A population-based genomic epidemiological study of the source of tuberculosis infections in an emerging city: Shenzhen, China

BACKGROUND: Tuberculosis (TB) in emerging cities is often a disease of recent immigrants, and understanding this epidemiology is crucial for designing effective control and prevention strategies. METHODS: We conducted a retrospective population-based genomic epidemiological study of culture-positive pulmonary TB patients diagnosed between June 2014 and November 2017 in the Bao'an District of Shenzhen, a Chinese city with dramatic recent growth. After whole genome sequencing, transmission clusters were defined as strains differing by no more than 12 SNPs. FINDINGS: Of 1696 culture-positive TB patients, 93•8% (1591/1696) were migrants, with 51•6% (821/1591) employed in housekeeping or unemployed. Of the 1460 migrants with known residence time, 47•7% (697/1460) developed TB within two years after arriving in Bao'an. Only 12•2% (207/1696) of Bao'an isolates were in genomic clusters, indicating that recent transmission was not the primary cause of TB in Bao'an. The isolates’ median terminal branch length was 56 SNPs, more than could have accumulated since the arrival of the migrants in Bao'an. The migrants’ isolates had genotypic distributions similar to those in their home provinces. One strain isolated in Bao'an belonged to a clade circulating in the patient's home province, providing further evidence that the strains were brought to Bao'an with the migrants. INTERPRETATION: TB in the Bao'an District is principally caused by reactivation of infections acquired by migrants in their home provinces. Nearly half developed TB within two years after arriving in Bao'an, suggesting a need for increased TB screening of migrants, especially housekeeping workers and the unemployed. FUNDING: Sanming Project of Medicine in Shenzhen; National Science and Technology Major Project of China; Natural Science Foundation of China.