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Spatial and Genomic Data to Characterize Endemic Typhoid Transmission

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Spatial and Genomic Data to Characterize Endemic Typhoid Transmission. / Gauld, Jillian S; Olgemoeller, Franziska; Heinz, Eva et al.

In: Clinical Infectious Diseases, Vol. 74, No. 11, 01.06.2022, p. 1993-2000.

Research output: Contribution to Journal/MagazineJournal articlepeer-review

Harvard

Gauld, JS, Olgemoeller, F, Heinz, E, Nkhata, R, Bilima, S, Wailan, AM, Kennedy, N, Mallewa, J, Gordon, MA, Read, JM, Heyderman, RS, Thomson, NR, Diggle, PJ & Feasey, NA 2022, 'Spatial and Genomic Data to Characterize Endemic Typhoid Transmission', Clinical Infectious Diseases, vol. 74, no. 11, pp. 1993-2000. https://doi.org/10.1093/cid/ciab745

APA

Gauld, J. S., Olgemoeller, F., Heinz, E., Nkhata, R., Bilima, S., Wailan, A. M., Kennedy, N., Mallewa, J., Gordon, M. A., Read, J. M., Heyderman, R. S., Thomson, N. R., Diggle, P. J., & Feasey, N. A. (2022). Spatial and Genomic Data to Characterize Endemic Typhoid Transmission. Clinical Infectious Diseases, 74(11), 1993-2000. https://doi.org/10.1093/cid/ciab745

Vancouver

Gauld JS, Olgemoeller F, Heinz E, Nkhata R, Bilima S, Wailan AM et al. Spatial and Genomic Data to Characterize Endemic Typhoid Transmission. Clinical Infectious Diseases. 2022 Jun 1;74(11):1993-2000. Epub 2021 Aug 31. doi: 10.1093/cid/ciab745

Author

Gauld, Jillian S ; Olgemoeller, Franziska ; Heinz, Eva et al. / Spatial and Genomic Data to Characterize Endemic Typhoid Transmission. In: Clinical Infectious Diseases. 2022 ; Vol. 74, No. 11. pp. 1993-2000.

Bibtex

@article{f7ac45ac718744b68abacc96c9dc3cf0,
title = "Spatial and Genomic Data to Characterize Endemic Typhoid Transmission",
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 <15 to >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 <192 m apart.CONCLUSIONS: These findings reinforce the emerging view that hydrological systems play a key role in the transmission of typhoid fever. By combining genomic and spatial data, we show how multifaceted data can be used to identify high incidence areas, explain the connections between them, and inform targeted environmental surveillance, all of which will be critical to shape local and regional typhoid control strategies.",
keywords = "Cohort Studies, Genomics, Humans, Nucleotides, Salmonella typhi/genetics, Typhoid Fever/microbiology",
author = "Gauld, {Jillian S} and Franziska Olgemoeller and Eva Heinz and Rose Nkhata and Sithembile Bilima and Wailan, {Alexander M} and Neil Kennedy and Jane Mallewa and Gordon, {Melita A} and Read, {Jonathan M} and Heyderman, {Robert S} and Thomson, {Nicholas R} and Diggle, {Peter J} and Feasey, {Nicholas A}",
year = "2022",
month = jun,
day = "1",
doi = "10.1093/cid/ciab745",
language = "English",
volume = "74",
pages = "1993--2000",
journal = "Clinical Infectious Diseases",
issn = "1058-4838",
publisher = "BioMed Central",
number = "11",

}

RIS

TY - JOUR

T1 - Spatial and Genomic Data to Characterize Endemic Typhoid Transmission

AU - Gauld, Jillian S

AU - Olgemoeller, Franziska

AU - Heinz, Eva

AU - Nkhata, Rose

AU - Bilima, Sithembile

AU - Wailan, Alexander M

AU - Kennedy, Neil

AU - Mallewa, Jane

AU - Gordon, Melita A

AU - Read, Jonathan M

AU - Heyderman, Robert S

AU - Thomson, Nicholas R

AU - Diggle, Peter J

AU - Feasey, Nicholas A

PY - 2022/6/1

Y1 - 2022/6/1

N2 - 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 <15 to >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 <192 m apart.CONCLUSIONS: These findings reinforce the emerging view that hydrological systems play a key role in the transmission of typhoid fever. By combining genomic and spatial data, we show how multifaceted data can be used to identify high incidence areas, explain the connections between them, and inform targeted environmental surveillance, all of which will be critical to shape local and regional typhoid control strategies.

AB - 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 <15 to >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 <192 m apart.CONCLUSIONS: These findings reinforce the emerging view that hydrological systems play a key role in the transmission of typhoid fever. By combining genomic and spatial data, we show how multifaceted data can be used to identify high incidence areas, explain the connections between them, and inform targeted environmental surveillance, all of which will be critical to shape local and regional typhoid control strategies.

KW - Cohort Studies

KW - Genomics

KW - Humans

KW - Nucleotides

KW - Salmonella typhi/genetics

KW - Typhoid Fever/microbiology

U2 - 10.1093/cid/ciab745

DO - 10.1093/cid/ciab745

M3 - Journal article

C2 - 34463736

VL - 74

SP - 1993

EP - 2000

JO - Clinical Infectious Diseases

JF - Clinical Infectious Diseases

SN - 1058-4838

IS - 11

ER -