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He J, Yang Z, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Sun D, Tian B, He Y, Wu Z, Cheng A, Zhu D. Integrative and conjugative elements of Pasteurella multocida: Prevalence and signatures in population evolution. Virulence 2024; 15:2359467. [PMID: 38808732 PMCID: PMC11141479 DOI: 10.1080/21505594.2024.2359467] [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: 01/16/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
Pasteurella multocida (P. multocida) is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in P. multocida and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced P. multocida genomes obtained by high-throughput sequencing together with 393 publicly available P. multocida genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in P. multocida, including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICEHin1056 family, with the latter being widely prevalent in P. multocida and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene blaOXA-2 and the bleomycin gene bleO to P. multocida. Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in P. multocida were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in P. multocida and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.
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Affiliation(s)
- Jiao He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Yu He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Zhen Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
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Wen S, Zhao Y, Qi X, Cai M, Huang K, Liu H, Kong DX. Conformational plasticity of SpyCas9 induced by AcrIIA4 and AcrIIA2: Insights from molecular dynamics simulation. Comput Struct Biotechnol J 2024; 23:537-548. [PMID: 38235361 PMCID: PMC10791570 DOI: 10.1016/j.csbj.2023.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
CRISPR-Cas9 systems constitute bacterial adaptive immune systems that protect against phage infections. Bacteriophages encode anti-CRISPR proteins (Acrs) that mitigate the bacterial immune response. However, the structural basis for their inhibitory actions from a molecular perspective remains elusive. In this study, through microsecond atomistic molecular dynamics simulations, we demonstrated the remarkable flexibility of Streptococcus pyogenes Cas9 (SpyCas9) and its conformational adaptability during interactions with AcrIIA4 and AcrIIA2. Specifically, we demonstrated that the binding of AcrIIA4 and AcrIIA2 to SpyCas9 induces a conformational rearrangement that causes spatial separation between the nuclease and cleavage sites, thus making the endonuclease inactive. This separation disrupts the transmission of signals between the protospacer adjacent motif recognition and nuclease domains, thereby impeding the efficient processing of double-stranded DNA. The simulation also reveals that AcrIIA4 and AcrIIA2 cause different structural variations of SpyCas9. Our research illuminates the precise mechanisms underlying the suppression of SpyCas9 by AcrIIA4 and AcrIIA2, thus presenting new possibilities for controlling genome editing with higher accuracy.
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Affiliation(s)
- Shuixiu Wen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Yuxin Zhao
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Xinyu Qi
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Mingzhu Cai
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Kaisheng Huang
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Hui Liu
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - De-Xin Kong
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
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Hu Y, Wang Y, Hu X, Chao H, Li S, Ni Q, Zhu Y, Hu Y, Zhao Z, Chen M. T4SEpp: A pipeline integrating protein language models to predict bacterial type IV secreted effectors. Comput Struct Biotechnol J 2024; 23:801-812. [PMID: 38328004 PMCID: PMC10847861 DOI: 10.1016/j.csbj.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/20/2024] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Many pathogenic bacteria use type IV secretion systems (T4SSs) to deliver effectors (T4SEs) into the cytoplasm of eukaryotic cells, causing diseases. The identification of effectors is a crucial step in understanding the mechanisms of bacterial pathogenicity, but this remains a major challenge. In this study, we used the full-length embedding features generated by six pre-trained protein language models to train classifiers predicting T4SEs and compared their performance. We integrated three modules into a model called T4SEpp. The first module searched for full-length homologs of known T4SEs, signal sequences, and effector domains; the second module fine-tuned a machine learning model using data for a signal sequence feature; and the third module used the three best-performing pre-trained protein language models. T4SEpp outperformed other state-of-the-art (SOTA) software tools, achieving ∼0.98 accuracy at a high specificity of ∼0.99, based on the assessment of an independent validation dataset. T4SEpp predicted 13 T4SEs from Helicobacter pylori, including the well-known CagA and 12 other potential ones, among which eleven could potentially interact with human proteins. This suggests that these potential T4SEs may be associated with the pathogenicity of H. pylori. Overall, T4SEpp provides a better solution to assist in the identification of bacterial T4SEs and facilitates studies of bacterial pathogenicity. T4SEpp is freely accessible at https://bis.zju.edu.cn/T4SEpp.
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Affiliation(s)
- Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
- Department of Cell Biology and Genetics, College of Basic Medicine, Shenzhen University Medical School, Shenzhen, China
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sida Li
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qinyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanyan Zhu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yixue Hu
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ziyi Zhao
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Medical School, Shenzhen, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
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Chaguza C, Chibwe I, Chaima D, Musicha P, Ndeketa L, Kasambara W, Mhango C, Mseka UL, Bitilinyu-Bangoh J, Mvula B, Kipandula W, Bonongwe P, Munthali RJ, Ngwira S, Mwendera CA, Kalizang'oma A, Jambo KC, Kambalame D, Kamng'ona AW, Steele AD, Chauma-Mwale A, Hungerford D, Kagoli M, Nyaga MM, Dube Q, French N, Msefula CL, Cunliffe NA, Jere KC. Genomic insights into the 2022-2023Vibrio cholerae outbreak in Malawi. Nat Commun 2024; 15:6291. [PMID: 39060226 PMCID: PMC11282309 DOI: 10.1038/s41467-024-50484-w] [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: 06/08/2023] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Malawi experienced its deadliest Vibrio cholerae (Vc) outbreak following devastating cyclones, with >58,000 cases and >1700 deaths reported between March 2022 and May 2023. Here, we use population genomics to investigate the attributes and origin of the Malawi 2022-2023 Vc outbreak isolates. Our results demonstrate the predominance of ST69 clone, also known as the seventh cholera pandemic El Tor (7PET) lineage, expressing O1 Ogawa (~ 80%) serotype followed by Inaba (~ 16%) and sporadic non-O1/non-7PET serogroups (~ 4%). Phylogenetic reconstruction revealed that the Malawi outbreak strains correspond to a recent importation from Asia into Africa (sublineage AFR15). These isolates harboured known antimicrobial resistance and virulence elements, notably the ICEGEN/ICEVchHai1/ICEVchind5 SXT/R391-like integrative conjugative elements and a CTXφ prophage with the ctxB7 genotype compared to historical Malawian Vc isolates. These data suggest that the devastating cyclones coupled with the recent importation of 7PET serogroup O1 strains, may explain the magnitude of the 2022-2023 cholera outbreak in Malawi.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA.
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK.
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | - Innocent Chibwe
- Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi
| | - David Chaima
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Patrick Musicha
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Latif Ndeketa
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | | | | | - Upendo L Mseka
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | | | - Bernard Mvula
- Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi
| | - Wakisa Kipandula
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health profession, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Patrick Bonongwe
- Ministry of Health, Balaka District Hospital, Balaka, Machinga, Malawi
| | - Richard J Munthali
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Selemani Ngwira
- Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi
| | - Chikondi A Mwendera
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Akuzike Kalizang'oma
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Kondwani C Jambo
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Arox W Kamng'ona
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - A Duncan Steele
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, 0204, Pretoria, South Africa
| | | | - Daniel Hungerford
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Matthew Kagoli
- Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi
| | - Martin M Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, 9300, South Africa
| | - Queen Dube
- Malawi Ministry of Health, Lilongwe, Malawi
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Chisomo L Msefula
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Nigel A Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Khuzwayo C Jere
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi.
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health profession, Kamuzu University of Health Sciences, Blantyre, Malawi.
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK.
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, UK.
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Cinar M, Martinez-Medina L, Puvvula P, Arakelyan A, Vardarajan B, Anthony N, Nagaraju G, Park D, Feng L, Sheff F, Mosunjac M, Saxe D, Flygare S, Alese O, Kaufman J, Lonial S, Sarmiento J, Lossos I, Vertino P, Lopez J, El-Rayes B, Bernal-Mizrachi L. Transposon DNA sequences facilitate the tissue-specific gene transfer of circulating tumor DNA between human cells. Nucleic Acids Res 2024; 52:7539-7555. [PMID: 38783375 PMCID: PMC11260451 DOI: 10.1093/nar/gkae427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/01/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
The exchange of genes between cells is known to play an important physiological and pathological role in many organisms. We show that circulating tumor DNA (ctDNA) facilitates cell-specific gene transfer between human cancer cells and explain part of the mechanisms behind this phenomenon. As ctDNA migrates into the nucleus, genetic information is transferred. Cell targeting and ctDNA integration require ERVL, SINE or LINE DNA sequences. Chemically manufactured AluSp and MER11C sequences replicated multiple myeloma (MM) ctDNA cell targeting and integration. Additionally, we found that ctDNA may alter the treatment response of MM and pancreatic cancer models. This study shows that retrotransposon DNA sequences promote cancer gene transfer. However, because cell-free DNA has been detected in physiological and other pathological conditions, our findings have a broader impact than just cancer. Furthermore, the discovery that transposon DNA sequences mediate tissue-specific targeting will open up a new avenue for the delivery of genes and therapies.
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Affiliation(s)
- Munevver Cinar
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | | | | | - Arsen Arakelyan
- Bioinformatics group, Institute of Molecular Biology NAS RA, Yerevan, Armenia
| | | | - Neil Anthony
- Integrated Cellular Imaging Core, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Ganji P Nagaraju
- Division of hematology and oncology, O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dongkyoo Park
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Lei Feng
- Kodikaz Therapeutic Solutions, Inc, New York, NY, USA
| | - Faith Sheff
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Marina Mosunjac
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Debra Saxe
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Steven Flygare
- Department of Computational Biology/ Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Olatunji B Alese
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Jonathan L Kaufman
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Juan M Sarmiento
- Department of Surgery, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Izidore S Lossos
- Department of Medicine, Division of Hematology-Oncology and Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Paula M Vertino
- Department of Biomedical Genetics and the Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Jose A Lopez
- Bloodworks Northwest Research Institute, Division of Hematology, University of Washington School of Medicine, Seattle, WA, USA
| | - Bassel El-Rayes
- Division of hematology and oncology, O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leon Bernal-Mizrachi
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
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6
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Nazir R, Shua D, Shen JP, Hu HW, Wang JT, He JZ. Effect of meddling ARBs on ARGs dynamics in fungal infested soil and their selective dispersal along spatially distant mycelial networks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174594. [PMID: 38992349 DOI: 10.1016/j.scitotenv.2024.174594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
During the recent times, environmental antibiotic resistance genes (ARGs) and their potential transfer to other bacterial hosts of pathogenic importance are of serious concern. However, the dissemination strategies of such ARGs are largely unknown. We tested that saprotrophic soil fungi differentially enriched antibiotic resistant bacteria (ARBs) and subsequently contributed in spatial distribution of selective ARGs. Wafergen qPCR analysis of 295 different ARGs was conducted for manure treated pre-sterilized soil incubated or not with selected bacterial-fungal consortia. The qPCR assay detected unique ARGs specifically found in the mycosphere of ascomycetous and basidiomycetous fungi. Both fungi exerted potentially different selection pressures on ARBs, resulting in different patterns of ARGs dissemination (to distant places) along their respective growing fungal highways. The relative abundance of mobile genetic elements (MGEs) was significantly decreased along fungal highways compared to the respective inoculation points. Moreover, the decrease in MGEs and ARGs (along fungal highways) was more prominent over time which depicts the continuous selection pressure of growing fungi on ARBs for enrichment of particular ARGs in mycosphere. Such data also indicate the potential role of saprotrophic soil fungi to facilitate horizontal gene transfer within mycospheric environmental settings. Our study, therefore, advocates to emphasize the future investigations for such (bacteria-fungal) interactive microbial consortia for potential (spatial) dissemination of resistance determinants which may ultimately increase the exposure risks of ARGs.
