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Murray GGR, Hossain ASMM, Miller EL, Bruchmann S, Balmer AJ, Matuszewska M, Herbert J, Hadjirin NF, Mugabi R, Li G, Ferrando ML, Fernandes de Oliveira IM, Nguyen T, Yen PLK, Phuc HD, Zaw Moe A, Su Wai T, Gottschalk M, Aragon V, Valentin-Weigand P, Heegaard PMH, Vrieling M, Thein Maw M, Thidar Myint H, Tun Win Y, Thi Hoa N, Bentley SD, Clavijo MJ, Wells JM, Tucker AW, Weinert LA. The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs. Proc Natl Acad Sci U S A 2023; 120:e2307773120. [PMID: 37963246 PMCID: PMC10666105 DOI: 10.1073/pnas.2307773120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023] Open
Abstract
The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized.
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Affiliation(s)
- Gemma G. R. Murray
- Department of Genetics, Evolution and Environment, University College London, LondonWC1E 6BT, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | | | - Eric L. Miller
- Department of Biology, Haverford College, Haverford, PA19041
| | - Sebastian Bruchmann
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Andrew J. Balmer
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
- Department of Medicine, University of Cambridge, CambridgeCB2 2QQ, United Kingdom
| | - Josephine Herbert
- Centre for Enzyme Innovation, University of Portsmouth, PortsmouthPO1 2DD, United Kingdom
| | - Nazreen F. Hadjirin
- Nuffield Department of Population Health, University of Oxford, OxfordOX3 7LF, United Kingdom
| | - Robert Mugabi
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Ganwu Li
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Maria Laura Ferrando
- Animal Sciences Department, Wageningen University, 6700 AHWageningen, The Netherlands
| | | | - Thanh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phung L. K. Yen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Aung Zaw Moe
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Thiri Su Wai
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, QuébecJ2S 2M2, Canada
| | - Virginia Aragon
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Barcelona08193, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona08193, Spain
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover30559, Germany
| | - Peter M. H. Heegaard
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Manouk Vrieling
- Wageningen Bioveterinary Research, 8221 RALelystad, The Netherlands
| | - Min Thein Maw
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | | | - Ye Tun Win
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7LG, United Kingdom
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, CambridgeCB10 1RQ, United Kingdom
| | - Maria J. Clavijo
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Jerry M. Wells
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
- Animal Sciences Department, Wageningen University, 6700 AHWageningen, The Netherlands
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
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