Rigby, Jonathan, Wilson, Catherine N, Zuza, Allan, Diness, Yohane, Mkwanda, Charity, Tonthola, Katalina, Kanjerwa, Oscar, Salifu, Chifundo, Pearse, Oliver, Msefula, Chisomo et al (show 7 more authors)
(2025)
Diversity of Salmonella enterica isolates from urban river and sewage water in Blantyre, Malawi
PLOS NEGLECTED TROPICAL DISEASES, 19 (9).
e0012413-.
ISSN 1935-2735, 1935-2735
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Rigby etal 2025 Diversity of Salmonella enterica isolates from urban river and sewage water in Blantyre, Malawi - PLoS NTD.pdf - Open Access published version Available under License Creative Commons Attribution. Download (1MB) | Preview |
Abstract
Background Salmonella enterica encompasses over 2,600 serovars, including several commonly associated with severe infection in humans. Salmonella is a major cause of sepsis in Africa; however, diagnosis requires clinical microbiology facilities. Environmental surveillance has the potential to play a role in Salmonella surveillance. Methods We undertook water-based environmental surveillance in Blantyre, Malawi, from 2018-2020, taking samples from rivers (87.9%), a sewage plant (8.85%) and other water sources (3.24%), isolating and storing 1,042 non-typhoidal Salmonella (NTS) isolates in this period. Of these, 341 NTS isolates were whole genome sequenced, genome quality was checked, duplicate genomes from any given sample were removed and core genome phylogeny was reconstructed. AMRFinder, PathogenWatch and SISTR were used to further investigate serovar, sequence type and antimicrobial resistance determinants. Results After quality checks, and removal of duplicate genomes, 270 NTS genomes remained for further analysis. Multiple Salmonella serovars associated with human infection were detected, of which S. Typhimurium (55/270 isolates) was the most common, including 44 of Sequence Type (ST) 313, a serovar commonly associated with severe invasive disease (iNTS). Six lineage 2 ST313 genomes possessed AMR genes predicting multidrug resistance (MDR), while 29 lineage 3 isolates contained no AMR predictive genes. PCR based detection of staG has been proposed as a diagnostic marker of S. Typhi; however, all eight genomes that contained staG identified as Salmonella enterica serovar Orion, raising concerns about the specificity of this marker as a monoplex for environmental surveillance of S. Typhi. Discussion The study identified diverse Salmonella serovars in the environment, including those reported to cause invasive disease, emphasizing the complex but potentially valuable contribution of implementing environmental surveillance for Salmonella in high burden areas lacking diagnostic microbiology capacity.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | Humans, Salmonella enterica, Salmonella Infections, Anti-Bacterial Agents, Water Microbiology, Rivers, Sewage, Phylogeny, Genome, Bacterial, Malawi, Serogroup, Whole Genome Sequencing |
| Divisions: | Faculty of Health & Life Sciences Faculty of Health & Life Sciences > Inst. Infection, Vet & Ecological Sciences Faculty of Health & Life Sciences > Inst. Infection, Vet & Ecological Sciences > Inst. Infection, Vet & Ecological Sciences (T&R Staff) Faculty of Health & Life Sciences > Inst. Infection, Vet & Ecological Sciences > Clinical Infection, Microbiology & Immunology |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 08 Dec 2025 09:49 |
| Last Modified: | 16 Jun 2026 17:12 |
| DOI: | 10.1371/journal.pntd.0012413 |
| Related Websites: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3195902 |
| Disclaimer: | The University of Liverpool is not responsible for content contained on other websites from links within repository metadata. Please contact us if you notice anything that appears incorrect or inappropriate. |
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