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Affiliation(s)
- Rashid Nazir
- Department of Environmental Sciences, COMSATS University Islamabad (CUI), Abbottabad - Campus, Tobe Camp, University Road, 22060 Abbottabad, Pakistan; State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Du Shua
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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7
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Zalewska M, Błażejewska A, Gawor J, Adamska D, Goryca K, Szeląg M, Kalinowski P, Popowska M. The IncC and IncX1 resistance plasmids present in multi-drug resistant Escherichia coli strains isolated from poultry manure in Poland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:47727-47741. [PMID: 39007976 PMCID: PMC11297818 DOI: 10.1007/s11356-024-34283-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
The study describes the whole-genome sequencing of two antibiotic-resistant representative Escherichia coli strains, isolated from poultry manure in 2020. The samples were obtained from a commercial chicken meat production facility in Poland. The antibiotic resistance profile was characterized by co-resistance to β-lactam antibiotics, aminoglycosides, and fluoroquinolones. The three identified resistance plasmids (R-plasmids), pECmdr13.2, pECmdr13.3, and pECmdr14.1, harbored various genes conferring resistance to tetracyclines (tetR[A]) for, aminoglycoside (aph, aac, and aad families), β-lactam (blaCMY-2, blaTEM-176), sulfonamide (sul1, sul2), fluoroquinolone (qnrS1), and phenicol (floR). These plasmids, which have not been previously reported in Poland, were found to carry IS26 insertion elements, the intI1-integrase gene, and conjugal transfer genes, facilitating horizontal gene transfer. Plasmids pECmdr13.2 and pECmdr14.1 also possessed a mercury resistance gene operon related to transposon Tn6196; this promotes plasmid persistence even without antibiotic selection pressure due to co-selection mechanisms such as co-resistance. The chicken manure-derived plasmids belonged to the IncX1 (narrow host range) and IncC (broad host range) incompatibility groups. Similar plasmids have been identified in various environments, clinical isolates, and farm animals, including cattle, swine, and poultry. This study holds significant importance for the One Health approach, as it highlights the potential for antibiotic-resistant bacteria from livestock and food sources, particularly E. coli, to transfer through the food chain to humans and vice versa.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland
| | - Aleksandra Błażejewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Dorota Adamska
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, S. Banacha 2C, 02-097, Warsaw, Poland
| | - Krzysztof Goryca
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, S. Banacha 2C, 02-097, Warsaw, Poland
| | - Michał Szeląg
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, S. Banacha 2C, 02-097, Warsaw, Poland
| | - Patryk Kalinowski
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland.
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8
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Tatarenkov A, Muñoz-Gutiérrez I, Vargas I, Behnsen J, Mota-Bravo L. Pangenome Analysis Reveals Novel Contact-Dependent Growth Inhibition System and Phenazine Biosynthesis Operons in Proteus mirabilis BL95 That Are Located in An Integrative and Conjugative Element. Microorganisms 2024; 12:1321. [PMID: 39065090 PMCID: PMC11278526 DOI: 10.3390/microorganisms12071321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/15/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Proteus mirabilis is a leading cause of urinary tract infections and a common commensal of the gastrointestinal tract. Our recent study (JB) showed that P. mirabilis strain BL95 employs a novel contact-dependent killing system against enteric bacteria in the mouse gut and in vitro. To uncover the genetic determinants of this system, we performed whole-genome sequencing of BL95 and compared it with 98 complete genomes of P. mirabilis. BL95 carries 56 coding sequences (CDSs) not found in other P. mirabilis. Over half of these unique genes are located on a novel integrative conjugative element (ICE) named ICEPm2, inserted in tRNA-Phe and exclusive to BL95. ICEPm2 has integration, conjugation, and DNA replication modules nearly identical to ICEPm1 (common in P. mirabilis), but ICEPm2 of BL95 carries two unique operons for P. mirabilis-a phenazine biosynthesis and a contact-dependent growth inhibition (CDI) system. ICEPm2 is absent in the P. mirabilis (AR_0156) closest to BL95 and it is present in the genomes of several Escherichia coli from mouse intestines, indicating its recent horizontal mobilization. BL95 shares over 100 genes of five different secretion systems with other P. mirabilis, mostly poorly studied, making a large pool of candidate genes for the contact-dependent growth inhibition.
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Affiliation(s)
- Andrey Tatarenkov
- School of Biological Sciences, University of California, Irvine, CA 92697, USA; (A.T.); (I.M.-G.); (I.V.)
| | - Iván Muñoz-Gutiérrez
- School of Biological Sciences, University of California, Irvine, CA 92697, USA; (A.T.); (I.M.-G.); (I.V.)
| | - Isabel Vargas
- School of Biological Sciences, University of California, Irvine, CA 92697, USA; (A.T.); (I.M.-G.); (I.V.)
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60612, USA;
| | - Luis Mota-Bravo
- School of Biological Sciences, University of California, Irvine, CA 92697, USA; (A.T.); (I.M.-G.); (I.V.)
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9
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Oles RE, Terrazas MC, Loomis LR, Neal MJ, Paulchakrabarti M, Zuffa S, Hsu CY, Vasquez Ayala A, Lee MH, Tribelhorn C, Belda-Ferre P, Bryant M, Zemlin J, Young J, Dulai P, Sandborn WJ, Sivagnanam M, Raffatellu M, Pride D, Dorrestein PC, Zengler K, Choudhury B, Knight R, Chu H. Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599758. [PMID: 38948766 PMCID: PMC11213024 DOI: 10.1101/2024.06.19.599758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathogenic. To determine the genetic basis of its duality, we conducted a comparative genomic analysis of 813 B. fragilis strains, representing both commensal and pathogenic origins. Our findings reveal that pathogenic strains emerge across diverse phylogenetic lineages, due in part to rapid gene exchange and the adaptability of the accessory genome. We identified 16 phylogenetic groups, differentiated by genes associated with capsule composition, interspecies competition, and host interactions. A microbial genome-wide association study identified 44 genes linked to extra-intestinal survival and pathogenicity. These findings reveal how genomic diversity within commensal species can lead to the emergence of pathogenic traits, broadening our understanding of microbial evolution in the gut.
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Affiliation(s)
- Renee E. Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | | | - Luke R. Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Maxwell J. Neal
- Department of Bioengineering, University of California, San Diego, La Jolla, CA
| | | | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | | | - Michael H. Lee
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Caitlin Tribelhorn
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Pedro Belda-Ferre
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - MacKenzie Bryant
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA
| | - Jocelyn Young
- Division of Gastroenterology, Hepatology and Nutrition, University of California, San Diego and Rady Children’s Hospital, San Diego, CA
| | - Parambir Dulai
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Division of Gastroenterology, Northwestern University, Chicago, Illinois
| | - William J. Sandborn
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Mamata Sivagnanam
- Division of Gastroenterology, Hepatology and Nutrition, University of California, San Diego and Rady Children’s Hospital, San Diego, CA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Center for Innovative Phage Applications and Therapeutics (IPATH), University of California, San Diego, La Jolla, CA
- Center of Advanced Laboratory Medicine (CALM), University of California, San Diego, La Jolla, CA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA
| | - Karsten Zengler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, CA
| | - Biswa Choudhury
- GlycoAnalytics Core, University of California San Diego, San Diego, CA
| | - Rob Knight
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA
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10
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Dadeh Amirfard K, Moriyama M, Suzuki S, Sano D. Effect of environmental factors on conjugative transfer of antibiotic resistance genes in aquatic settings. J Appl Microbiol 2024; 135:lxae129. [PMID: 38830804 DOI: 10.1093/jambio/lxae129] [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: 09/27/2023] [Revised: 04/25/2024] [Accepted: 06/02/2024] [Indexed: 06/05/2024]
Abstract
Antimicrobial-resistance genes (ARGs) are spread among bacteria by horizontal gene transfer, however, the effect of environmental factors on the dynamics of the ARG in water environments has not been very well understood. In this systematic review, we employed the regression tree algorithm to identify the environmental factors that facilitate/inhibit the transfer of ARGs via conjugation in planktonic/biofilm-formed bacterial cells based on the results of past relevant research. Escherichia coli strains were the most studied genus for conjugation experiments as donor/recipient in the intra-genera category. Conversely, Pseudomonas spp., Acinetobacter spp., and Salmonella spp. were studied primarily as recipients across inter-genera bacteria. The conjugation efficiency (ce) was found to be highly dependent on the incubation period. Some antibiotics, such as nitrofurantoin (at ≥0.2 µg ml-1) and kanamycin (at ≥9.5 mg l-1) as well as metallic compounds like mercury (II) chloride (HgCl2, ≥3 µmol l-1), and vanadium (III) chloride (VCl3, ≥50 µmol l-1) had enhancing effect on conjugation. The highest ce value (-0.90 log10) was achieved at 15°C-19°C, with linoleic acid concentrations <8 mg l-1, a recognized conjugation inhibitor. Identifying critical environmental factors affecting ARG dissemination in aquatic environments will accelerate strategies to control their proliferation and combat antibiotic resistance.
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Affiliation(s)
- Katayoun Dadeh Amirfard
- Department of Frontier Science for Advanced Environment, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Miyagi 980-8579, Japan
| | - Momoko Moriyama
- Department of Frontier Science for Advanced Environment, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Miyagi 980-8579, Japan
| | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University, Bunkyōchō 2-5, Matsuyama, Ehime 790-8577, Japan
| | - Daisuke Sano
- Department of Frontier Science for Advanced Environment, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Miyagi 980-8579, Japan
- Department of Civil and Environmental Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Miyagi 980-8579, Japan
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11
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Yi S, Zhou K, Xu X. Characterization of erm(B)-Carrying Integrative and Conjugative Elements Transferred from Streptococcus anginosus to Other Streptococci and Enterococci. Microb Drug Resist 2024; 30:243-253. [PMID: 38608246 DOI: 10.1089/mdr.2023.0342] [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] [Indexed: 04/14/2024] Open
Abstract
Integrative and conjugative elements (ICEs) are important vectors of lateral gene transfer and contribute to the evolution of bacterial pathogens. However, studies on the transfer among species and the physiological consequences of ICEs are rare. The objective of this study was to investigate the cross-species transferability of newly identified erm(B)-carried ICE in Streptococcus anginosus San95 and its physiological consequences after transfer. The erm(B)-carried ICE, characterized by a triple serine integrase module, integrated into hsdM genes, thus designated ICESan95_hsdM. Analysis of ICESan95_hsdM revealed 32 additional ICESan95-like ICEs in the available NCBI genome (n = 24) and sequence of clinical isolates (n = 8). Polymerase chain reaction (PCR) was used to evaluate the 467 clinical isolates, of which 84 were positive for core genes (integrase, relaxase, and T4SS genes) of ICESan95_hsdM. Cross-species transfer experiments demonstrated that ICESan95_hsdM could transfer from S. anginosus to different streptococcal and enterococcal recipients. Growth and competitive culture assays showed acquisition of ICESan95_hsdM incurred no fitness cost. Our work discovered a group of ICEs in Streptococci and Enterococci. For the first time, we demonstrated the broad cross-species transferability to different species or genera of ICEs with no fitness cost that enables commensal S. anginosus to deliver antimicrobial resistance genes to other streptococci and enterococci.
