{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T07:03:17Z","timestamp":1787727797931,"version":"build-2784847793"},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T00:00:00Z","timestamp":1707350400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1217093"],"award-info":[{"award-number":["OPP1217093"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"\nBackground<\/jats:title>\nEnvironmental surveillance, using detection of Salmonella<\/jats:italic> Typhi DNA, has emerged as a potentially useful tool to identify typhoid-endemic settings; however, it is relatively costly and requires molecular diagnostic capacity. We sought to determine whether S<\/jats:italic>. Typhi bacteriophages are abundant in water sources in a typhoid-endemic setting, using low-cost assays.<\/jats:p>\n<\/jats:sec>\n\nMethodology<\/jats:title>\nWe collected drinking and surface water samples from urban, peri-urban and rural areas in 4 regions of Nepal. We performed a double agar overlay with S<\/jats:italic>. Typhi to assess the presence of bacteriophages. We isolated and tested phages against multiple strains to assess their host range. We performed whole genome sequencing of isolated phages, and generated phylogenies using conserved genes.<\/jats:p>\n<\/jats:sec>\n\nFindings<\/jats:title>\nS<\/jats:italic>. Typhi-specific bacteriophages were detected in 54.9% (198\/361) of river and 6.3% (1\/16) drinking water samples from the Kathmandu Valley and Kavrepalanchok. Water samples collected within or downstream of population-dense areas were more likely to be positive (72.6%, 193\/266) than those collected upstream from population centers (5.3%, 5\/95) (p=0.005). In urban Biratnagar and rural Dolakha, where typhoid incidence is low, only 6.7% (1\/15, Biratnagar) and 0% (0\/16, Dolakha) river water samples contained phages. All S<\/jats:italic>. Typhi phages were unable to infect other Salmonella<\/jats:italic> and non-Salmonella<\/jats:italic> strains, nor a Vi-knockout S<\/jats:italic>. Typhi strain. Representative strains from S<\/jats:italic>. Typhi lineages were variably susceptible to the isolated phages. Phylogenetic analysis showed that S<\/jats:italic>. Typhi phages belonged to the class Caudoviricetes<\/jats:italic> and clustered in three distinct groups.<\/jats:p>\n<\/jats:sec>\n\nConclusions<\/jats:title>\nS<\/jats:italic>. Typhi bacteriophages were highly abundant in surface waters of typhoid-endemic communities but rarely detected in low typhoid burden communities. Bacteriophages recovered were specific for S<\/jats:italic>. Typhi and required Vi polysaccharide for infection. Screening small volumes of water with simple, low-cost (~$2) plaque assays enables detection of S<\/jats:italic>. Typhi phages and should be further evaluated as a scalable tool for typhoid environmental surveillance.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pntd.0011912","type":"journal-article","created":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T18:21:53Z","timestamp":1707416513000},"page":"e0011912","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":13,"title":["Detection of Salmonella Typhi bacteriophages in surface waters as a scalable approach to environmental surveillance"],"prefix":"10.1371","volume":"18","author":[{"given":"Sneha","family":"Shrestha","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8593-1119","authenticated-orcid":true,"given":"Kesia Esther","family":"Da Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jivan","family":"Shakya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander T.","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nishan","family":"Katuwal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajeev","family":"Shrestha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mudita","family":"Shakya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabin Bikram","family":"Shahi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiva Ram","family":"Naga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"LeBoa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristen","family":"Aiemjoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isaac I.","family":"Bogoch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Senjuti","family":"Saha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dipesh","family":"Tamrakar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason R.","family":"Andrews","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,2,8]]},"reference":[{"key":"pntd.0011912.ref001","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1007\/s11684-020-0777-6","article-title":"Antibiotic resistome of Salmonella typhi: molecular determinants for the emergence of drug resistance","volume":"15","author":"A Kumar","year":"2021","journal-title":"Front Med"},{"key":"pntd.0011912.ref002","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S1473-3099(18)30685-6","article-title":"The global burden of typhoid and paratyphoid fevers: a systematic analysis for the Global Burden of Disease Study 2017","volume":"19","author":"JD Stanaway","year":"2019","journal-title":"Lancet Infect Dis"},{"key":"pntd.0011912.ref003","doi-asserted-by":"crossref","first-page":"S268","DOI":"10.1093\/infdis\/jiy494","article-title":"Integrating Facility-Based Surveillance with Healthcare Utilization Surveys to Estimate Enteric Fever Incidence","volume":"218","author":"JR Andrews","year":"2018","journal-title":"Methods and Challenges. 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