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From Research to Surveillance: Leveraging the State of Whole Genome Sequencing for Precision Public Health in a High-Burden Tuberculosis Setting

K VB Lima(1,2) A Sharma(5) D J Marcon(1,2) R SS Guimarães(4) A van Rie(5) R M Warren(3) P N Suffys(6) E C Conceicao(3)

1:Instituto Evandro Chagas, Seção de Bacteriologia e Micologia, Ananindeua-PA, Brazil; 2:Universidade do Estado do Pará, Instituto de Ciências Biológicas e da Saúde, Pós-Graduação em Biologia Parasitária na Amazônia, Belém-PA, Brazil; 3:Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; 4:Instituto Evandro Chagas, Laboratório de Geoprocessamento, Ananindeua-PA, Brazil; 5:Department of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; 6:Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Biologia Molecular Aplicado à Micobactérias, Rio de Janeiro, RJ, Brazil

Tuberculosis (TB) continues to pose a significant public health challenge in 30 high-burden TB countries, including Brazil. Whole-genome sequencing (WGS) offers promising prospects in the realm of precision public health. By facilitating the pinpointing of individuals involved in recent TB transmission chains, WGS emerges as a valuable asset for TB surveillance. Through a literature review, we aimed to assess all Mycobacterium tuberculosis complex genomes isolated in Brazil that are publicly accessible to evaluate TB transmission and drug resistance. We employed the MAGMA pipeline utilizing two distinct cut-off analyses involving 5 and 12 Single Nucleotide Polymorphisms (SNPs). Drug resistance prefiling (DRP) was obtained using TB-Profiler v.6.2.0. From 23 studies, we obtained 2182 FASTQ paired-end files, of which 65 failed quality control. Of the 2118 genomes analysed, 1340 were identified within 333 clusters using a 12 SNP cut-off, while 789 genomes clustered into 286 clusters with a 5 SNP cut-off. Based on 12 SNPs, 21 clusters harboured strains from different states and regions: Southeast-Southeast (5), Southeast-South (5), South-Mideast (5), Southeast-Midwest (4), South-South (1), and Southeast-Southeast-Midwest (1). This suggests transmission chains across these Brazilian regions. Lineage 4 (1994/94.15%) was the most frequent. The DRP was: pan-susceptible (1364/64.40%), multidrug-resistant (298/14.07%), mono-isoniazid (149/7.03%), pre-extensively resistant (76/3.59%),  mono-rifampicin (46/2.17%) and others (185/8.73%). No resistance was detected to para-aminosalicylic acid, clofazimine, linezolid, bedaquiline, or delamanid. This is preliminary data that will be accessible for research and TB surveillance purposes in Brazil within the GEMIBRA (Genome of Mycobacteria in Brazil) web platform v.2 which is currently under development.

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