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Affiliation(s)
- Sida Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Kaixin Zhou
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
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12
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Koo H, Morrow CD. Bacteroidales-Specific Antimicrobial Genes Can Influence the Selection of the Dominant Fecal Strain of Bacteroides vulgatus and Bacteroides uniformis from the Gastrointestinal Tract Microbial Community. Life (Basel) 2024; 14:555. [PMID: 38792577 PMCID: PMC11121782 DOI: 10.3390/life14050555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Bacteroides vulgatus and Bacteroides uniformis are known to be abundant in the human fecal microbial community. Although these strains typically remain stable over time in humans, disruption of this microbial community following antibiotics resulted in the transient change to new strains suggesting that a complex, dynamic strain community exists in humans. To further study the selection of dominant fecal microbial strains from the gastrointestinal tract (GIT) community, we analyzed three longitudinal metagenomic sequencing data sets using BLAST+ to identify genes encoding Bacteroidales-specific antimicrobial proteins (BSAP) that have known functions to restrict species-specific replication of B. uniformis (BSAP-2) or B. vulgatus (BSAP-3) and have been postulated to provide a competitive advantage in microbial communities. In the HMP (Human Microbiome Project) data set, we found fecal samples from individuals had B. vulgatus or B. uniformis with either complete or deleted BSAP genes that did not change over time. We also examined fecal samples from two separate longitudinal data sets of individuals who had been given either single or multiple antibiotics. The BSAP gene pattern from most individuals given either single or multiple antibiotics recovered to be the same as the pre-antibiotic strain. However, in a few individuals, we found incomplete BSAP-3 genes at early times during the recovery that were replaced by B. vulgatus with the complete BSAP-3 gene, consistent with the function of the BSAP to specifically restrict Bacteroides spp. The results of these studies provide insights into the fluxes that occur in the Bacteroides spp. GIT community following perturbation and the dynamics of the selection of a dominant fecal strain of Bacteroides spp.
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Affiliation(s)
- Hyunmin Koo
- Department of Genetics, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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13
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Lin ZJ, Zhou ZC, Shuai XY, Shan XY, Zhou JY, Chen H. Deciphering Multidrug-Resistant Plasmids in Disinfection Residual Bacteria from a Wastewater Treatment Plant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6793-6803. [PMID: 38574343 DOI: 10.1021/acs.est.3c10895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Current disinfection processes pose an emerging environmental risk due to the ineffective removal of antibiotic-resistant bacteria, especially disinfection residual bacteria (DRB) carrying multidrug-resistant plasmids (MRPs). However, the characteristics of DRB-carried MRPs are poorly understood. In this study, qPCR analysis reveals that the total absolute abundance of four plasmids in postdisinfection effluent decreases by 1.15 log units, while their relative abundance increases by 0.11 copies/cell compared to investigated wastewater treatment plant (WWTP) influent. We obtain three distinctive DRB-carried MRPs (pWWTP-01-03) from postdisinfection effluent, each carrying 9-11 antibiotic-resistant genes (ARGs). pWWTP-01 contains all 11 ARGs within an ∼25 Kbp chimeric genomic island showing strong patterns of recombination with MRPs from foodborne outbreaks and hospitals. Antibiotic-, disinfectant-, and heavy-metal-resistant genes on the same plasmid underscore the potential roles of disinfectants and heavy metals in the coselection of ARGs. Additionally, pWWTP-02 harbors an adhesin-type virulence operon, implying risks of both antibiotic resistance and pathogenicity upon entering environments. Furthermore, some MRPs from DRB are capable of transferring and could confer selective advantages to recipients under environmentally relevant antibiotic pressure. Overall, this study advances our understanding of DRB-carried MRPs and highlights the imminent need to monitor and control wastewater MRPs for environmental security.
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Affiliation(s)
- Ze-Jun Lin
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhen-Chao Zhou
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin-Yi Shuai
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Yu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jin-Yu Zhou
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou 310058, China
- International Cooperation Base of Environmental Pollution and Ecological Health, Science and Technology Agency of Zhejiang, Zhejiang University, Hangzhou 310058, China
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14
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Che Y, Wu R, Li H, Wang L, Wu X, Chen Q, Chen R, Zhou L. Molecular characterization of the integrative and conjugative elements harbouring multidrug resistance genes in Glaesserella parasuis. Vet Microbiol 2024; 291:110014. [PMID: 38335675 DOI: 10.1016/j.vetmic.2024.110014] [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: 07/08/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
It is widely known that integrative and conjugative elements (ICEs) play an important role in the transmission of resistance genes and other exogenous genes. The present study aimed to characterize the three novel ICEs including ICEGpa76, ICEGpa44, and ICEGpa11, from Glaesserella parasuis. The ICEs from G. parasuis strains d76, Z44, and XP11 were predicted and identified by whole-genome sequencing (WGS) analysis, ICEfinder, and PCR. Characterization of G. parasuis strains carrying ICEs were determined by conjugation assay, antimicrobial susceptibility testing, WGS, phylogenetic analysis, and comparative sequence analysis.The WGS results showed that three ICEs from G. parasuis have a common genetic backbone belonging to characteristics ofthe ICEHpa1 family. The sequence comparison showed that the ICEHpa1 family has five hot spots (HSs) determined by IS6, IS110, and IS256. Moreover, two variable regions (VRs), VR1 and VR2 were determined by multidrug resistance genes and the rearrangement hotspot (rhs) family, respectively. VR1 consists of multidrug resistance genes, ISApl1s, and other accessory genes, while VR2 is composed of IS4, rhs family, transposase, and hypothetical protein genes. Conjugation experiments and MICs revealed that three ICEs could be transferred to G. parasuis strain IV52, indicating these three ICEs could be transmitted horizontally among G. parasuis strains. Additionally, the difference in resistance genes from ICEs might be due to the insertion function of the ISApl1s in VR1, and the rhs family in VR2 might evolve andthen be stably inherited in G. parasuis. These results further elucidated the transmission mechanism of exogenous genes in G. parasuis.
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Affiliation(s)
- Yongliang Che
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, China
| | - Renjie Wu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Hongjie Li
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Longbai Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, China
| | - Xuemin Wu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, China
| | - Qiuyong Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, China
| | - Rujing Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, China
| | - Lunjiang Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China; Fujian Animal Diseases Control Technology Development Center, Fuzhou, China.
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15
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Kehlet-Delgado H, Montoya AP, Jensen KT, Wendlandt CE, Dexheimer C, Roberts M, Torres Martínez L, Friesen ML, Griffitts JS, Porter SS. The evolutionary genomics of adaptation to stress in wild rhizobium bacteria. Proc Natl Acad Sci U S A 2024; 121:e2311127121. [PMID: 38507447 PMCID: PMC10990125 DOI: 10.1073/pnas.2311127121] [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: 07/05/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024] Open
Abstract
Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.
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Affiliation(s)
| | | | - Kyson T. Jensen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT84602
| | | | | | - Miles Roberts
- School of Biological Sciences, Washington State University, Vancouver, WA98686
| | | | - Maren L. Friesen
- Department of Plant Pathology, Washington State University, Pullman, WA99164
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA99164
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT84602
| | - Stephanie S. Porter
- School of Biological Sciences, Washington State University, Vancouver, WA98686
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16
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Colombi E, Bertels F, Doulcier G, McConnell E, Pichugina T, Sohn KH, Straub C, McCann HC, Rainey PB. Rapid dissemination of host metabolism-manipulating genes via integrative and conjugative elements. Proc Natl Acad Sci U S A 2024; 121:e2309263121. [PMID: 38457521 PMCID: PMC10945833 DOI: 10.1073/pnas.2309263121] [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: 06/01/2023] [Accepted: 01/08/2024] [Indexed: 03/10/2024] Open
Abstract
Integrative and conjugative elements (ICEs) are self-transmissible mobile elements that transfer functional genetic units across broad phylogenetic distances. Accessory genes shuttled by ICEs can make significant contributions to bacterial fitness. Most ICEs characterized to date encode readily observable phenotypes contributing to symbiosis, pathogenicity, and antimicrobial resistance, yet the majority of ICEs carry genes of unknown function. Recent observations of rapid acquisition of ICEs in a pandemic lineage of Pseudomonas syringae pv. actinidae led to investigation of the structural and functional diversity of these elements. Fifty-three unique ICE types were identified across the P. syringae species complex. Together they form a distinct family of ICEs (PsICEs) that share a distant relationship to ICEs found in Pseudomonas aeruginosa. PsICEs are defined by conserved backbone genes punctuated by an array of accessory cargo genes, are highly recombinogenic, and display distinct evolutionary histories compared to their bacterial hosts. The most common cargo is a recently disseminated 16-kb mobile genetic element designated Tn6212. Deletion of Tn6212 did not alter pathogen growth in planta, but mutants displayed fitness defects when grown on tricarboxylic acid (TCA) cycle intermediates. RNA-seq analysis of a set of nested deletion mutants showed that a Tn6212-encoded LysR regulator has global effects on chromosomal gene expression. We show that Tn6212 responds to preferred carbon sources and manipulates bacterial metabolism to maximize growth.
