Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana

Chelsea R. Baker; Ivan Barilar; Leonardo S. de Araujo; Anne W. Rimoin; Daniel M. Parker; Rosanna Boyd; James L. Tobias; Patrick K. Moonan; Eleanor S. Click; Alyssa Finlay; John E. Oeltmann; Vladimir N. Minin; Chawangwa Modongo; Nicola M. Zetola; Stefan Niemann; Sanghyuk S. Shin

doi:10.3201/eid2905.220796

Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana

Chelsea R. Baker, Ivan Barilar, Leonardo S. de Araujo, Anne W. Rimoin, Daniel M. Parker, Rosanna Boyd, James L. Tobias, Patrick K. Moonan, Eleanor S. Click, Alyssa Finlay, John E. Oeltmann, Vladimir N. Minin, Chawangwa Modongo, Nicola M. Zetola, Stefan Niemann, Sanghyuk S. Shin

Research output: Contribution to journal › Article › peer-review

Abstract

Combining genomic and geospatial data can be useful for understanding Mycobacterium tuberculosis transmission in high-burden tuberculosis (TB) settings. We performed whole-genome sequencing on M. tuberculosis DNA extracted from sputum cultures from a population-based TB study conducted in Gaborone, Botswana, during 2012–2016. We determined spatial distribution of cases on the basis of shared genotypes among isolates. We considered clusters of isolates with ≤5 single-nucleotide polymorphisms identified by whole-genome sequencing to indicate recent transmission and clusters of ≥10 persons to be outbreaks. We obtained both molecular and geospatial data for 946/1,449 (65%) participants with culture-confirmed TB; 62 persons belonged to 5 outbreaks of 10–19 persons each. We detected geospatial clustering in just 2 of those 5 outbreaks, suggesting heterogeneous spatial patterns. Our findings indicate that targeted interventions applied in smaller geographic areas of high-burden TB identified using integrated genomic and geospatial data might help interrupt TB transmission during outbreaks.

Original language	English (US)
Pages (from-to)	977-987
Number of pages	11
Journal	Emerging Infectious Diseases
Volume	29
Issue number	5
DOIs	https://doi.org/10.3201/eid2905.220796
State	Published - May 2023
Externally published	Yes

ASJC Scopus subject areas

Epidemiology
Microbiology (medical)
Infectious Diseases

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.3201/eid2905.220796

Cite this

Baker, C. R., Barilar, I., de Araujo, L. S., Rimoin, A. W., Parker, D. M., Boyd, R., Tobias, J. L., Moonan, P. K., Click, E. S., Finlay, A., Oeltmann, J. E., Minin, V. N., Modongo, C., Zetola, N. M., Niemann, S., & Shin, S. S. (2023). Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana. Emerging Infectious Diseases, 29(5), 977-987. https://doi.org/10.3201/eid2905.220796

Baker, CR, Barilar, I, de Araujo, LS, Rimoin, AW, Parker, DM, Boyd, R, Tobias, JL, Moonan, PK, Click, ES, Finlay, A, Oeltmann, JE, Minin, VN, Modongo, C, Zetola, NM, Niemann, S & Shin, SS 2023, 'Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana', Emerging Infectious Diseases, vol. 29, no. 5, pp. 977-987. https://doi.org/10.3201/eid2905.220796

@article{175772de04d144f5ab0fefe47d2f8efe,

title = "Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana",

abstract = "Combining genomic and geospatial data can be useful for understanding Mycobacterium tuberculosis transmission in high-burden tuberculosis (TB) settings. We performed whole-genome sequencing on M. tuberculosis DNA extracted from sputum cultures from a population-based TB study conducted in Gaborone, Botswana, during 2012–2016. We determined spatial distribution of cases on the basis of shared genotypes among isolates. We considered clusters of isolates with ≤5 single-nucleotide polymorphisms identified by whole-genome sequencing to indicate recent transmission and clusters of ≥10 persons to be outbreaks. We obtained both molecular and geospatial data for 946/1,449 (65%) participants with culture-confirmed TB; 62 persons belonged to 5 outbreaks of 10–19 persons each. We detected geospatial clustering in just 2 of those 5 outbreaks, suggesting heterogeneous spatial patterns. Our findings indicate that targeted interventions applied in smaller geographic areas of high-burden TB identified using integrated genomic and geospatial data might help interrupt TB transmission during outbreaks.",

