Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi

Catherine N. Wilson (), Patrick Musicha, Mathew A. Beale, Yohane Diness, Oscar Kanjerwa, Chifundo Salifu, Zefaniah Katuah, Patricia Duncan, John Nyangu, Andrew Mungu, Muonaouza Deleza, Lawrence Banda, Lumbani Makhaza, Nicola Elviss, Christopher P. Jewell, Gina Pinchbeck, Nicholas A. Feasey, Eric M. Fèvre () and Nicholas R. Thomson
Additional contact information
Catherine N. Wilson: University of Liverpool
Patrick Musicha: Malawi Liverpool Wellcome Programme
Mathew A. Beale: Wellcome Sanger Institute
Yohane Diness: Malawi Liverpool Wellcome Programme
Oscar Kanjerwa: Malawi Liverpool Wellcome Programme
Chifundo Salifu: Malawi Liverpool Wellcome Programme
Zefaniah Katuah: Malawi Liverpool Wellcome Programme
Patricia Duncan: Ministry of Agriculture and Food Security
John Nyangu: Ministry of Agriculture and Food Security
Andrew Mungu: Ministry of Agriculture and Food Security
Muonaouza Deleza: Lilongwe University of Agriculture and Natural Resources
Lawrence Banda: Lilongwe University of Agriculture and Natural Resources
Lumbani Makhaza: Malawi Liverpool Wellcome Programme
Nicola Elviss: UK Health Security Agency
Christopher P. Jewell: Lancaster University
Gina Pinchbeck: University of Liverpool
Nicholas A. Feasey: Malawi Liverpool Wellcome Programme
Eric M. Fèvre: University of Liverpool
Nicholas R. Thomson: Wellcome Sanger Institute

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Diverse salmonellae have the potential to cause disease and may be carried asymptomatically within the intestine of many vertebrate species. The relative contribution of human, animal, and environmental hosts to the transmission of Salmonella is unknown within and between households in low-income settings, especially where humans and animals may live in close contact and sanitary infrastructure is often inadequate. Between November 2018 and December 2019, we isolated Salmonella spp. from thirty households in urban and rural locations in Malawi, sampling at three time points from the stool of humans, animals, and their household environment. Using whole genome sequencing and fine-resolution bioinformatic and phylogenetic analyses we found evidence of sharing of Salmonella species and strains between humans, animals and the environment, both within and between households. The intricate web of interconnected salmonellae within this ecosystem underscores the importance of adopting a multi-faceted ‘One Health’ strategy when considering control of Salmonella in low-intensity agricultural systems.

Date: 2025
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DOI: 10.1038/s41467-025-65266-1

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