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Affiliation(s)
- Elena Colombi
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Guilhem Doulcier
- Laboratoire Biophysique et Évolution, Institut Chemie Biologie Innovation, École Supérieure de Physique et de Chemie Industrielles de la Ville de Paris, Université Paris Science et Lettres, Centre National de al Reserche Scientifique, Paris 75005, France
| | - Ellen McConnell
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Tatyana Pichugina
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Kee Hoon Sohn
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Christina Straub
- Health and Environment, Institute of Environmental Science and Research, Auckland 1025, New Zealand
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Honour C McCann
- Plant Pathogen Evolution Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Laboratoire Biophysique et Évolution, Institut Chemie Biologie Innovation, École Supérieure de Physique et de Chemie Industrielles de la Ville de Paris, Université Paris Science et Lettres, Centre National de al Reserche Scientifique, Paris 75005, France
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17
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Cai J, Geng Y, Zhang B, Li Y. Discovery of a Novel Integrative Conjugative Element ICE AplChn2 Related to SXT/R391 in Actinobacillus pleuropneumoniae. Microb Drug Resist 2024; 30:134-140. [PMID: 38181173 DOI: 10.1089/mdr.2023.0108] [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] [Indexed: 01/07/2024] Open
Abstract
Objective: The objective of this study was to characterize ICEAplChn2, a novel SXT/R391-related integration and conjugation element (ICE) carrying 19 drug resistance genes, in a clinical isolate of Actinobacillus pleuropneumoniae from swine. Methods: Whole genome sequencing (WGS) of A. pleuropneumoniae CP063424 strain was completed using a combination of third-generation PacBio and second-generation Illumina. The putative ICE was predicted by the online tool ICEfinder. ICEAplChn2 was analyzed by PCR, conjugation experiments, and bioinformatics tools. Results: A. pleuropneumoniae CP063424 strain exhibited high minimum inhibitory concentrations of clindamycin (1,024 mg/L). The WGS data revealed that ICEAplChn2, with a length of 167,870 bp and encoding 151 genes, including multiple antibiotic resistance genes such as erm(42), VanE, LpxC, dfrA1, golS, aadA3, EreA, dfrA32, tetR(C), tet(C), sul2, aph(3)″-lb, aph(6)-l, floR, dfrA, ANT(3″)-IIa, catB11, and VanRE, was found to be related to the SXT/R391 family on the chromosome of A. pleuronipneumoniae CP063424. The circular intermediate of ICEAplChn2 was detected by PCR, but conjugation experiments showed that it was not self-transmissible. Conclusions: To our knowledge, ICEAplChn2 is the longest member with the most resistance genes in the SXT/R391 family. Meanwhile, ATP-binding cassette superfamily was found to be inserted in the ICEAplChn2 and possessed a new insertion region, which is the first description in the SXT/R391 family.
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Affiliation(s)
- Jinshuang Cai
- Key Laboratory of Bacteriology, College of Veterinary Medicine, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yan Geng
- Key Laboratory of Bacteriology, College of Veterinary Medicine, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Baoge Zhang
- Key Laboratory of Bacteriology, College of Veterinary Medicine, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Li
- Key Laboratory of Bacteriology, College of Veterinary Medicine, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
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18
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Dechêne-Tempier M, de Boisséson C, Lucas P, Bougeard S, Libante V, Marois-Créhan C, Payot S. Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France. Microb Genom 2024; 10:001224. [PMID: 38536216 PMCID: PMC10995628 DOI: 10.1099/mgen.0.001224] [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: 11/16/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024] Open
Abstract
Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.
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Affiliation(s)
- Manon Dechêne-Tempier
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Claire de Boisséson
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
| | - Pierrick Lucas
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Génétique Virale et Biosécurité, BP53 22440 Ploufragan, France
| | - Stéphanie Bougeard
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Épidémiologie, santé et bien-être, BP53 22440 Ploufragan, France
| | | | - Corinne Marois-Créhan
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
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19
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Yu MK, Fogarty EC, Eren AM. Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess. Nat Microbiol 2024; 9:830-847. [PMID: 38443576 PMCID: PMC10914615 DOI: 10.1038/s41564-024-01610-3] [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: 07/21/2022] [Accepted: 01/17/2024] [Indexed: 03/07/2024]
Abstract
Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive 'plasmid systems' using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems.
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Affiliation(s)
- Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL, USA.
| | - Emily C Fogarty
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee On Microbiology, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany.
- Marine 'Omics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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20
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Lyu B, Song Q. The intricate relationship of G-Quadruplexes and bacterial pathogenicity islands. eLife 2024; 12:RP91985. [PMID: 38391174 PMCID: PMC10942614 DOI: 10.7554/elife.91985] [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] [Indexed: 02/24/2024] Open
Abstract
The dynamic interplay between guanine-quadruplex (G4) structures and pathogenicity islands (PAIs) represents a captivating area of research with implications for understanding the molecular mechanisms underlying pathogenicity. This study conducted a comprehensive analysis of a large-scale dataset from reported 89 pathogenic strains of bacteria to investigate the potential interactions between G4 structures and PAIs. G4 structures exhibited an uneven and non-random distribution within the PAIs and were consistently conserved within the same pathogenic strains. Additionally, this investigation identified positive correlations between the number and frequency of G4 structures and the GC content across different genomic features, including the genome, promoters, genes, tRNA, and rRNA regions, indicating a potential relationship between G4 structures and the GC-associated regions of the genome. The observed differences in GC content between PAIs and the core genome further highlight the unique nature of PAIs and underlying factors, such as DNA topology. High-confidence G4 structures within regulatory regions of Escherichia coli were identified, modulating the efficiency or specificity of DNA integration events within PAIs. Collectively, these findings pave the way for future research to unravel the intricate molecular mechanisms and functional implications of G4-PAI interactions, thereby advancing our understanding of bacterial pathogenicity and the role of G4 structures in pathogenic diseases.
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Affiliation(s)
- Bo Lyu
- Division of Plant Science and Technology, University of MissouriColumbiaUnited States
| | - Qisheng Song
- Division of Plant Science and Technology, University of MissouriColumbiaUnited States
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21
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Xu M, Chen M, Pan C, Xu RZ, Gao P, Chen HQ, Shen XX. Microplastics shape microbial interactions and affect the dissemination of antibiotic resistance genes in different full-scale wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168313. [PMID: 38007128 DOI: 10.1016/j.scitotenv.2023.168313] [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: 08/22/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 11/27/2023]
Abstract
Wastewater treatment plants (WWTPs) pose a potential threat to the environment because of the accumulation of antibiotic resistance genes (ARGs) and microplastics (MPs). However, the interactions between ARGs and MPs, which have both indirect and direct effects on ARG dissemination in WWTPs, remain unclear. In this study, spatiotemporal variations in different types of MPs, ten ARGs (sul1, sul2, tetA, tetO, tetM, tetX, tetW, qnrS, ermB, and ermC), class 1 integron integrase (intI1) and transposon Tn916/1545 in three typical WWTPs were characterized. Sul1, tetO, and sul2 were the predominant ARGs in the targeted WWTPs, whereas the intI1 and transposon Tn916/1545 were positively correlated with most of the targeted ARGs. Saccharimonadales (4.15 %), Trichococcus (2.60 %), Nitrospira (1.96 %), Candidatus amarolinea (1.79 %), and SC-I-84 (belonging to phylum Proteobacteria) (1.78 %) were the dominant genera. Network and redundancy analyses showed that Trichococcus, Faecalibacterium, Arcobacter, and Prevotella copri were potential hosts of ARGs, whereas Candidatus campbellbacteria and Candidatus kaiserbacteria were negatively correlated with ARGs. The potential hosts of ARGs had a strong positive correlation with polyethylene terephthalate, silicone resin, and fluor rubber and a negative correlation with polyurethane. Candidatus campbellbacteria and Candidatus kaiserbacteria were positively correlated with polyurethane, whereas potential hosts of ARGs were positively correlated with polypropylene and fluor rubber. Structural equation modeling highlighted that intI1, transposon Tn916/1545 and microbial communities, particularly microbial diversity, dominated the dissemination of ARGs, whereas MPs had a significant positive correlation with microbial abundance. Our study deepens the understanding of the relationships between ARGs and MPs in WWTPs, which will be helpful in designing strategies for inhibiting ARG hosts in WWTPs.
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Affiliation(s)
- Ming Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Mengkai Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Chengyu Pan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Run-Ze Xu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Peng Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Hao-Qiang Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Xiao-Xiao Shen
- Institute of Water Science and Technology, Hohai University, Nanjing 210098, China; The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China.
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22
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Zhang J, Li W, Zhang X, Wang X, Lv L. Combined applications of UV and chlorine on antibiotic resistance control: A critical review. ENVIRONMENTAL RESEARCH 2024; 243:117884. [PMID: 38072103 DOI: 10.1016/j.envres.2023.117884] [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: 10/01/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Environmental health problems caused by antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) have become a global concern. ARB and ARGs have been continuously detected in various water environments, which pose a new challenge for water quality safety assurance. Disinfection is a key water treatment process to eliminate pathogenic microorganisms in water, and combined chlorine and UV processes (the UV/Cl2 process, the UV-Cl2 process, and the Cl2-UV process) are considered potential disinfection methods to control antibiotic resistance. This review documented the efficacy and mechanism of combined UV and chlorine processes for the control of antibiotic resistance, as well as the effects of chlorine dose, solution pH, UV wavelength, and water matrix on the effectiveness of the processes. There are knowledge gaps in research on the combined chlorine and UV processes for antibiotic resistance control, in particular the UV-Cl2 process and the Cl2-UV process. In addition, changes in the structure of microbial communities and the distribution of ARGs, which are closely related to the spread of antibiotic resistance in the water, induced by combined processes were also addressed. Whether these changes could lead to the re-transmission of antibiotic resistance and harm human health may need to be further evaluated.
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Affiliation(s)
- Jingyi Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Weiguang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Xinran Zhang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xuhui Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Longyi Lv
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, 300401, China
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23
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Charubin K, Hill JD, Papoutsakis ET. DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture. mBio 2024; 15:e0313323. [PMID: 38214507 PMCID: PMC10865971 DOI: 10.1128/mbio.03133-23] [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: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024] Open
Abstract
Prokaryotic evolution is driven by random mutations and horizontal gene transfer (HGT). HGT occurs via transformation, transduction, or conjugation. We have previously shown that in syntrophic cocultures of Clostridium acetobutylicum and Clostridium ljungdahlii, heterologous cell fusion leads to a large-scale exchange of proteins and RNA between the two organisms. Here, we present evidence that heterologous cell fusion facilitates the exchange of DNA between the two organisms. Using selective subculturing, we isolated C. acetobutylicum cells which acquired and integrated into their genome portions of plasmid DNA from a plasmid-carrying C. ljungdahlii strain. Limiting-dilution plating and DNA methylation data based on PacBio Single-Molecule Real Time (SMRT) sequencing support the existence of hybrid C. acetobutylicum/C. ljungdahlii cells. These findings expand our understanding of multi-species microbiomes, their survival strategies, and evolution.IMPORTANCEInvestigations of natural multispecies microbiomes and synthetic microbial cocultures are attracting renewed interest for their potential application in biotechnology, ecology, and medical fields. Previously, we have shown the syntrophic coculture of C. acetobutylicum and C. ljungdahlii undergoes heterologous cell-to-cell fusion, which facilitates the exchange of cytoplasmic protein and RNA between the two organisms. We now show that heterologous cell fusion between the two Clostridium organisms can facilitate the exchange of DNA. By applying selective pressures to this coculture system, we isolated clones of wild-type C. acetobutylicum which acquired the erythromycin resistance (erm) gene from the C. ljungdahlii strain carrying a plasmid with the erm gene. Single-molecule real-time sequencing revealed that the erm gene was integrated into the genome in a mosaic fashion. Our data also support the persistence of hybrid C. acetobutylicum/C. ljungdahlii cells displaying hybrid DNA-methylation patterns.
