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Liu S, Yang X, Li R, Wang S, Han Z, Yang M, Zhang Y. IS6 family insertion sequences promote optrA dissemination between plasmids varying in transfer abilities. Appl Microbiol Biotechnol 2024; 108:132. [PMID: 38229329 DOI: 10.1007/s00253-023-12858-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/25/2023] [Accepted: 11/13/2023] [Indexed: 01/18/2024]
Abstract
Plasmids are the primary vectors for intercellular transfer of the oxazolidinone and phenicol cross-resistance gene optrA, while insertion sequences (ISs) are mobile genetic elements that can mobilize plasmid-borne optrA intracellularly. However, little is known about how the IS-mediated intracellular mobility facilitates the dissemination of the optrA gene between plasmid categories that vary in transfer abilities, including non-mobilizable, mobilizable, and conjugative plasmids. Here, we performed a holistic genomic study of 52 optrA-carrying plasmids obtained from searches guided by the Comprehensive Antibiotic Resistance Database. Among the 132 ISs identified within 10 kbp from the optrA gene in the plasmids, IS6 family genes were the most prevalent (86/132). Homologous gene arrays containing IS6 family genes were shared between different plasmids, especially between mobilizable and conjugative plasmids. All these indicated the central role of IS6 family genes in disseminating plasmid-borne optrA. Thirty-three of the 52 plasmids were harbored by Enterococcus faecalis found mainly in humans and animals. By Nanopore sequencing and inverse PCR, the potential of the enterococcal optrA to be transmitted from a mobilizable plasmid to a conjugative plasmid mediated by IS6 family genes was further confirmed in Enterococcus faecalis strains recovered from the effluents of anaerobic digestion systems for treating chicken manure. Our findings highlight the increased intercellular transfer abilities and dissemination risk of plasmid-borne optrA gene caused by IS-mediated intracellular mobility, and underscore the importance of routinely monitoring the dynamic genetic contexts of clinically important antibiotic resistance genes to effectively control this critical public health threat. KEY POINTS: • IS6 was prevalent in optrA-plasmids varying in intercellular transfer abilities. • Enterococcal optrA-plasmids were widespread among human, animal, and the environment. • IS6 elevated the dissemination risk of enterococcal optrA-plasmids.
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Affiliation(s)
- Shihai Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Shaolin Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Wu K, Li Z, Fang M, Yuan Y, Fox EM, Liu Y, Li R, Bai L, Zhang W, Zhang WM, Yang Q, Chang L, Li P, Wang X, Wang J, Yang Z. Genome characteristics of the optrA-positive Clostridium perfringens strain QHY-2 carrying a novel plasmid type. mSystems 2023; 8:e0053523. [PMID: 37458450 PMCID: PMC10469678 DOI: 10.1128/msystems.00535-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/04/2023] [Indexed: 09/01/2023] Open
Abstract
Clostridium perfringens is a bacterial species of importance to both public and animal health. The gene optrA is the first gene that confers resistance to the tedizolid, a last-resort antimicrobial agent in human medicine. Herein, we whole-genome sequenced and analyzed one optrA-positive C. perfringens strain QHY-2 from Tibetan sheep in Qinghai province and identified one optrA plasmid pQHY-2. The plasmid shared similar structure with the optrA-positive plasmids p2C45 and p21-D-5b previously identified in C. perfringens, demonstrating the potential horizontal transmission of the optrA plasmids among C. perfringens strains. Annotation of the optrA-positive plasmids showed optrA and erm(A) located on a segment flanked by IS element IS1216E, and fexA, optrA, and erm(A) located on a segment flanked by IS element ISVlu1, which revealed the possible dissemination mechanism. Additionally, a Tn6218-like transposon carrying aac(6')-aph(2″) and erm(B) was also detected on pQHY-2, demonstrating the transposition of Tn6218 and spread of antibiotic resistance among Clostridium bacteria. Molecular analysis indicated the optrA-positive plasmids belonged to a plasmid type distinct from the pCW3-like plasmids, pCP13-like plasmids, or pIP404-like plasmids. Further structure analysis showed they might be formed by inserting segments into plasmid pCPCPI53k-r1_1, which coexist with two pCW3-like plasmids and one pCP13-like plasmid in C. perfringens strain CPI 53k-r1 isolated from a healthy human in Finland. IMPORTANCE Antimicrobial resistance is now a global concern posing threats to food safety and public health. The pCW3-like plasmids can encode several main toxin genes and three antibiotic resistance genes (ARGs), including tetA(P), tetB(P), and erm(B), which used to be considered as the main carrier of ARGs in Clostridium perfringens. In this study, we found the optrA plasmids, which belonged to a novel plasmid type, could also harbor many other ARGs, indicating this type of plasmid might be the potential repository of ARGs in C. perfringens. Additionally, this type of plasmid could coexist with the pCW3-like plasmids and pCP13-like plasmids that encoded toxin genes associated with gastrointestinal diseases, which showed the potential threat to public health.
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Affiliation(s)
- Ke Wu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Zhe Li
- Bureau of Agriculture and Rural Affairs, Junan, China
| | - Mingjin Fang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Yuan Yuan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Edward M. Fox
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Yingqiu Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Ruichao Li
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Li Bai
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing, China
| | - Wen Zhang
- Ningxia Supervision Institute for Veterinary Drugs and Animal Feedstuffs, Yinchuan, Ningxia, China
| | - Wei-Min Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Qi Yang
- Ningxia Supervision Institute for Veterinary Drugs and Animal Feedstuffs, Yinchuan, Ningxia, China
| | - Lingling Chang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Pu Li
- Department of Critical Care Medicine, the Second Affiliated Hospital of Air Force Medical University, Shaanxi, China
| | - Xinglong Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Juan Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing, China
| | - Zengqi Yang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
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