Dataset Information

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs.

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.

SUBMITTER: Murray GGR

PROVIDER: S-EPMC10666105 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs.

Murray Gemma G R GGR Hossain A S Md Mukarram ASMM Miller Eric L EL Bruchmann Sebastian S Balmer Andrew J AJ Matuszewska Marta M Herbert Josephine J Hadjirin Nazreen F NF Mugabi Robert R Li Ganwu G Ferrando Maria Laura ML Fernandes de Oliveira Isabela Maria IM Nguyen Thanh T Yen Phung L K PLK Phuc Ho D HD Zaw Moe Aung A Su Wai Thiri T Gottschalk Marcelo M Aragon Virginia V Valentin-Weigand Peter P Heegaard Peter M H PMH Vrieling Manouk M Thein Maw Min M Thidar Myint Hnin H Tun Win Ye Y Thi Hoa Ngo N Bentley Stephen D SD Clavijo Maria J MJ Wells Jerry M JM Tucker Alexander W AW Weinert Lucy A LA

Proceedings of the National Academy of Sciences of the United States of America 20231114 47

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 <i>Streptococcus suis</i>, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathoge ...[more]

PMID: 37963246

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Project description:EC Directive 2001/93 requires that all pigs have access to proper investigation and manipulation materials. Intensively farmed pigs in Europe are frequently provided with a short metal chain with or without an indestructible object attached to the chain. To date authorities are regarding this as proper enrichment, perhaps with (in)direct reference to the RICHPIG model as a justification. However, it has become increasingly clear that the chains do not provide proper enrichment, and that adding an indestructible object to the end of the chain may even reduce rather than improve pig welfare. To test this hypothesis an expert survey was conducted containing 26 more or less compound questions. On a scale from 0 to 10 experts specified their level of agreement with the hypothesis, the prevalence and welfare scores of nine indestructible enrichment materials. In total 36 experts, mostly pig-welfare scientists, responded (response rate: 39%). Indestructible objects are less prevalent in countries that provide straw (like Sweden and the UK) and outside the EU (US). They are more prevalent in the Netherlands, Belgium, France and Finland, while the prevalence seems to be low in Spain. Balls, wood and pipes were provided most frequently: hard wood especially in the UK (as specified in farm assurance); indestructible balls and pipes in Germany and the Netherlands. The experts' score for agreement with the hypothesis was only 4.6 on average (scale 0-10; n = 25). Enrichment materials, ranked from high to low welfare score, were grouped in 5 significance levels as indicated by different superscripts based on Wilcoxon signed rank tests: Branched chains (5.1a), Chain on the floor (4.4b), Hard wood (3.7bc), Pipe (3.5c), Bare chain (3.3c), Short chain (3.1d), Small ball (2.8d), Big ball (2.5d), and Chain hanging too high (1.3e). Branched chains scored significantly better than all other indestructible materials and its welfare score (5.1 on average) was close to the pre-defined level of acceptability (5.5 on a scale from 0, worst, to 10, best). The welfare benefits of adding balls, pipes or hard wood to the metal chain were marginal, and well below what the experts considered acceptable enrichment. The branched-chains design, by contrast, appears to be the most viable alternative. It involves providing a longer chain, i.e. with the free end reaching to floor level, adding 'branches', i.e. several short chains ending at the nose height of the pigs, and providing more chains per pen (i.e. 1 branched chain per 5 pigs). Branched chains should be implemented widely and in the short term as a first step towards, and benchmark for, providing proper enrichment to intensively-farmed pigs.

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Dataset Information

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs.

Publications

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs.

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