Piecing together the puzzle: source tracing for pediatric tuberculosis patient with a multifaceted approach

Tuberculosis (TB) remains a global public health concern, with limited reductions in disease incidence rates. Investigating TB transmission chains is crucial for improving control measures. We retrospectively studied a cluster of eight epidemiologically linked TB patients (S1-S8) using whole genome sequencing (WGS) data of Mycobacterium tuberculosis (Mtb) isolates integrated with clinical and epidemiological information. We focused on identifying the possible source of infection for a pediatric TB patient diagnosed at four months of age (S7). All Mtb isolates represented one active TB episode, except for one case of a single prolonged TB episode (S4.1 and S4.2). One patient had three episodes (S1.1-S1.3). Active TB cases linked to the S7 included relatives and neighbors. In silico Mtb isolate spoligotyping revealed three genotypes: SIT42 (LAM9) for three isolates (S2, S4.1, and S4.2), SIT254 (LAM-RUS) for three isolates (S5, S6, and S8), and SIT1 (Beijing) for four isolates (S1.2, S1.3, S3, and S7). It also indicated the presence of mixed strain infection in the S1.1 case (SIT1 and SIT254), confirmed by differing SNV analysis, showing small genetic distances of 2-6 SNVs with all three SIT254 and two SIT1 isolates (S1.2 and S1.3). Phenotypic and WGS-based drug susceptibility testing revealed differing resistance patterns among SIT1 isolates: S1.1, S1.2, and S1.3 isolates were isoniazid-resistant, S3 was multidrug-resistant, and only S7 isolate was drug-susceptible. WGS data showed distances of 113-165 SNVs between S7 and other SIT1 isolates, confirming that the source of TB infection for S7 was not among the identified contacts. This study highlights the possibility of wide Mtb strain variability within epidemiologically linked TB patient clusters and underscores the importance of a comprehensive approach in TB source case investigation.