{"doi":"10.1371/journal.pgph.0004040","title":"Distribution and transmission of M. tuberculosis in a high-HIV prevalence city in Malawi: A genomic and spatial analysis","abstract":"<jats:p>Delays in identifying and treating individuals with infectious tuberculosis (TB) contribute to poor health outcomes and allow ongoing community transmission of <jats:italic>M. tuberculosis</jats:italic> (<jats:italic>Mtb</jats:italic>). Current recommendations for screening for tuberculosis specify community characteristics (e.g., areas with high local tuberculosis prevalence) that can be used to target screening within the general population. However, areas of higher tuberculosis burden are not necessarily areas with higher rates of transmission. We investigated the transmission of <jats:italic>Mtb</jats:italic> using high-resolution surveillance data in Blantyre, Malawi. We extracted and performed whole genome sequencing on mycobacterial DNA from cultured <jats:italic>M. tuberculosis</jats:italic> isolates obtained from culture-positive tuberculosis cases at the time of tuberculosis (TB) notification in Blantyre, Malawi between 2015-2019. We constructed putative transmission networks identified using TransPhylo and investigated individual and pair-wise demographic, clinical, and spatial factors associated with person-to-person transmission. We found that 56% of individuals with sequenced isolates had a probable transmission link to at least one other individual in the study. We identified thirteen putative transmission networks that included five or more individuals. Five of these networks had a single spatial focus of transmission in the city, and each focus centered in a distinct neighborhood in the city. We also found that approximately two-thirds of inferred transmission links occurred between individuals residing in different geographic zones of the city. While the majority of detected tuberculosis transmission events in Blantyre occurred between people living in different zones, there was evidence of distinct geographical concentration for five transmission networks. These findings suggest that targeted interventions in areas with evidence of localized transmission may be an effective local tactic, but will likely need to be augmented by city-wide interventions to improve case finding to have sustained impact.</jats:p>","journal":"PLOS Global Public Health","year":2025,"id":635265,"datarank":0.24141568686511508,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.0,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":292871,"name":"Elizabeth L. Corbett","orcid":"0000-0002-3552-3181","position":1,"is_corresponding":false},{"id":1648098,"name":"Victor Ndhlovu","orcid":"0000-0003-1606-0959","position":2,"is_corresponding":false},{"id":861625,"name":"Benjamin Sobkowiak","orcid":"0000-0002-1382-1137","position":3,"is_corresponding":false},{"id":470062,"name":"Caroline Colijn","orcid":"0000-0001-6097-6708","position":4,"is_corresponding":false},{"id":231886,"name":"Jason R. Andrews","orcid":"0000-0002-5967-251X","position":5,"is_corresponding":false},{"id":670593,"name":"Rachael M. Burke","orcid":"0000-0002-2156-5030","position":6,"is_corresponding":false},{"id":479251,"name":"Patrick Cudahy","orcid":"0000-0003-4462-9567","position":7,"is_corresponding":false},{"id":438383,"name":"Peter J. Dodd","orcid":"0000-0001-5825-9347","position":8,"is_corresponding":false},{"id":539310,"name":"Jeffrey W. Eaton","orcid":"0000-0001-7728-728X","position":9,"is_corresponding":false},{"id":376250,"name":"David M. Engelthaler","orcid":"0000-0001-5945-059X","position":10,"is_corresponding":false},{"id":481302,"name":"Megan Folkerts","orcid":"0000-0001-7430-1701","position":11,"is_corresponding":false},{"id":1648106,"name":"Helena R.A. Feasey","orcid":null,"position":12,"is_corresponding":false},{"id":956914,"name":"Yu Lan","orcid":"0000-0003-0373-1944","position":13,"is_corresponding":false},{"id":1648109,"name":"Jen Lewis","orcid":"0000-0002-3765-1566","position":14,"is_corresponding":false},{"id":1648111,"name":"Jennifer McNichol","orcid":null,"position":15,"is_corresponding":false},{"id":308322,"name":"Nicolas A. Menzies","orcid":"0000-0002-2571-016X","position":16,"is_corresponding":false},{"id":1608469,"name":"Geoffrey Chipungu","orcid":"0000-0002-3819-0300","position":17,"is_corresponding":false},{"id":732784,"name":"Marriott Nliwasa","orcid":"0000-0002-3100-5512","position":18,"is_corresponding":false},{"id":106838,"name":"Daniel M. Weinberger","orcid":"0000-0003-1178-8086","position":19,"is_corresponding":false},{"id":106837,"name":"Joshua L. Warren","orcid":"0000-0002-6274-6970","position":20,"is_corresponding":false},{"id":22312,"name":"Joshua A. Salomon","orcid":"0000-0003-3929-5515","position":21,"is_corresponding":false},{"id":670594,"name":"Peter MacPherson","orcid":"0000-0002-0329-9613","position":22,"is_corresponding":false},{"id":226284,"name":"Ted Cohen","orcid":"0000-0002-8091-7198","position":23,"is_corresponding":false},{"id":552195,"name":"Melanie H. Chitwood","orcid":"0000-0002-9289-5694","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Distribution and transmission of M. tuberculosis in a high-HIV prevalence city in Malawi: A genomic and spatial analysis","abstract":"<jats:p>Delays in identifying and treating individuals with infectious tuberculosis (TB) contribute to poor health outcomes and allow ongoing community transmission of <jats:italic>M. tuberculosis</jats:italic> (<jats:italic>Mtb</jats:italic>). Current