author = "Baker, {Chelsea R.} and Ivan Barilar and {de Araujo}, {Leonardo S.} and Rimoin, {Anne W.} and Parker, {Daniel M.} and Rosanna Boyd and Tobias, {James L.} and Moonan, {Patrick K.} and Click, {Eleanor S.} and Alyssa Finlay and Oeltmann, {John E.} and Minin, {Vladimir N.} and Chawangwa Modongo and Zetola, {Nicola M.} and Stefan Niemann and Shin, {Sanghyuk S.}",

year = "2023",

month = may,

doi = "10.3201/eid2905.220796",

language = "English (US)",

volume = "29",

pages = "977--987",

journal = "Emerging Infectious Diseases",

issn = "1080-6040",

publisher = "Centers for Disease Control and Prevention (CDC)",

number = "5",

}

TY - JOUR

T1 - Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana

AU - Baker, Chelsea R.

AU - Barilar, Ivan

AU - de Araujo, Leonardo S.

AU - Rimoin, Anne W.

AU - Parker, Daniel M.

AU - Boyd, Rosanna

AU - Tobias, James L.

AU - Moonan, Patrick K.

AU - Click, Eleanor S.

AU - Finlay, Alyssa

AU - Oeltmann, John E.

AU - Minin, Vladimir N.

AU - Modongo, Chawangwa

AU - Zetola, Nicola M.

AU - Niemann, Stefan

AU - Shin, Sanghyuk S.

PY - 2023/5

Y1 - 2023/5

N2 - Combining genomic and geospatial data can be useful for understanding Mycobacterium tuberculosis transmission in high-burden tuberculosis (TB) settings. We performed whole-genome sequencing on M. tuberculosis DNA extracted from sputum cultures from a population-based TB study conducted in Gaborone, Botswana, during 2012–2016. We determined spatial distribution of cases on the basis of shared genotypes among isolates. We considered clusters of isolates with ≤5 single-nucleotide polymorphisms identified by whole-genome sequencing to indicate recent transmission and clusters of ≥10 persons to be outbreaks. We obtained both molecular and geospatial data for 946/1,449 (65%) participants with culture-confirmed TB; 62 persons belonged to 5 outbreaks of 10–19 persons each. We detected geospatial clustering in just 2 of those 5 outbreaks, suggesting heterogeneous spatial patterns. Our findings indicate that targeted interventions applied in smaller geographic areas of high-burden TB identified using integrated genomic and geospatial data might help interrupt TB transmission during outbreaks.

AB - Combining genomic and geospatial data can be useful for understanding Mycobacterium tuberculosis transmission in high-burden tuberculosis (TB) settings. We performed whole-genome sequencing on M. tuberculosis DNA extracted from sputum cultures from a population-based TB study conducted in Gaborone, Botswana, during 2012–2016. We determined spatial distribution of cases on the basis of shared genotypes among isolates. We considered clusters of isolates with ≤5 single-nucleotide polymorphisms identified by whole-genome sequencing to indicate recent transmission and clusters of ≥10 persons to be outbreaks. We obtained both molecular and geospatial data for 946/1,449 (65%) participants with culture-confirmed TB; 62 persons belonged to 5 outbreaks of 10–19 persons each. We detected geospatial clustering in just 2 of those 5 outbreaks, suggesting heterogeneous spatial patterns. Our findings indicate that targeted interventions applied in smaller geographic areas of high-burden TB identified using integrated genomic and geospatial data might help interrupt TB transmission during outbreaks.

UR - http://www.scopus.com/inward/record.url?scp=85153425822&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85153425822&partnerID=8YFLogxK

U2 - 10.3201/eid2905.220796

DO - 10.3201/eid2905.220796

M3 - Article

C2 - 37081530

AN - SCOPUS:85153425822

SN - 1080-6040

VL - 29

SP - 977

EP - 987

JO - Emerging Infectious Diseases

JF - Emerging Infectious Diseases

IS - 5

ER -

Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana

Abstract

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this