Spatial and Genomic Data to Characterize Endemic Typhoid Transmission.
| Title: | Spatial and Genomic Data to Characterize Endemic Typhoid Transmission. |
|---|---|
| Authors: | Gauld JS; Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle, Washington, USA.; Centre for Health Informatics, Computing, and Statistics, Lancaster University, Lancaster, United Kingdom.; Olgemoeller F; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.; Malawi -Liverpool Wellcome Programme, Blantyre, Malawi.; Heinz E; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.; Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.; Nkhata R; Malawi -Liverpool Wellcome Programme, Blantyre, Malawi.; Bilima S; Malawi -Liverpool Wellcome Programme, Blantyre, Malawi.; Wailan AM; Wellcome Sanger Institute, Cambridge, United Kingdom.; Kennedy N; Department of Paediatrics, University of Malawi the College of Medicine, Blantyre, Malawi.; School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, United Kingdom.; Mallewa J; Adult Medicine, University of Malawi the College of Medicine, Blantyre, Malawi.; Gordon MA; Malawi -Liverpool Wellcome Programme, Blantyre, Malawi.; Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, United Kingdom.; Adult Medicine, University of Malawi the College of Medicine, Blantyre, Malawi.; Read JM; Centre for Health Informatics, Computing, and Statistics, Lancaster University, Lancaster, United Kingdom.; Heyderman RS; Division of Infection and Immunity, University College London, London, United Kingdom.; Thomson NR; Wellcome Sanger Institute, Cambridge, United Kingdom.; Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom.; Diggle PJ; Centre for Health Informatics, Computing, and Statistics, Lancaster University, Lancaster, United Kingdom.; Feasey NA; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.; Malawi -Liverpool Wellcome Programme, Blantyre, Malawi. |
| Source: | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America [Clin Infect Dis] 2022 Jun 10; Vol. 74 (11), pp. 1993-2000. |
| Publication Type: | Journal Article; Research Support, Non-U.S. Gov't |
| Language: | English |
| Journal Info: | Publisher: Oxford University Press Country of Publication: United States NLM ID: 9203213 Publication Model: Print Cited Medium: Internet ISSN: 1537-6591 (Electronic) Linking ISSN: 10584838 NLM ISO Abbreviation: Clin Infect Dis Subsets: MEDLINE |
| Imprint Name(s): | Publication: Jan. 2011- : Oxford : Oxford University Press; Original Publication: Chicago, IL : The University of Chicago Press, c1992- |
| MeSH Terms: | Typhoid Fever*/microbiology; Salmonella typhi/genetics ; Cohort Studies ; Genomics ; Humans ; Nucleotides |
| Abstract: | Background: Diverse environmental exposures and risk factors have been implicated in the transmission of Salmonella Typhi, but the dominant transmission pathways through the environment to susceptible humans remain unknown. Here, we use spatial, bacterial genomic, and hydrological data to refine our view of typhoid transmission in an endemic setting.; Methods: A total of 546 patients presenting to Queen Elizabeth Central Hospital in Blantyre, Malawi, with blood culture-confirmed typhoid fever between April 2015 and January 2017 were recruited to a cohort study. The households of a subset of these patients were geolocated, and 256 S. Typhi isolates were whole-genome sequenced. Pairwise single-nucleotide variant distances were incorporated into a geostatistical modeling framework using multidimensional scaling.; Results: Typhoid fever was not evenly distributed across Blantyre, with estimated minimum incidence ranging across the city from 100 cases per 100 000 population per year. Pairwise single-nucleotide variant distance and physical household distances were significantly correlated (P = .001). We evaluated the ability of river catchment to explain the spatial patterns of genomics observed, finding that it significantly improved the fit of the model (P = .003). We also found spatial correlation at a smaller spatial scale, of households living |
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| Grant Information: | United Kingdom Wellcome Trust; R01 AI160780 United States AI NIAID NIH HHS; 206454 United Kingdom WT_ Wellcome Trust |
| Contributed Indexing: | Keywords: Salmonella typhi; environmental transmission; genomics; spatial patterns; typhoid fever |
| Substance Nomenclature: | 0 (Nucleotides) |
| Entry Date(s): | Date Created: 20210831 Date Completed: 20220614 Latest Revision: 20230211 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC9187325 |
| DOI: | 10.1093/cid/ciab745 |
| PMID: | 34463736 |
| Database: | MEDLINE |
Journal Article; Research Support, Non-U.S. Gov't