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Affiliation(s)
- Kamil Charubin
- Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - John D. Hill
- Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Eleftherios Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
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Han Y, Gao YF, Xu HT, Li JP, Li C, Song CL, Lei CW, Chen X, Wang Q, Ma BH, Wang HN. Characterization and risk assessment of novel SXT/R391 integrative and conjugative elements with multidrug resistance in Proteus mirabilis isolated from China, 2018-2020. Microbiol Spectr 2024; 12:e0120923. [PMID: 38197656 PMCID: PMC10871549 DOI: 10.1128/spectrum.01209-23] [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: 03/25/2023] [Accepted: 11/09/2023] [Indexed: 01/11/2024] Open
Abstract
Proteus mirabilis can transfer transposons, insertion sequences, and gene cassettes to the chromosomes of other hosts through SXT/R391 integrative and conjugative elements (ICEs), significantly increasing the possibility of antibiotic resistance gene (ARG) evolution and expanding the risk of ARGs transmission among bacteria. A total of 103 strains of P. mirabilis were isolated from 25 farms in China from 2018 to 2020. The positive detection rate of SXT/R391 ICEs was 25.2% (26/103). All SXT/R391 ICEs positive P. mirabilis exhibited a high level of overall drug resistance. Conjugation experiments showed that all 26 SXT/R391 ICEs could efficiently transfer to Escherichia coli EC600 with a frequency of 2.0 × 10-7 to 6.0 × 10-5. The acquired ARGs, genetic structures, homology relationships, and conservation sequences of 26 (19 different subtypes) SXT/R391 ICEs were investigated by high-throughput sequencing, whole-genome typing, and phylogenetic tree construction. ICEPmiChnHBRJC2 carries erm (42), which have never been found within an SXT/R391 ICE in P. mirabilis, and ICEPmiChnSC1111 carries 19 ARGs, including clinically important cfr, blaCTX-M-65, and aac(6')-Ib-cr, making it the ICE with the most ARGs reported to date. Through genetic stability, growth curve, and competition experiments, it was found that the transconjugant of ICEPmiChnSCNNC12 did not have a significant fitness cost on the recipient bacterium EC600 and may have a higher risk of transmission and dissemination. Although the transconjugant of ICEPmiChnSCSZC20 had a relatively obvious fitness cost on EC600, long-term resistance selection pressure may improve bacterial fitness through compensatory adaptation, providing scientific evidence for risk assessment of horizontal transfer and dissemination of SXT/R391 ICEs in P. mirabilis.IMPORTANCEThe spread of antibiotic resistance genes (ARGs) is a major public health concern. The study investigated the prevalence and genetic diversity of integrative and conjugative elements (ICEs) in Proteus mirabilis, which can transfer ARGs to other hosts. The study found that all of the P. mirabilis strains carrying ICEs exhibited a high level of drug resistance and a higher risk of transmission and dissemination of ARGs. The analysis of novel multidrug-resistant ICEs highlighted the potential for the evolution and spread of novel resistance mechanisms. These findings emphasize the importance of monitoring the spread of ICEs carrying ARGs and the urgent need for effective strategies to combat antibiotic resistance. Understanding the genetic diversity and potential for transmission of ARGs among bacteria is crucial for developing targeted interventions to mitigate the threat of antibiotic resistance.
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Affiliation(s)
- Yun Han
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yu-Feng Gao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - He-ting Xu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jin-Peng Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Cai-Liang Song
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chang-Wei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuan Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Qin Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Bo-Heng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hong-Ning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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Ryan MP, Carraro N, Slattery S, Pembroke JT. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Crit Rev Microbiol 2024; 50:105-126. [PMID: 36634159 DOI: 10.1080/1040841x.2022.2161870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.
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Affiliation(s)
- Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon, Limerick, Ireland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shannon Slattery
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
- Bernal Institute, University of Limerick, Ireland
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Murata T, Gotoh Y, Hayashi T. A comprehensive list of genes required for the efficient conjugation of plasmid Rts1 was determined by systematic deletion analysis. DNA Res 2024; 31:dsae002. [PMID: 38300630 PMCID: PMC10838148 DOI: 10.1093/dnares/dsae002] [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: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024] Open
Abstract
While conjugation-related genes have been identified in many plasmids by genome sequencing, functional analyses have not yet been performed in most cases, and a full set of conjugation genes has been identified for only a few plasmids. Rts1, a prototype IncT plasmid, is a conjugative plasmid that was originally isolated from Proteus vulgaris. Here, we conducted a systematic deletion analysis of Rts1 to fully understand its conjugation system. Through this analysis along with complementation assays, we identified 32 genes that are required for the efficient conjugation of Rts1 from Escherichia coli to E. coli. In addition, the functions of the 28 genes were determined or predicted; 21 were involved in mating-pair formation, three were involved in DNA transfer and replication, including a relaxase gene belonging to the MOBH12 family, one was involved in coupling, and three were involved in transcriptional regulation. Among the functionally well-analysed conjugation systems, most of the 28 genes showed the highest similarity to those of the SXT element, which is an integrative conjugative element of Vibrio cholerae. The Rts1 conjugation gene set included all 23 genes required for the SXT system. Two groups of plasmids with conjugation systems nearly identical or very similar to that of Rts1 were also identified.
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Affiliation(s)
- Takahiro Murata
- Department of Pediatrics, Teikyo University School of Medicine, Mizonokuchi Hospital, Takatsu-ku, Kawasaki, Kanagawa 213-8507, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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27
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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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Ivanovski I, Zylstra GJ. Genetic and Functional Characterization of a Salicylate 1-monooxygenase Located on an Integrative and Conjugative Element (ICE) in Pseudomonas stutzeri AJR13. J Microbiol 2023; 61:1025-1032. [PMID: 38100000 DOI: 10.1007/s12275-023-00093-x] [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: 06/29/2023] [Revised: 11/02/2023] [Accepted: 11/05/2023] [Indexed: 01/11/2024]
Abstract
Pseudomonas stutzeri strain AJR13 was isolated for growth on the related compounds biphenyl (BPH) and diphenylmethane (DPM). The BPH and DPM degradative pathway genes are present on an integrative and conjugative element (ICE) in the chromosome. Examination of the genome sequence of AJR13 revealed a gene encoding a salicylate 1-monooxygenase (salA) associated with the ICE even though AJR13 did not grow on salicylate. Transfer of the ICE to the well-studied Pseudomonas putida KT2440 resulted in a KT2440 strain that could grow on salicylate. Knockout mutagenesis of the salA gene on the ICE in KT2440 eliminated the ability to grow on salicylate. Complementation of the knockout with the cloned salA gene restored growth on salicylate. Transfer of the cloned salA gene under control of the lac promoter to KT2440 resulted in a strain that could grow on salicylate. Heterologous expression of the salA gene in E. coli BL21 DE3 resulted in the production of catechol from salicylate, confirming that it is indeed a salicylate 1-monooxygenase. Interestingly, transfer of the cloned salA gene under control of the lac promoter to AJR13 resulted in a strain that could now grow on salicylate, suggesting that gene expression for the downstream catechol pathway is intact.
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Affiliation(s)
- Igor Ivanovski
- Department of Biology, St. Joseph's University, Patchogue, NY, 11772, USA.
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.
| | - Gerben J Zylstra
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
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29
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Cai T, Tang H, Du X, Wang W, Tang K, Wang X, Liu D, Wang P. Genomic Island-Encoded Diguanylate Cyclase from Vibrio alginolyticus Regulates Biofilm Formation and Motility in Pseudoalteromonas. Microorganisms 2023; 11:2725. [PMID: 38004737 PMCID: PMC10672970 DOI: 10.3390/microorganisms11112725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
Many bacteria use the second messenger c-di-GMP to regulate exopolysaccharide production, biofilm formation, motility, virulence, and other phenotypes. The c-di-GMP level is controlled by the complex network of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) that synthesize and degrade c-di-GMP. In addition to chromosomally encoded DGCs, increasing numbers of DGCs were found to be located on mobile genetic elements. Whether these mobile genetic element-encoded DGCs can modulate the physiological phenotypes in recipient bacteria after horizontal gene transfer should be investigated. In our previous study, a genomic island encoding three DGC proteins (Dgc137, Dgc139, and Dgc140) was characterized in Vibrio alginolyticus isolated from the gastric cavity of the coral Galaxea fascicularis. Here, the effect of the three DGCs in four Pseudoalteromonas strains isolated from coral Galaxea fascicularis and other marine environments was explored. The results showed that when dgc137 is present rather than the three DGC genes, it obviously modulates biofilm formation and bacterial motility in these Pseudoalteromonas strains. Our findings implied that mobile genetic element-encoded DGC could regulate the physiological status of neighboring bacteria in a microbial community by modulating the c-di-GMP level after horizontal gene transfer.
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Affiliation(s)
- Tongxuan Cai
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China; (T.C.); (H.T.); (X.D.); (W.W.); (K.T.); (X.W.)
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Huan Tang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China; (T.C.); (H.T.); (X.D.); (W.W.); (K.T.); (X.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofei Du
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China; (T.C.); (H.T.); (X.D.); (W.W.); (K.T.); (X.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China; (T.C.); (H.T.); (X.D.); (W.W.); (K.T.); (X.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China; (T.C.); (H.T.); (X.D.); (W.W.); (K.T.); (X.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China; (T.C.); (H.T.); (X.D.); (W.W.); (K.T.); (X.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Pengxia Wang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, No.1119, Haibin Road, Nansha District, Guangzhou 511458, China; (T.C.); (H.T.); (X.D.); (W.W.); (K.T.); (X.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No.1119, Haibin Road, Nansha District, Guangzhou 511458, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Peng K, Li Y, Wang Q, Yang P, Wang Z, Li R. Integrative conjugative elements mediate the high prevalence of tmexCD3-toprJ1b in Proteus spp. of animal source. mSystems 2023; 8:e0042923. [PMID: 37707055 PMCID: PMC10654056 DOI: 10.1128/msystems.00429-23] [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: 04/29/2023] [Accepted: 07/23/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE The emergence and spread of tmexCD-toprJ have greatly weakened the function of tigecycline. Although studies have demonstrated the significance of Proteus as carriers for tmexCD-toprJ, the epidemic mechanism and characteristics of tmexCD-toprJ in Proteus remain unclear. Herein, we deciphered that the umuC gene in VRIII of SXT/R391 ICEs was a hotspot for the integration of tmexCD3-toprJ1b-bearing mobile genetic elements by genomic analysis. The mobilization and dissemination of tmexCD3-toprJ1b in Proteus were mediated by highly prevalent ICEs. Furthermore, the co-occurrence of tmexCD3-toprJ1b-bearing ICEs with other chromosomally encoded multidrug resistance gene islands warned that the chromosomes of Proteus are significant reservoirs of ARGs. Overall, our results provide significant insights for the prevention and control of tmexCD3-toprJ1b in Proteus.
