Comprehensive genomic surveillance reveals transmission profiles of extensively drug-resistant tuberculosis cases in Pará, Brazil

Bedaquiline, an antimicrobial used to treat drug-resistant tuberculosis (DR-TB), was introduced in Brazil in October 2021. Monitoring the emergence and transmission of DR-TB is crucial for implementing public health to control the spread of DR strains of <i>Mycobacterium tuberculosis</i>. To measure its impact on the multi-drug treatment scheme in the state of Pará, we aimed to conduct genomic surveillance of DR-TB after bedaquiline was introduced in Brazil. Individuals treated for DR-TB between October 2021 and December 2022, in the reference hospital to treat DR-TB cases from the state of Pará, were included in the study. Clinical and bacteriological information was obtained from the National Laboratory Management Environment and the Special TB Treatment Information System. Genomic DNA was extracted from bacterial cultures performed at the Pará Central Laboratory (LACEN-PA). Whole-genome sequencing (WGS) was obtained using Illumina Nextera-XT and NextSeq 550 and genomes were analyzed using the MAGMA and TB-Profiler pipelines interpreted according to the World Health Organization (WHO) mutations catalog 2nd edition. Geoprocessing was performed based on the patient's residences. Cutoffs of 5-12 single nucleotide polymorphisms (SNPs) were used for transmission analysis. From the 103 patients reported as DR-TB, viable cultures were obtained from 67. Forty isolates were selected randomly for WGS. Among these, a mixed infection of <i>M. tuberculosis</i> L1 and L4 and a co-infection of <i>M. tuberculosis</i> and <i>Mycobacterium chelonae</i> were observed. The genotypic drug susceptibility profile of TB stains (39/40) was as follows: sensitive (1/2, 5%), rifampicin mono-resistant (RR) (4/10%), isoniazid mono-resistant (1/2%), multidrug-resistant (MDR) (21/52%), extensively drug-resistant (XDR) (3/7%), pre-XDR (8/20%), and other (1/2%). Among the 38 isolates of <i>M. tuberculosis</i> strains without mixed infection, using a cutoff of 12 SNPs and suggestive of recent TB transmission, 14 (37%) were grouped into five clusters (C1-C5) and included RR (C5), MDR (C3, C4, C5), pre-XDR, and XDR (C2) strains. We recommend greater attention from the regional public health authorities to detect and track resistance to new drugs, especially in areas with pre-XDR and XDR cases. This is the first report on the detection and transmission of XDR-TB in Pará, Brazil, after the recent re-definition of XDR-TB by the WHO in 2021.