Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis

Author summary Why was this study done? The transmission of multidrug-resistant tuberculosis (MDR-TB) poses a major challenge for tuberculosis (TB) control in several countries, but a detailed understanding of the local dynamics of TB and MDR-TB transmission in these high MDR-TB burden settings has been elusive.The increasing availability of whole genome sequencing, and the development of new statistical approaches for combining spatial, epidemiological, and genomic data to infer transmission, offers new opportunities to identify TB transmission with high resolution. What did the researchers do and find? We prospectively enrolled all individuals with incident culture-positive TB from the Republic of Moldova, a high MDR-TB burden setting, between January 2018 and December 2019 and sequenced a diagnostic isolate from each individual.We found that that nearly all extant MDR-TB in Moldova is likely the result of recent transmission and that multidrug resistance (MDR) is highly concentrated within 2 . lineages (Beijing and Ural).Phylogeographic analyses revealed geographically distinct patterns of transmission for the Beijing MDR strains, which were predominantly localized within the Transnistrian region to the east of the country, while Ural MDR strains were less geographically restricted.Each putative MDR-TB transmission cluster had distinct second-line drugs resistance-conferring mutations. Population genetic analyses revealed both long periods of local population expansion as well as more recent introduction of specific MDR-TB strains into the country. What do these findings mean? To our knowledge, this is first study to comprehensively sequence all . isolates from an entire high MDR incidence country and offers unique insights into the complexity MDR-TB transmission in Moldova.Local transmission of distinct highly drug-resistant . strains suggests that public health and clinical interventions tailored to address such local heterogeneities may be needed to interrupt transmission and improve treatment outcomes. BackgroundThe incidence of multidrug-resistant tuberculosis (MDR-TB) remains critically high in countries of the former Soviet Union, where >20% of new cases and >50% of previously treated cases have resistance to rifampin and isoniazid. Transmission of resistant strains, as opposed to resistance selected through inadequate treatment of drug-susceptible tuberculosis (TB), is the main driver of incident MDR-TB in these countries. Methods and findingsWe conducted a prospective, genomic analysis of all culture-positive TB cases diagnosed in 2018 and 2019 in the Republic of Moldova. We used phylogenetic methods to identify putative transmission clusters; spatial and demographic data were analyzed to further describe local transmission of Mycobacterium tuberculosis. Of 2,236 participants, 779 (36%) had MDR-TB, of whom 386 (50%) had never been treated previously for TB. Moreover, 92% of multidrug-resistant (MDR) M. tuberculosis strains belonged to putative transmission clusters. Phylogenetic reconstruction identified 3 large clades that were comprised nearly uniformly of MDR-TB: 2 of these clades were of Beijing lineage, and 1 of Ural lineage, and each had additional distinct clade-specific second-line drug resistance mutations and geographic distributions. Spatial and temporal proximity between pairs of cases within a cluster was associated with greater genomic similarity. Our study lasted for only 2 years, a relatively short duration compared with the natural history of TB, and, thus, the ability to infer the full extent of transmission is limited. ConclusionsThe MDR-TB epidemic in Moldova is associated with the local transmission of multiple M. tuberculosis strains, including distinct clades of highly drug-resistant M. tuberculosis with varying geographic distributions and drug resistance profiles. This study demonstrates the role of comprehensive genomic surveillance for understanding the transmission of M. tuberculosis and highlights the urgency of interventions to interrupt transmission of highly drug-resistant M. tuberculosis.