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Affiliation(s)
- Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yangfan 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
| | - Qiaojun 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
| | - Pengbin Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 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
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, 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
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31
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Nishida AH, Ochman H. Origins and Evolution of Novel Bacteroides in Captive Apes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563286. [PMID: 37961372 PMCID: PMC10634691 DOI: 10.1101/2023.10.20.563286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Bacterial strains evolve in response to the gut environment of their hosts, with genomic changes that influence their interactions with hosts as well as with other members of the gut community. Great apes in captivity have acquired strains of Bacteroides xylanisolvens, which are common within gut microbiome of humans but not typically found other apes, thereby enabling characterization of strain evolution following colonization. Here, we isolate, sequence and reconstruct the history of gene gain and loss events in numerous captive-ape-associated strains since their divergence from their closest human-associated strains. We show that multiple captive-ape-associated B. xylanisolvens lineages have independently acquired gene complexes that encode functions related to host mucin metabolism. Our results support the finding of high genome fluidity in Bacteroides, in that several strains, in moving from humans to captive apes, have rapidly gained large genomic regions that augment metabolic properties not previously present in their relatives.
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Affiliation(s)
- Alexandra H. Nishida
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 USA
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 USA
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32
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Abante J, Wang PL, Salzman J. DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery. Genome Biol 2023; 24:240. [PMID: 37864197 PMCID: PMC10589994 DOI: 10.1186/s13059-023-03038-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/14/2023] [Indexed: 10/22/2023] Open
Abstract
Diversity-generating and mobile genetic elements are key to microbial and viral evolution and can result in evolutionary leaps. State-of-the-art algorithms to detect these elements have limitations. Here, we introduce DIVE, a new reference-free approach to overcome these limitations using information contained in sequencing reads alone. We show that DIVE has improved detection power compared to existing reference-based methods using simulations and real data. We use DIVE to rediscover and characterize the activity of known and novel elements and generate new biological hypotheses about the mobilome. Building on DIVE, we develop a reference-free framework capable of de novo discovery of mobile genetic elements.
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Affiliation(s)
- Jordi Abante
- Biomedical Data Science, Stanford University, 1265 Welch Rd, Palo Alto, 94305, CA, USA
- Center for Computational, Evolutionary and Human Genomics, Stanford University, 327 Campus Drive, Stanford, 94305, CA, USA
- Current address: Department of Biomedical Sciences, Universitat de Barcelona, Casanova 143, Barcelona, 08036, Spain
| | - Peter L Wang
- Biomedical Data Science, Stanford University, 1265 Welch Rd, Palo Alto, 94305, CA, USA
- Department of Biochemistry, Stanford University, 279 Campus Drive, Stanford, 94305, CA, USA
| | - Julia Salzman
- Biomedical Data Science, Stanford University, 1265 Welch Rd, Palo Alto, 94305, CA, USA.
- Department of Biochemistry, Stanford University, 279 Campus Drive, Stanford, 94305, CA, USA.
- Department of Statistics, Stanford University, 390 Serra Mall, Stanford, 94305, CA, USA.
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Weiss A, Wang T, You L. Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities. Cell Syst 2023; 14:895-905.e5. [PMID: 37820728 PMCID: PMC10591896 DOI: 10.1016/j.cels.2023.09.002] [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: 10/17/2022] [Revised: 05/09/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Transferable plasmids play a critical role in shaping the functions of microbial communities. Previous studies suggested multiple mechanisms underlying plasmid persistence and abundance. Here, we focus on the interplay between heterogeneous community partitioning and plasmid fates. Natural microbiomes often experience partitioning that creates heterogeneous local communities with reduced population sizes and biodiversity. Little is known about how population partitioning affects the plasmid fate through the modulation of community structure. By modeling and experiments, we show that heterogeneous community partitioning can paradoxically promote the persistence of a plasmid that would otherwise not persist in a global community. Among the local communities created by partitioning, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance by serving as a local plasmid haven. Our results provide insights into plasmid maintenance and suggest a generalizable approach to modulate plasmid persistence for engineering and medical applications.
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Affiliation(s)
- Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Quantitative Biodesign, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA.
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Huang J, Dai X, Wu Z, Hu X, Sun J, Tang Y, Zhang W, Han P, Zhao J, Liu G, Wang X, Mao S, Wang Y, Call DR, Liu J, Wang L. Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes. THE ISME JOURNAL 2023; 17:1467-1481. [PMID: 37369704 PMCID: PMC10432423 DOI: 10.1038/s41396-023-01463-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Prophages play important roles in the transduction of various functional traits, including virulence factors, but remain debatable in harboring and transmitting antimicrobial resistance genes (ARGs). Herein we characterize a prevalent family of prophages in Streptococcus, designated SMphages, which harbor twenty-five ARGs that collectively confer resistance to ten antimicrobial classes, including vanG-type vancomycin resistance locus and oxazolidinone resistance gene optrA. SMphages integrate into four chromosome attachment sites by utilizing three types of integration modules and undergo excision in response to phage induction. Moreover, we characterize four subtypes of Alp-related surface proteins within SMphages, the lethal effects of which are extensively validated in cell and animal models. SMphages transfer via high-frequency conjugation that is facilitated by integrative and conjugative elements from either donors or recipients. Our findings explain the widespread of SMphages and the rapid dissemination of ARGs observed in members of the Streptococcus genus.
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Affiliation(s)
- Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingyang Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yijun Tang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanqiu Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peizhao Han
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaqi Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangjin Liu
- Key Lab of Animal Bacteriology, Ministry of Agriculture, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, 99164, USA
| | - Jinxin Liu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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Zhang J, Yang Y, Sun H, Luo X, Cui X, Miao Q, He D, Zhao J, Yan F, Pan Y, Zhai Y, Hu G. Prevalence of the optrA gene among Streptococcus suis isolates from diseased pigs and identification of a novel integrative conjugative element ICESsu988S. Res Microbiol 2023; 174:104078. [PMID: 37149078 DOI: 10.1016/j.resmic.2023.104078] [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: 12/10/2022] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/08/2023]
Abstract
Aim of this study was to investigate the prevalence and genetic environment of the oxazolidinone resistance gene optrA in Streptococcus suis (S. suis) isolates from diseased pigs in China. A total of 178 S. suis isolates were screened for the optrA gene by PCR. The phenotypes and genotypes of optrA-positive isolates were investigated by antimicrobial susceptibility testing, core genome Multilocus Sequence Typing (cgMLST), capsular serotypes determination and whole-genome sequencing (WGS). Fifty-one (28.7%) S. suis isolates were positive for optrA. Phylogenetic analysis indicated that the spread of the optrA among S. suis isolates was primarily due to horizontal transfer. Analysis of S. suis serotypes from diseased pigs revealed substantial diversity. The genetic environment of optrA was complex and diverse and could be divided into 12 different types. Interestingly, we identified a novel integrative and conjugative element ICESsu988S, carrying optrA and erm(T) genes. This is to the best of our knowledge the first report of the optrA and erm(T) co-located on an ICE in S. suis. Our results showed a high prevalence of optrA gene in S. suis isolates in China. Further research is needed to evaluate the importance of ICEs, as they horizontally propagate important clinical resistance genes.
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Affiliation(s)
- Junkai Zhang
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yingying Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, China.
| | - Huarun Sun
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China.
| | - Xingwei Luo
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Xiaodie Cui
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Qingqing Miao
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Dandan He
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Jinfeng Zhao
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Fengbin Yan
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yushan Pan
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yajun Zhai
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Gongzheng Hu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
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Jowsey W, Morris CP, Hall D, Sullivan J, Fagerlund R, Eto K, Solomon P, Mackay J, Bond C, Ramsay J, Ronson C. DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria. Nucleic Acids Res 2023; 51:6841-6856. [PMID: 37246713 PMCID: PMC10359603 DOI: 10.1093/nar/gkad457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 05/30/2023] Open
Abstract
Horizontal gene transfer is tightly regulated in bacteria. Often only a fraction of cells become donors even when regulation of horizontal transfer is coordinated at the cell population level by quorum sensing. Here, we reveal the widespread 'domain of unknown function' DUF2285 represents an 'extended-turn' variant of the helix-turn-helix domain that participates in both transcriptional activation and antiactivation to initiate or inhibit horizontal gene transfer. Transfer of the integrative and conjugative element ICEMlSymR7A is controlled by the DUF2285-containing transcriptional activator FseA. One side of the DUF2285 domain of FseA has a positively charged surface which is required for DNA binding, while the opposite side makes critical interdomain contacts with the N-terminal FseA DUF6499 domain. The QseM protein is an antiactivator of FseA and is composed of a DUF2285 domain with a negative surface charge. While QseM lacks the DUF6499 domain, it can bind the FseA DUF6499 domain and prevent transcriptional activation by FseA. DUF2285-domain proteins are encoded on mobile elements throughout the proteobacteria, suggesting regulation of gene transfer by DUF2285 domains is a widespread phenomenon. These findings provide a striking example of how antagonistic domain paralogues have evolved to provide robust molecular control over the initiation of horizontal gene transfer.
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Affiliation(s)
- William J Jowsey
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Calum R P Morris
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Drew A Hall
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Karina Y Eto
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Paul D Solomon
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Charles S Bond
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Marshall Centre for Infectious Disease Research and Training, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Joshua P Ramsay
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
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Soares-Castro P, Soares F, Reis F, Lino-Neto T, Santos PM. Bioprospection of the bacterial β-myrcene-biotransforming trait in the rhizosphere. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12650-w. [PMID: 37405434 PMCID: PMC10386936 DOI: 10.1007/s00253-023-12650-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023]
Abstract
The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr+). Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr+ isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches. Furthermore, the characterization of isolates not harboring the Myr+-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation. KEY POINTS: • The isolation of 150 Myr+ bacteria hints the ubiquity of such trait in the rhizosphere. • The Myr+ trait is spread across different bacterial taxonomic classes. • The core-code for the Myr+ trait was detected in a novel ICE, only found in Pseudomonas spp.
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Affiliation(s)
- Pedro Soares-Castro
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal
| | - Filipa Soares
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Francisca Reis
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Teresa Lino-Neto
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Pedro M Santos
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal.
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Murthy AC, Aleksanyan N, Morton GM, Toyoda HC, Kalashyan M, Chen S, Ragucci AE, Broulidakis MP, Swerdlow KJ, Bui MNN, Muccioli M, Berkmen MB. Characterization of ConE, the VirB4 Homolog of the Integrative and Conjugative Element ICE Bs1 of Bacillus subtilis. J Bacteriol 2023; 205:e0003323. [PMID: 37219457 PMCID: PMC10294652 DOI: 10.1128/jb.00033-23] [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: 02/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
Conjugation is a major form of horizontal gene transfer, contributing to bacterial evolution and the acquisition of new traits. During conjugation, a donor cell transfers DNA to a recipient through a specialized DNA translocation channel classified as a type IV secretion system (T4SS). Here, we focused on the T4SS of ICEBs1, an integrative and conjugative element in Bacillus subtilis. ConE, encoded by ICEBs1, is a member of the VirB4 family of ATPases, the most conserved component of T4SSs. ConE is required for conjugation and localizes to the cell membrane, predominantly at the cell poles. In addition to Walker A and B boxes, VirB4 homologs have conserved ATPase motifs C, D, and E. Here, we created alanine substitutions in five conserved residues within or near ATPase motifs in ConE. Mutations in all five residues drastically decreased conjugation frequency but did not affect ConE protein levels or localization, indicating that an intact ATPase domain is critical for DNA transfer. Purified ConE is largely monomeric with some oligomers and lacks enzymatic activity, suggesting that ATP hydrolysis may be regulated or require special solution conditions. Finally, we investigated which ICEBs1 T4SS components interact with ConE using a bacterial two-hybrid assay. ConE interacts with itself, ConB, and ConQ, but these interactions are not required to stabilize ConE protein levels and largely do not depend on conserved residues within the ATPase motifs of ConE. The structure-function characterization of ConE provides more insight into this conserved component shared by all T4SSs. IMPORTANCE Conjugation is a major form of horizontal gene transfer and involves the transfer of DNA from one bacterium to another through the conjugation machinery. Conjugation contributes to bacterial evolution by disseminating genes involved in antibiotic resistance, metabolism, and virulence. Here, we characterized ConE, a protein component of the conjugation machinery of the conjugative element ICEBs1 of the bacterium Bacillus subtilis. We found that mutations in the conserved ATPase motifs of ConE disrupt mating but do not alter ConE localization, self-interaction, or levels. We also explored which conjugation proteins ConE interacts with and whether these interactions contribute to stabilizing ConE. Our work contributes to the understanding of the conjugative machinery of Gram-positive bacteria.
