Genomic diversity of the rarely observed genotype of the Mycobacterium tuberculosis Central Asian (CAS) lineage 3 from North Brazil

This research was funded by CNPQ, grant number 207,071/2014-4, and grant number Finance Code 001 and CAPES (Finance Code 001).Stellenbosch University. Faculty of Medicine and Health Sciences. Division of Molecular Biology and Human Genetics. South African Medical Research Council Centre for Tuberculosis Research. National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research. Department of Science and Innovation. Tygerberg, South Africa / Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade Federal do Pará. Centro de Genômica e Biologia de Sistemas. Belém, PA, Brazil.Stellenbosch University. Faculty of Medicine and Health Sciences. Division of Molecular Biology and Human Genetics. South African Medical Research Council Centre for Tuberculosis Research. National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research. Department of Science and Innovation. Tygerberg, South Africa.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Centro Universitário do Pará. Departamento de Medicina. Belém, PA, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade do Estado do Pará. Programa de Pós-graduação Biologia Parasitária na Amazônia. Belém, PA, Brazil.Liverpool John Moores University. Faculty of Engineering and Technology. Liverpool, UK / Seqera Labs. Bacelona, Spain.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular Aplicada a Micobactéria. Rio de Janeiro, RJ, Brazil.Ministério da Saúde. Secretaria de Vigilância em Saúde e Ambiente. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade do Estado do Pará. Programa de Pós-graduação Biologia Parasitária na Amazônia. Belém, PA, Brazil.Mycobacterium tuberculosis (Mtb) Central Asian Strain (CAS) Lineage 3 (L3) genotype is predominantly found in East-Africa, Central-Asia, Western-Asia, and South-Asia; however, a new spoligotyping CAS/SIT2545 was found in northern regions of Brazil. We aimed to characterize and describe the genetic diversity and perform a phylogenetic assessment of this novel genotype. We performed 24-MIRU-VNTR loci and Whole-genome sequencing (WGS) of six Brazilian isolates previously spoligotyped. The libraries were prepared using a Nextera-XT kit and sequenced in a NextSeq 550 Illumina instrument. We performed lineage assignment and genomic characterization. From publicly available genomes of Mtb L3 and other lineages, we created a robust dataset to run the MTBSeq pipeline and perform a phylogenetic analysis. MIRU-VNTR and WGS confirmed CAS/SIT2545 belongs to L3. Out of 1691 genomes, 1350 (79.83%) passed in quality control (genomic coverage > 95%). Strain 431 differed in 52 single nucleotide variants (SNV), confirming it does not belong to the same transmission chain. The eight genomes from a global dataset clustered closer to Brazilian strains differed in >52 SNVs. We hypothesized L3 and L1 were introduced in Brazilian Northern in the same historical event; however, there is a need for additional studies exploring the genetic diversity of Mtb Brazilian Northern