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

• Autor(a) principal: Conceição, Emilyn Costa
• Data de Publicação: 2023
• Outros Autores: Conceição, Marília Lima da, Marcon, Davi Josué, Loubser, Johannes, Andrade, Gabrielly Leite, Silva, Sandro Patroca da, Cruz, Ana Cecília Ribeiro, Sharma, Abhinav, Suffys, Philip, Lima, Karla Valéria Batista
• Tipo de documento: Artigo
• Idioma: eng
• Título da fonte: Repositório Digital do Instituto Evandro Chagas (Patuá)
• Texto Completo: https://patua.iec.gov.br/handle/iec/6729
• topic: Tuberculose; Mycobacterium tuberculosis / classificação; Mycobacterium tuberculosis / isolamento & purificação; Linhagem; Variação Genética / genética; Sequenciamento Completo do Genoma / métodos

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.