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Affiliation(s)
- Anastasia C. Murthy
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Naira Aleksanyan
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Georgeanna M. Morton
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Hunter C. Toyoda
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Meri Kalashyan
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Sirui Chen
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Adelyn E. Ragucci
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
- Cancer Immunology and Virology Department, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew P. Broulidakis
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Kyle J. Swerdlow
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Minh N. N. Bui
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Maria Muccioli
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
| | - Melanie B. Berkmen
- Department of Chemistry and Biochemistry, Suffolk University, Boston, Massachusetts, USA
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Dai X, Sun J, Zhu B, Lv M, Chen L, Chen L, Wang X, Huang J, Wang L. Various Mobile Genetic Elements Involved in the Dissemination of the Phenicol-Oxazolidinone Resistance Gene optrA in the Zoonotic Pathogen Streptococcus suis: a Nonignorable Risk to Public Health. Microbiol Spectr 2023; 11:e0487522. [PMID: 37070987 PMCID: PMC10269897 DOI: 10.1128/spectrum.04875-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
The rapid increase of phenicol-oxazolidinone (PhO) resistance in Streptococcus suis due to transferable resistance gene optrA is a matter of concern. However, genetic mechanisms for the dissemination of the optrA gene remain to be discovered. Here, we selected 33 optrA-positive S. suis isolates for whole-genome sequencing and analysis. The IS1216E element was present in 85% of the optrA-carrying contigs despite genetic variation observed in the flanking region. IS1216E-optrA-carrying segments could be inserted into larger mobile genetic elements (MGEs), including integrative and conjugative elements, plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated circularization occurred to form the IS1216E-optrA-carrying translocatable units, suggesting a crucial role of IS1216E in optrA spreading. Three optrA-carrying MGEs (ICESsuAKJ47_SSU1797, plasmid pSH0918, and prophage ΦSsuFJSM5_rum) were successfully transferred via conjugation at different transfer frequencies. Interestingly, two types of transconjugants were observed due to the multilocus integration of ICESsuAKJ47 into an alternative SSU1943 attachment site along with the primary SSU1797 attachment site (type 1) or into the single SSU1797 attachment site (type 2). In addition, conjugative transfer of an optrA-carrying plasmid and prophage in streptococci was validated for the first time. Considering the abundance of MGEs in S. suis and the mobility of IS1216E-optrA-carrying translocatable units, attention should be paid to the potential risks to public health from the emergence and spread of PhO-resistant S. suis. IMPORTANCE Antimicrobial resistance to phenicols and oxazolidinones by the dissemination of the optrA gene leads to treatment failure in both veterinary and human medicine. However, information about the profile of these MGEs (mobilome) that carry optrA and their transferability in streptococci was limited, especially for the zoonotic pathogen S. suis. This study showed that the optrA-carrying mobilome in S. suis includes integrative and conjugative elements (ICEs), plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated formation of optrA-carrying translocatable units played important roles in optrA spreading between types of MGEs, and conjugative transfer of various optrA-carrying MGEs (ICEs, plasmids, and prophages) further facilitated the transfer of optrA across strains, highlighting a nonignorable risk to public health of optrA dissemination to other streptococci and even to bacteria of other genera.
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Affiliation(s)
- Xingyang Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Boqin Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Mingsiyi Lv
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Liye Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Li Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing, China
- Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing, China
- Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing, China
- Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing, China
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40
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Fujihara H, Hirose J, Suenaga H. Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria. Front Microbiol 2023; 14:1168246. [PMID: 37350784 PMCID: PMC10282184 DOI: 10.3389/fmicb.2023.1168246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture. Further, host bacteria that can use energy effectively by controlling the expression of organized gene clusters involved in xenobiotic degradation will have a survival advantage in harsh xenobiotic-rich environments. In this review, we summarize the current understanding of evolutionary mechanisms operative in bacteria, with a focus on biphenyl/PCB-degrading bacteria. We then discuss metagenomic approaches that are useful for such investigation.
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Affiliation(s)
- Hidehiko Fujihara
- Department of Food and Fermentation Sciences, Faculty of Food and Nutrition Sciences, Beppu University, Beppu, Japan
| | - Jun Hirose
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
| | - Hikaru Suenaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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Liu C, Zhu X, You L, Gin KYH, Chen H, Chen B. Per/polyfluoroalkyl substances modulate plasmid transfer of antibiotic resistance genes: A balance between oxidative stress and energy support. WATER RESEARCH 2023; 240:120086. [PMID: 37257295 DOI: 10.1016/j.watres.2023.120086] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/22/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
Emerging contaminants can accelerate the transmission of antibiotic resistance genes (ARGs) from environmental bacteria to human pathogens via plasmid conjugation, posing a great challenge to the public health. Although the toxic effects of per/polyfluoroalkyl substances (PFAS) as persistent organic pollutants have been understood, it is still unclear whether and how PFAS modulate the transmission of ARGs. In this study, we for the first time reported that perfluorooctanoic acid (PFOA), perfluorododecanoic acid (PFDoA) and ammonium perfluoro (2-methyl-3-oxahexanoate) (GenX) at relatively low concentrations (0.01, 0.1 mg/L) promoted the conjugative transfer of plasmid RP4 within Escherichia coli, while the plasmid conjugation was inhibited by PFOA, PFDoA and GenX at relatively high concentrations (1, 10 mg/L). The non-unidirectional conjugation result was ascribed to the co-regulation of ROS overproduction, enhanced cell membrane permeability, shortage of energy support as well as l-arginine pool depletion. Taking the well-known PFOA as an example, it significantly enhanced the conjugation frequency by 1.4 and 3.4 times at relatively low concentrations (0.01, 0.1 mg/L), respectively. Exposure to PFOA resulted in enhanced cell membrane permeability and ROS overproduction in donor cells. At high concentrations of PFOA (1, 10 mg/L), although enhanced oxidative stress and cell membrane permeability still occurred, the ATP contents in E. coli decreased, which contributed to the inhibited conjugation. Transcriptome analysis further showed that the expression levels of genes related to arginine biosynthesis (argA, argC, argF, argG, argI) and transport (artJ, artM, artQ) pathways were significantly increased. Intracellular l-arginine concentration deficiency were observed at high concentrations of PFOA. With the supplementary exogenous arginine, it was demonstrated that arginine upregulated conjugation transfer- related genes (trfAp, trbBp) and restores the cell number of transconjugants in PFOA-treated group. Therefore, the inhibited conjugation at high concentrations PFOA were attributed to the shortage of ATP and the depletion of L-arginine pool. These findings provide important insights into the effect environmental concentrations of PFAS on the conjugative transfer of ARGs, and update the regulation mechanism of plasmid conjugation, which is critical for the management of antibiotic resistance in aquatic environments.
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Affiliation(s)
- Congcong Liu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Xiangyu Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China
| | - Luhua You
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou 310058, China.
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Haq IU, Mukhtar Z, Anwar-Ul-Haq M, Liaqat S. Deciphering host-pathogen interaction during Streptomyces spp. infestation of potato. Arch Microbiol 2023; 205:222. [PMID: 37149838 DOI: 10.1007/s00203-023-03560-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
Potato crop, currently, is the staple food crop of about 1.3 billion global population. Potato is attaining even more admiration globally day by day owing to its public acceptability. However, potato sustainable production is distinctly challenged by multiple factors like diseases, pests and climate change etc. Among diseases, common scab is one of the prime threats to potato crop due to its soil-borne nature and versatility in phytotoxins' secretion. Common scab is caused multiple number of phytopathogenic streptomyces strains. Despite extensive research programs, researchers are still unable to identify a significant solution to this threat that is proliferating exceptional rate across the globe. To develop feasible remedies, adequate information regarding host-pathogen interaction should be available. This review possesses insights on existing pathogenic species, the evolution of novel pathogenic streptomyces spp. and phytotoxins produced by the pathogenic strains. Furthermore, which type of physiological, biochemical and genetic activities occur during pathogen's infestation of the host are also canvassed.
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Affiliation(s)
- Ihtisham Ul Haq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.
- Ayub Agricultural Research Institute, Faisalabad, Pakistan.
| | - Zahid Mukhtar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | | | - Sana Liaqat
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
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Song J, Zhang H, Wu Z, Qiu M, Zhan X, Zheng C, Shi N, Zhang Q, Zhang L, Yu Y, Fang H. A novel bidirectional regulation mechanism of mancozeb on the dissemination of antibiotic resistance. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131559. [PMID: 37163893 DOI: 10.1016/j.jhazmat.2023.131559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023]
Abstract
The high abundance of antibiotic resistance genes (ARGs) in the fungicide residual environment, posing a threat to the environment and human health, raises the question of whether and how fungicide promotes the prevalence and dissemination of antibiotic resistance. Here, we reported a novel mechanism underlying bidirectional regulation of a typical heavy-metal-containing fungicide mancozeb on the horizontal transfer of ARGs. Our findings revealed that mancozeb exposure significantly exerted oxidative and osmotic stress on the microbes and facilitated plasmid-mediated ARGs transfer, but its metallic portions (Mn and Zn) were potentially utilized as essential ions by microbes for metalating enzymes to deal with cellular stress and thus reduce the transfer. The results of transcriptome analysis with RT-qPCR confirmed that the expression levels of cellular stress responses and conjugation related genes were drastically altered. It can be concluded mancozeb bidirectionally regulated the ARGs dissemination which may be attributed to the diverse effects on the microbes by its different portions. This novel mechanism provides an updated understanding of neglected fungicide-triggered ARGs dissemination and crucial insight for comprehensive risk assessment of fungicides.
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Affiliation(s)
- Jiajin Song
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Zishan Wu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengting Qiu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiuping Zhan
- Shanghai Agricultural Technology Extension Service Center, Shanghai 201103, China
| | - Conglai Zheng
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nan Shi
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| | - Qianke Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Luqing Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China.