recommendations for screening for tuberculosis specify community characteristics (e.g., areas with high local tuberculosis prevalence) that can be used to target screening within the general population. However, areas of higher tuberculosis burden are not necessarily areas with higher rates of transmission. We investigated the transmission of <jats:italic>Mtb</jats:italic> using high-resolution surveillance data in Blantyre, Malawi. We extracted and performed whole genome sequencing on mycobacterial DNA from cultured <jats:italic>M. tuberculosis</jats:italic> isolates obtained from culture-positive tuberculosis cases at the time of tuberculosis (TB) notification in Blantyre, Malawi between 2015-2019. We constructed putative transmission networks identified using TransPhylo and investigated individual and pair-wise demographic, clinical, and spatial factors associated with person-to-person transmission. We found that 56% of individuals with sequenced isolates had a probable transmission link to at least one other individual in the study. We identified thirteen putative transmission networks that included five or more individuals. Five of these networks had a single spatial focus of transmission in the city, and each focus centered in a distinct neighborhood in the city. We also found that approximately two-thirds of inferred transmission links occurred between individuals residing in different geographic zones of the city. While the majority of detected tuberculosis transmission events in Blantyre occurred between people living in different zones, there was evidence of distinct geographical concentration for five transmission networks. These findings suggest that targeted interventions in areas with evidence of localized transmission may be an effective local tactic, but will likely need to be augmented by city-wide interventions to improve case finding to have sustained impact.</jats:p>","is_dataset_classified":null,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"40173177","pmcid":"PMC11964229","openalex_id":"https://openalex.org/W4409103486","authors":[],"funders":[{"funder_name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","grant_id":"R01AI147854","title":null},{"funder_name":"Bill and Melinda Gates Foundation","grant_id":"INV-006733, INV-002606","title":null},{"funder_name":"Medical Research Council","grant_id":"MR/X020258/1","title":"MRC Centre for Global Infectious Disease Analysis (MRC GIDA)"},{"funder_name":"Gates Foundation","grant_id":"INV-002606","title":null},{"funder_name":"Gates Foundation","grant_id":"INV-006733","title":null},{"funder_name":"National Institutes of Health","grant_id":"5R01AI147854-03","title":"Integrating genomic and spatial approaches for targeted control of HIV-associated tuberculosis epidemics"}],"total_grants":6,"fwci":3.1804,"citation_percentile":0.9097114,"influential_citations":0,"citation_trend":[{"year":2025,"count":2},{"year":2026,"count":2}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://unhabitat.org/sites/default/files/download-manager-files/Malawi%20Blantyre%20Urban%20Profile.pdf","host_type":"journal"},{"url":"https://unhabitat.org/sites/default/files/download-manager-files/Malawi%20Blantyre%20Urban%20Profile.pdf","host_type":"publisher"},{"url":"https://dx.plos.org/10.1371/journal.pgph.0004040","host_type":"publisher"},{"url":"https://doi.org/10.1371/journal.pgph.0004040","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/40173177","host_type":"repository"},{"url":"https://eprints.gla.ac.uk/view/journal_volume/PLoS_Global_Public_Health.html>,","host_type":"journal"},{"url":"https://orcid.org/0000-0002-9289-5694>;","host_type":"repository"},{"url":"https://doaj.org/article/34c156b107954e76b802a68dc77f192d","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11964229","host_type":"repository"},{"url":"https://researchonline.lshtm.ac.uk/id/eprint/4677360/1/Chitwood-etal-2025-Distribution-and-transmission.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC11964229","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC11964229?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1371/journal.pgph.0004040","host_type":""},{"url":"https://eprints.whiterose.ac.uk/id/eprint/225566/","host_type":""},{"url":"https://hdl.handle.net/10023/31911","host_type":""},{"url":"https://www.scopus.com/pages/publications/105002177176","host_type":""}],"fields_of_study":["Tuberculosis Research and Epidemiology","Mycobacterium research and diagnosis","HIV Research and Treatment","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["Tuberculosis","Transmission (telecommunications)","Mycobacterium tuberculosis","Population","Psychological intervention","Environmental health","Medicine","Demography","Geography","Biology","Pathology","MCC","Prevention","DAS","Human Geography","Human Society","Emerging Infectious Diseases","Rare Diseases","Infectious Diseases","SDG 3 - Good Health and Well-being","RA0421","Clinical Research","RA0421 Public health. Hygiene. Preventive Medicine","Biodefense","Factors relating to the physical environment","Health Sciences","Sexually Transmitted Infections","HIV/AIDS","Public aspects of medicine","RA1-1270","Infection","Research Article"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"No poverty"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"refseq"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T14:52:00.223622Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}