Whole genome sequencing to characterize the molecular epidemiology and drug-resistance of tuberculosis in Huzhou, China.

BACKGROUND: Whole-genome sequencing (WGS) has emerged as a powerful tool for elucidating Mycobacterium tuberculosis (MTB) transmission dynamics and drug resistance patterns. In China, the application of WGS in TB surveillance has been rapidly expanding. However, molecular epidemiological studies based on WGS data from low-incidence areas remain limited. Huzhou City, located in northern Zhejiang Province, reported a TB incidence rate of 27.16 per 100,000 population in 2024, which was lower than both the national and provincial averages. In July 2023, Huzhou pioneered China’s first “TB-Free City” initiative. To support public health efforts and facilitate the development of a WGS-based molecular surveillance network tailored for low-incidence settings, we performed WGS on 350 MTB isolates obtained from culture-positive TB patients in Huzhou between March 2023 and September 2024. Phylogenetic analysis, drug resistance profiling, and transmission cluster identification (using a ≤ 12 SNP threshold) were conducted to characterize the molecular epidemiology of TB in this region.

RESULTS: Lineage 2.2.1 (Beijing genotype) was predominant (80.0%). A total of 86 isolates (24.6%) harbored drug resistance-associated mutations, including 2.0% MDR-TB and 1.7% pre-XDR-TB, with no XDR-TB or resistance to bedaquiline, linezolid, or delamanid detected. We identified 28 genomic clusters comprising 65 isolates (18.6%), with a clustering rate of 11.6% among DR-TB cases. Furthermore, 79.1% (68/86) of drug-resistant TB (DR-TB) cases were likely attributable to recent transmission, with clustered DR-TB strains sharing identical resistance-conferring mutations. Comparative analysis revealed that patients under 60 years of age were significantly more likely to be involved in recent transmission events ( = 0.035), while lineage, gender, occupation, treatment history, and local residency were not statistically associated with clustering.

CONCLUSIONS: Our findings suggest that recent transmission, particularly among younger individuals, contributes substantially to the DR-TB burden in Huzhou. WGS-based surveillance revealed moderate resistance levels and limited transmission, supporting the ongoing “TB-Free City” initiative. Enhanced genomic monitoring and early intervention targeting younger, mobile populations may further curb TB transmission in low-incidence settings.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12202-8.