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Huang Q, Huang Y, Li B, Li X, Guo Y, Jiang Z, Liu X, Yang Z, Ning Z, Xiao T, Jiang C, Hao L. Metagenomic analysis characterizes resistomes of an acidic, multimetal(loid)-enriched coal source mine drainage treatment system. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130898. [PMID: 36731323 DOI: 10.1016/j.jhazmat.2023.130898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/07/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Heavy metal(loid) contaminations caused by mine activities are potential hot spots of antibiotic resistance genes (ARGs) because of heavy metal(loid)-induced co-selection of ARGs and heavy metal(loid) resistance genes (MRGs). This study used high-throughput metagenomic sequencing to analyze the resistome characteristics of a coal source acid mine drainage passive treatment system. The multidrug efflux mechanism dominated the antibiotic resistome, and a highly diverse heavy metal(loid) resistome was dominated by mercury-, iron-, and arsenic--associated resistance. Correlation analysis indicated that mobile gene elements had a greater influence on the dynamic of MRGs than ARGs. Among the metagenome-assembled genomes, six potential pathogens carrying multiple resistance genes resistant to several antibiotics and heavy metal(loid)s were recovered. Pseudomonas spp. contained the highest numbers of resistance genes, with resistance to two types of antibiotics and 12 types of heavy metal(loid)s. Thus, high contents of heavy metal(loid)s drove the co-selection of ARGs and MRGs. The occurrence of potential pathogens containing multiple resistance genes might increase the risk of ARG dissemination in the environment.
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Affiliation(s)
- Qiang Huang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bao Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiutong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yuan Guo
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiaoling Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Zhenni Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Tangfu Xiao
- Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, PR China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Likai Hao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, PR China.
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45
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Daveri A, Benigno V, van der Meer JR. Characterization of an atypical but widespread type IV secretion system for transfer of the integrative and conjugative element (ICEclc) in Pseudomonas putida. Nucleic Acids Res 2023; 51:2345-2362. [PMID: 36727472 PMCID: PMC10018362 DOI: 10.1093/nar/gkad024] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/23/2022] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Conjugation of DNA relies on multicomponent protein complexes bridging two bacterial cytoplasmic compartments. Whereas plasmid conjugation systems have been well documented, those of integrative and conjugative elements (ICEs) have remained poorly studied. We characterize here the conjugation system of the ICEclc element in Pseudomonas putida UWC1 that is a model for a widely distributed family of ICEs. By in frame deletion and complementation, we show the importance on ICE transfer of 22 genes in a 20-kb conserved ICE region. Protein comparisons recognized seven homologs to plasmid type IV secretion system components, another six homologs to frequent accessory proteins, and the rest without detectable counterparts. Stationary phase imaging of P. putida ICEclc with in-frame fluorescent protein fusions to predicted type IV components showed transfer-competent cell subpopulations with multiple fluorescent foci, largely overlapping in dual-labeled subcomponents, which is suggestive for multiple conjugation complexes per cell. Cross-dependencies between subcomponents in ICE-type IV secretion system assembly were revealed by quantitative foci image analysis in a variety of ICEclc mutant backgrounds. In conclusion, the ICEclc family presents an evolutionary distinct type IV conjugative system with transfer competent cells specialized in efficient transfer.
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Affiliation(s)
- Andrea Daveri
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valentina Benigno
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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46
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Lee K, Raguideau S, Sirén K, Asnicar F, Cumbo F, Hildebrand F, Segata N, Cha CJ, Quince C. Population-level impacts of antibiotic usage on the human gut microbiome. Nat Commun 2023; 14:1191. [PMID: 36864029 PMCID: PMC9981903 DOI: 10.1038/s41467-023-36633-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.
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Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
- CJ Bioscience, Seoul, 04527, Republic of Korea
| | | | - Kimmo Sirén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Falk Hildebrand
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK.
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK.
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47
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Engin AB, Engin ED, Engin A. Effects of co-selection of antibiotic-resistance and metal-resistance genes on antibiotic-resistance potency of environmental bacteria and related ecological risk factors. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 98:104081. [PMID: 36805463 DOI: 10.1016/j.etap.2023.104081] [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: 08/11/2022] [Revised: 01/23/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
The inadequate elimination of micropollutants in wastewater treatment plants (WWTP), cause to increase in the incidence of antibiotic resistant bacterial strains. Growth of microbial pathogens in WWTP is one of the serious public health problems. The widespread and simultaneous emergence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment with heavy metals create persistent and selective pressure for co-selection of both genes on environmental microorganisms. Co-localization of ARGs and HMRGs on the same horizontal mobile genetic elements (MGEs) allows the spreading of numerous antibiotic-resistant strains of bacteria in aquatic and terrestrial environment. The biofilm formation and colonization potential of environmental bacteria leads to the co-selection of multi-antibiotic resistance and multi-metal tolerance. Horizontal gene transfer (HGT), co-localization of both ARGs and HMRGs on the same MGEs, and the shared resistomes are important bacteria-associated ecological risks factors, which reduce the effectiveness of antibiotics against bacterial infections.
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Affiliation(s)
- Ayse Basak Engin
- Gazi University, Faculty of Pharmacy, Department of Toxicology, Ankara, Turkey.
| | - Evren Doruk Engin
- Ankara University, Biotechnology Institute, Gumusdere Campus, Kecioren, Ankara, Turkey
| | - Atilla Engin
- Gazi University, Faculty of Medicine, Department of General Surgery, Ankara, Turkey
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48
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Arbel-Goren R, McKeithen-Mead SA, Voglmaier D, Afremov I, Teza G, Grossman AD, Stavans J. Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer. Nucleic Acids Res 2023; 51:3116-3129. [PMID: 36762480 PMCID: PMC10123120 DOI: 10.1093/nar/gkad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that can transfer by conjugation to recipient cells. Some ICEs integrate into a unique site in the genome of their hosts. We studied quantitatively the process by which an ICE searches for its unique integration site in the Bacillus subtilis chromosome. We followed the motion of both ICEBs1 and the chromosomal integration site in real time within individual cells. ICEBs1 exhibited a wide spectrum of dynamical behaviors, ranging from rapid sub-diffusive displacements crisscrossing the cell, to kinetically trapped states. The chromosomal integration site moved sub-diffusively and exhibited pronounced dynamical asymmetry between longitudinal and transversal motions, highlighting the role of chromosomal structure and the heterogeneity of the bacterial interior in the search. The successful search for and subsequent recombination into the integration site is a key step in the acquisition of integrating mobile genetic elements. Our findings provide new insights into intracellular transport processes involving large DNA molecules.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Dominik Voglmaier
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idana Afremov
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gianluca Teza
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alan D Grossman
- Department of Biology Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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49
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Sun H, Yang Y, Yi K, Zhang M, Luo X, He D, Hu G, Wu H. ICEGpa1804, a novel integrative and conjugative element carrying eight resistance genes, identified in Glaesserella parasuis. Int J Antimicrob Agents 2023; 61:106740. [PMID: 36736498 DOI: 10.1016/j.ijantimicag.2023.106740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/10/2021] [Accepted: 01/23/2023] [Indexed: 02/05/2023]
Abstract
ICEGpa1804 was identified in the genome of a serovar 2, ST279 isolate EHP1804 carrying eight different resistance genes from 200 Glaesserella parasuis strains isolated from swine with lower respiratory tract infection in seven provinces of China. Susceptibility testing for EHP1804 was determined by broth microdilution, and its genetic profile was determined by whole-genome sequencing. The complete ICEGpa1804 was analysed by polymerase chain reaction, conjugation assay and bioinformatics tools. The conjugation assay was performed using EHP1804 as the donor and G. parasuis V43 (rifampicin-resistant) as the recipient. ICEGpa1804 has a size of 71,880 bp and contains 83 genes, including eight resistance genes [tet(B), blaRob-1, aphA1, strA, strB, aac(3)-IId, catA3 and sul2]. The conjugation assay showed that ICEGpa1804 could be transferred to G. parasuis V43 with frequencies of 4.3 × 10-7. To the best of the authors' knowledge, this is the first study to identify a novel integrative and conjugative element (ICE) carrying eight resistance genes and seven insertion sequence (IS) elements from a G. parasuis isolate. Tn6743, a novel transposon carrying six resistance genes, was identified. Moreover, ISGpa1, a novel IS256 family insertion element, is the first characterized example of a G. parasuis insertion element. Multiple mobile genetic elements involved in resistance genes were located in chromosomal ICEGpa1804, which showed that ICEs may serve as a vital platform for the accumulation of resistance genes.
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Affiliation(s)
- Huarun Sun
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Department of Animal Science, Henan Institute of Science and Technology, Xinxiang, 453000, China
| | - Yingying Yang
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kaifang Yi
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Mengke Zhang
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xingwei Luo
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Dandan He
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Gongzheng Hu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Hua Wu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
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50
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Radovanovic M, Kekic D, Gajic I, Kabic J, Jovicevic M, Kekic N, Opavski N, Ranin L. Potential influence of antimicrobial resistance gene content in probiotic bacteria on the gut resistome ecosystems. Front Nutr 2023; 10:1054555. [PMID: 36819705 PMCID: PMC9928729 DOI: 10.3389/fnut.2023.1054555] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a substantial threat to human health. The commensal bacteria of the gut microbiome were shown to serve as a reservoir of antibiotic resistance genes (ARGs), termed the gut resistome, which has the potential to transfer horizontally to pathogens and contribute to the emergence of drug-resistant bacteria. Namely, AMR traits are generally linked with mobile genetic elements (MGEs), which apart from disseminating vertically to the progeny, may cross horizontally to the distantly related microbial species. On the other hand, while probiotics are generally considered beneficiary to human health, and are therefore widely consumed in recent years most commonly in conjunction with antibiotics, the complexities and extent of their impact on the gut microbiome and resistome have not been elucidated. By reviewing the latest studies on ARG containing commercial probiotic products and common probiotic supplement species with their actual effects on the human gut resistome, this study aims to demonstrate that their contribution to the spread of ARGs along the GI tract merits additional attention, but also indicates the changes in sampling and profiling of the gut microbiome which may allow for the more comprehensive studying of the effects of probiotics in this part of the resistome.
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Affiliation(s)
- Marina Radovanovic
- Department of Biochemistry, Institute for Biological Research “Siniša Stanković”, National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Dusan Kekic
- Institute of Microbiology and Immunology, Medical Faculty, University of Belgrade, Belgrade, Serbia,*Correspondence: Dusan Kekic,
| | - Ina Gajic
- Institute of Microbiology and Immunology, Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Jovana Kabic
- Institute of Microbiology and Immunology, Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Milos Jovicevic
- Institute of Microbiology and Immunology, Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Natalija Kekic
- Clinic for Infectious and Tropical Diseases, University Clinical Centre of Serbia, Belgrade, Serbia
| | - Natasa Opavski
- Institute of Microbiology and Immunology, Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Lazar Ranin
- Institute of Microbiology and Immunology, Medical Faculty, University of Belgrade, Belgrade, Serbia
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