Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China
Clostridioides difficile is the most common pathogen causing antibiotic-associated diarrhea. Previous studies showed that diverse sources, aside from C. difficile infection (CDI) patients, played a major role in C. difficile hospital transmission. This study aimed to investigate relationships and tr...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2021-01-01
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| Series: | Emerging Microbes and Infections |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/22221751.2021.2005453 |
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| author | Yanzi Zhou Wangxiao Zhou Tingting Xiao Yunbo Chen Tao Lv Yuan Wang Shuntian Zhang Hongliu Cai Xiaohui Chi Xiaoyang Kong Kai Zhou Ping Shen Tongling Shan Yonghong Xiao |
| author_facet | Yanzi Zhou Wangxiao Zhou Tingting Xiao Yunbo Chen Tao Lv Yuan Wang Shuntian Zhang Hongliu Cai Xiaohui Chi Xiaoyang Kong Kai Zhou Ping Shen Tongling Shan Yonghong Xiao |
| author_sort | Yanzi Zhou |
| collection | DOAJ |
| description | Clostridioides difficile is the most common pathogen causing antibiotic-associated diarrhea. Previous studies showed that diverse sources, aside from C. difficile infection (CDI) patients, played a major role in C. difficile hospital transmission. This study aimed to investigate relationships and transmission potential of C. difficile strains from different sources. A prospective study was conducted both in the intensive care unit (ICU) and six livestock farms in China in 2018–2019. Ninety-eight strains from CDI patients (10 isolates), asymptomatic hospitalized carriers (55), the ICU environment (12), animals (14), soil (4), and farmers (3) were collected. Sequence type (ST) 3/ribotype (RT) 001, ST35/RT046, and ST48/RT596 were dominant types, distributed widely in multiple sources. Core-genome single-nucleotide polymorphism (cgSNP) analysis showed that hospital and farm strains shared several common clonal groups (CGs, strains separated by ≤ 2 cgSNPs) (CG4/ST3/RT001, CG7/ST35/RT046, CG11/ST48/RT596). CDI patients, asymptomatic carriers, and the ICU environment strains also shared several common CGs. The number of virulence genes was not statistically different between strains from different sources. Multi-source strains in the same CG carried identical virulence gene sequences, including pathogenicity genes at the pathogenicity locus and adhesion-related genes at S-layer cassette. Resistance genes (ermB, tetM, etc.) were widespread in multiple sources, and multi-source strains in the same CG had similar resistance phenotypes and carried consistent transposons and plasmid types. The study indicated that interspecies and cross-regional transmission of C. difficile occurs between animals, the environment, and humans. Community-associated strains from both farms and asymptomatic hospitalized carriers were important reservoirs of CDI in hospitals. |
| format | Article |
| id | doaj-art-82ef11a49332437e8a209a34adffa43b |
| institution | DOAJ |
| issn | 2222-1751 |
| language | English |
| publishDate | 2021-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj-art-82ef11a49332437e8a209a34adffa43b2025-08-20T02:59:11ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512021-01-011012244225510.1080/22221751.2021.2005453Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in ChinaYanzi Zhou0Wangxiao Zhou1Tingting Xiao2Yunbo Chen3Tao Lv4Yuan Wang5Shuntian Zhang6Hongliu Cai7Xiaohui Chi8Xiaoyang Kong9Kai Zhou10Ping Shen11Tongling Shan12Yonghong Xiao13State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaDepartment of Intensive Care Unit, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaShenzhen Institute of Respiratory Diseases, the First Affiliated Hospital (Shenzhen People’s Hospital), Southern University of Science and Technology, and Second Clinical Medical College, Jinan University, Shenzhen, People’s Republic of ChinaState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaDepartment of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR People’s Republic of China.State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of ChinaClostridioides difficile is the most common pathogen causing antibiotic-associated diarrhea. Previous studies showed that diverse sources, aside from C. difficile infection (CDI) patients, played a major role in C. difficile hospital transmission. This study aimed to investigate relationships and transmission potential of C. difficile strains from different sources. A prospective study was conducted both in the intensive care unit (ICU) and six livestock farms in China in 2018–2019. Ninety-eight strains from CDI patients (10 isolates), asymptomatic hospitalized carriers (55), the ICU environment (12), animals (14), soil (4), and farmers (3) were collected. Sequence type (ST) 3/ribotype (RT) 001, ST35/RT046, and ST48/RT596 were dominant types, distributed widely in multiple sources. Core-genome single-nucleotide polymorphism (cgSNP) analysis showed that hospital and farm strains shared several common clonal groups (CGs, strains separated by ≤ 2 cgSNPs) (CG4/ST3/RT001, CG7/ST35/RT046, CG11/ST48/RT596). CDI patients, asymptomatic carriers, and the ICU environment strains also shared several common CGs. The number of virulence genes was not statistically different between strains from different sources. Multi-source strains in the same CG carried identical virulence gene sequences, including pathogenicity genes at the pathogenicity locus and adhesion-related genes at S-layer cassette. Resistance genes (ermB, tetM, etc.) were widespread in multiple sources, and multi-source strains in the same CG had similar resistance phenotypes and carried consistent transposons and plasmid types. The study indicated that interspecies and cross-regional transmission of C. difficile occurs between animals, the environment, and humans. Community-associated strains from both farms and asymptomatic hospitalized carriers were important reservoirs of CDI in hospitals.https://www.tandfonline.com/doi/10.1080/22221751.2021.2005453Clostridioides difficile infectionasymptomatic carriermultiple sourcescomparative genometransmission |
| spellingShingle | Yanzi Zhou Wangxiao Zhou Tingting Xiao Yunbo Chen Tao Lv Yuan Wang Shuntian Zhang Hongliu Cai Xiaohui Chi Xiaoyang Kong Kai Zhou Ping Shen Tongling Shan Yonghong Xiao Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China Emerging Microbes and Infections Clostridioides difficile infection asymptomatic carrier multiple sources comparative genome transmission |
| title | Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China |
| title_full | Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China |
| title_fullStr | Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China |
| title_full_unstemmed | Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China |
| title_short | Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China |
| title_sort | comparative genomic and transmission analysis of clostridioides difficile between environmental animal and clinical sources in china |
| topic | Clostridioides difficile infection asymptomatic carrier multiple sources comparative genome transmission |
| url | https://www.tandfonline.com/doi/10.1080/22221751.2021.2005453 |
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