PMC9030810 DOI: 10.3390/antibiotics11040512] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Cities that are densely populated are reservoirs of antibiotic resistant genes (ARGs). The overall presence of all resistance genes in a specific environment is defined as a resistome. Spatial proximity of surfaces and different hygienic conditions leads to the transfer of antibiotic resistant bacteria (ARB) within urban environments. Built environments, public transportation, green spaces, and citizens’ behaviors all support persistence and transfer of antimicrobial resistances (AMR). Various unique aspects of urban settings that promote spread and resilience of ARGs/ARB are discussed: (i) the role of hospitals and recreational parks as reservoirs; (ii) private and public transportation as carriers of ARGs/ARB; (iii) the role of built environments as a hub for horizontal gene transfer even though they support lower microbial biodiversity than outdoor environments; (iv) the need to employ ecological and evolutionary concepts, such as modeling the fate of a specific ARG/ARB, to gain enhanced health risk assessments. Our understanding and our ability to control the rise of AMR in an urban setting is linked to our knowledge of the network connecting urban reservoirs and the environment.
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Xu Z, Chen L, Chen X, Tang A, Huang D, Pan Q, Fang Z. Prevalence and Molecular Characterization of Methicillin-Resistant Staphylococci Recovered from Public Shared Bicycles in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084492. [PMID: 35457359 PMCID: PMC9027712 DOI: 10.3390/ijerph19084492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 12/04/2022]
Abstract
Millions of public shared bicycles (PSBs) have been launched in China, and PSBs are a potential reservoir of antimicrobial-resistant staphylococci. However, no national data to elucidate the dissemination, antimicrobial resistance and genotypes of staphylococci has been recovered from public shared bicycles located in different cities in China. Antimicrobial susceptibility, SCCmec types and sequence types of staphylococci were determined. A total of 146 staphylococci were recovered in this study, and 87% staphylococcal isolates were resistant to at least one antibiotic. In total, 29 (20%) staphylococcal isolates harbored mecA gene, and SCCmec types were determined as follows: SCCmec type II (n = 1), IV(n = 3), V (n = 4), VI (n = 1), VIII (n = 2), A/1 (n = 6), A/5 (n = 2), C/1 (n = 2), C/2 (n = 1), C/3 (n = 1), (n = 5) and Pseudo (ψ)-SCCmec (n = 1). Sequence types of 16 Staphylococcus epidermidis were determined, including ST10, ST17, ST59, ST60, ST65, ST130, ST184, ST262, ST283, ST337, ST360, ST454, ST567, ST820, ST878 and ST934. PSBs are a reservoir of diverse antimicrobial-resistant staphylococci, and staphylococcal species differences were observed in isolates that were recovered from public shared bicycles in the south and north of China. PSBs are a source of antimicrobial resistance and genetic diverse staphylococci.
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Affiliation(s)
- Zhen Xu
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China; (L.C.); (X.C.); (A.T.); (D.H.); (Q.P.)
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
- Correspondence: (Z.X.); (Z.F.); Tel.: +86-83336608 (Z.X.)
| | - Liqin Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China; (L.C.); (X.C.); (A.T.); (D.H.); (Q.P.)
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
| | - Xiaowei Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China; (L.C.); (X.C.); (A.T.); (D.H.); (Q.P.)
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
| | - Amei Tang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China; (L.C.); (X.C.); (A.T.); (D.H.); (Q.P.)
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
| | - Dengmin Huang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China; (L.C.); (X.C.); (A.T.); (D.H.); (Q.P.)
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
| | - Qin Pan
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China; (L.C.); (X.C.); (A.T.); (D.H.); (Q.P.)
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
| | - Zhongze Fang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China; (L.C.); (X.C.); (A.T.); (D.H.); (Q.P.)
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
- Center for International Collaborative Research on Environment, Nutrition and Public Health, School of Public Health, Tianjin Medical University, Qixiang Road No. 22, Tianjin 300070, China
- Correspondence: (Z.X.); (Z.F.); Tel.: +86-83336608 (Z.X.)
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Rogers LA, Strong K, Cork SC, McAllister TA, Liljebjelke K, Zaheer R, Checkley SL. The Role of Whole Genome Sequencing in the Surveillance of Antimicrobial Resistant Enterococcus spp.: A Scoping Review. Front Public Health 2021; 9:599285. [PMID: 34178909 PMCID: PMC8222819 DOI: 10.3389/fpubh.2021.599285] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 05/04/2021] [Indexed: 12/19/2022] Open
Abstract
Enterococcus spp. have arisen as important nosocomial pathogens and are ubiquitous in the gastrointestinal tracts of animals and the environment. They carry many intrinsic and acquired antimicrobial resistance genes. Because of this, surveillance of Enterococcus spp. has become important with whole genome sequencing emerging as the preferred method for the characterization of enterococci. A scoping review was designed to determine how the use of whole genome sequencing in the surveillance of Enterococcus spp. adds to our knowledge of antimicrobial resistance in Enterococcus spp. Scoping review design was guided by the PRISMA extension and checklist and JBI Reviewer's Guide for scoping reviews. A total of 72 articles were included in the review. Of the 72 articles included, 48.6% did not state an association with a surveillance program and 87.5% of articles identified Enterococcus faecium. The majority of articles included isolates from human clinical or screening samples. Significant findings from the articles included novel sequence types, the increasing prevalence of vancomycin-resistant enterococci in hospitals, and the importance of surveillance or screening for enterococci. The ability of enterococci to adapt and persist within a wide range of environments was also a key finding. These studies emphasize the importance of ongoing surveillance of enterococci from a One Health perspective. More studies are needed to compare the whole genome sequences of human enterococcal isolates to those from food animals, food products, the environment, and companion animals.
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Affiliation(s)
- Lindsay A Rogers
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Kayla Strong
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Susan C Cork
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Karen Liljebjelke
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Sylvia L Checkley
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. Clin Microbiol Rev 2021; 34:e0018820. [PMID: 34076490 DOI: 10.1128/cmr.00188-20] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.
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