Kristin N Nelson1, N Sarita Shah1,2, Barun Mathema3, Nazir Ismail4,5, James C M Brust6, Tyler S Brown7, Sara C Auld1,8, Shaheed Vally Omar4, Natashia Morris9, Angie Campbell1, Salim Allana1, Pravi Moodley10,11, Koleka Mlisana10,11, Neel R Gandhi1,8. 1. Rollins School of Public Health, Emory University, Atlanta, Georgia. 2. Centers for Disease Control and Prevention, Atlanta, Georgia. 3. Mailman School of Public Health, Columbia University, New York, New York. 4. National Institute for Communicable Diseases, Johannesburg. 5. University of Pretoria, South Africa. 6. Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York. 7. Infectious Diseases Division, Massachusetts General Hospital, Boston. 8. Emory University School of Medicine, Atlanta, Georgia. 9. Environment and Health Research Unit, South African Medical Research Council, Johannesburg. 10. National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa. 11. School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
Abstract
Background: Transmission is driving the global drug-resistant tuberculosis (TB) epidemic; nearly three-quarters of drug-resistant TB cases are attributable to transmission. Geographic patterns of disease incidence, combined with information on probable transmission links, can define the spatial scale of transmission and generate hypotheses about factors driving transmission patterns. Methods: We combined whole-genome sequencing data with home Global Positioning System coordinates from 344 participants with extensively drug-resistant (XDR) TB in KwaZulu-Natal, South Africa, diagnosed from 2011 to 2014. We aimed to determine if genomically linked (difference of ≤5 single-nucleotide polymorphisms) cases lived close to one another, which would suggest a role for local community settings in transmission. Results: One hundred eighty-two study participants were genomically linked, comprising 1084 case-pairs. The median distance between case-pairs' homes was 108 km (interquartile range, 64-162 km). Between-district, as compared to within-district, links accounted for the majority (912/1084 [84%]) of genomic links. Half (526 [49%]) of genomic links involved a case from Durban, the urban center of KwaZulu-Natal. Conclusions: The high proportions of between-district links with Durban provide insight into possible drivers of province-wide XDR-TB transmission, including urban-rural migration. Further research should focus on characterizing the contribution of these drivers to overall XDR-TB transmission in KwaZulu-Natal to inform design of targeted strategies to curb the drug-resistant TB epidemic.
Background: Transmission is driving the global drug-resistant tuberculosis (TB) epidemic; nearly three-quarters of drug-resistant TB cases are attributable to transmission. Geographic patterns of disease incidence, combined with information on probable transmission links, can define the spatial scale of transmission and generate hypotheses about factors driving transmission patterns. Methods: We combined whole-genome sequencing data with home Global Positioning System coordinates from 344 participants with extensively drug-resistant (XDR) TB in KwaZulu-Natal, South Africa, diagnosed from 2011 to 2014. We aimed to determine if genomically linked (difference of ≤5 single-nucleotide polymorphisms) cases lived close to one another, which would suggest a role for local community settings in transmission. Results: One hundred eighty-two study participants were genomically linked, comprising 1084 case-pairs. The median distance between case-pairs' homes was 108 km (interquartile range, 64-162 km). Between-district, as compared to within-district, links accounted for the majority (912/1084 [84%]) of genomic links. Half (526 [49%]) of genomic links involved a case from Durban, the urban center of KwaZulu-Natal. Conclusions: The high proportions of between-district links with Durban provide insight into possible drivers of province-wide XDR-TB transmission, including urban-rural migration. Further research should focus on characterizing the contribution of these drivers to overall XDR-TB transmission in KwaZulu-Natal to inform design of targeted strategies to curb the drug-resistant TB epidemic.
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