Utility of Mycobacterium Tuberculosis Genome Sequencing Snapshots to Assess Transmission Dynamics Over Time

Overview

Journal J Infect Dis

Publisher Oxford University Press

Specialty Infectious Diseases

Date 2023 Nov 23

PMID 37995298

Authors

Courtney M Yuen

Chuan-Chin Huang

Ana Karina Millones

Roger I Calderon

Abigail L Manson

Judith Jimenez

Carmen Contreras

Ashlee M Earl

Mercedes C Becerra

Leonid Lecca

Megan B Murray

Affiliations

Soon will be listed here.

Abstract

We explored the utility of brief Mycobacterium tuberculosis whole-genome sequencing (WGS) "snapshots" at a sentinel site within Lima, Peru, for evaluating local transmission dynamics over time. Within a 17-km2 area, 15 of 70 (21%) isolates with WGS collected during 2011-2012 and 22 of 81 (27%) collected during 2020-2021 were clustered (P = .414), and additional isolates clustered with those from outside the area. Isolates from the later period were disproportionately related to large historic clusters in Lima from the earlier period. WGS snapshots at a sentinel site may not be useful for monitoring transmission, but monitoring the persistence of large transmission clusters might be.

References

Nikolayevskyy V, Niemann S, Anthony R, van Soolingen D, Tagliani E, Kodmon C . Role and value of whole genome sequencing in studying tuberculosis transmission. Clin Microbiol Infect. 2019; 25(11):1377-1382. DOI: 10.1016/j.cmi.2019.03.022. View

Smith J, Cohen T, Dowdy D, Shrestha S, Gandhi N, Hill A . Quantifying Mycobacterium tuberculosis Transmission Dynamics Across Global Settings: A Systematic Analysis. Am J Epidemiol. 2022; 192(1):133-145. PMC: 10144641. DOI: 10.1093/aje/kwac181. View

Becerra M, Huang C, Lecca L, Bayona J, Contreras C, Calderon R . Transmissibility and potential for disease progression of drug resistant : prospective cohort study. BMJ. 2019; 367:l5894. PMC: 6812583. DOI: 10.1136/bmj.l5894. View

Saavedra Cervera B, Lopez M, Chiner-Oms A, Garcia A, Cancino-Munoz I, Torres-Puente M . Fine-grain population structure and transmission patterns of in southern Mozambique, a high TB/HIV burden area. Microb Genom. 2022; 8(7). PMC: 9455694. DOI: 10.1099/mgen.0.000844. View

Nelson K, Shah N, Mathema B, Ismail N, Brust J, Brown T . Spatial Patterns of Extensively Drug-Resistant Tuberculosis Transmission in KwaZulu-Natal, South Africa. J Infect Dis. 2018; 218(12):1964-1973. PMC: 6217717. DOI: 10.1093/infdis/jiy394. View

Ngabonziza J, Rigouts L, Torrea G, Decroo T, Kamanzi E, Lempens P . Multidrug-resistant tuberculosis control in Rwanda overcomes a successful clone that causes most disease over a quarter century. J Clin Tuberc Other Mycobact Dis. 2022; 27:100299. PMC: 8802117. DOI: 10.1016/j.jctube.2022.100299. View

Li M, Guo M, Peng Y, Jiang Q, Xia L, Zhong S . High proportion of tuberculosis transmission among social contacts in rural China: a 12-year prospective population-based genomic epidemiological study. Emerg Microbes Infect. 2022; 11(1):2102-2111. PMC: 9448380. DOI: 10.1080/22221751.2022.2112912. View

Guerra-Assuncao J, Crampin A, Houben R, Mzembe T, Mallard K, Coll F . Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. Elife. 2015; 4. PMC: 4384740. DOI: 10.7554/eLife.05166. View

Yuen C, Brooks M, Millones A, Acosta D, Del Aguila-Rojas E, Campos H . Geospatial analysis of reported activity locations to identify sites for tuberculosis screening. Sci Rep. 2022; 12(1):14094. PMC: 9387880. DOI: 10.1038/s41598-022-18456-6. View

10.

Millones A, Lecca L, Acosta D, Campos H, Del Aguila-Rojas E, Farronay S . The impact of the COVID-19 pandemic on patients' experiences obtaining a tuberculosis diagnosis in Peru: a mixed-methods study. BMC Infect Dis. 2022; 22(1):829. PMC: 9645304. DOI: 10.1186/s12879-022-07832-2. View

11.

Yuen C, Amanullah F, Dharmadhikari A, Nardell E, Seddon J, Vasilyeva I . Turning off the tap: stopping tuberculosis transmission through active case-finding and prompt effective treatment. Lancet. 2015; 386(10010):2334-43. PMC: 7138065. DOI: 10.1016/S0140-6736(15)00322-0. View

12.

Huang C, Trevisi L, Becerra M, Calderon R, Contreras C, Jimenez J . Spatial scale of tuberculosis transmission in Lima, Peru. Proc Natl Acad Sci U S A. 2022; 119(45):e2207022119. PMC: 9659349. DOI: 10.1073/pnas.2207022119. View

13.

Hatherell H, Colijn C, Stagg H, Jackson C, Winter J, Abubakar I . Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review. BMC Med. 2016; 14:21. PMC: 4804562. DOI: 10.1186/s12916-016-0566-x. View