Dados do Trabalho

Título

Phylogenomic assessment of Mycobacterium tuberculosis Lineage 3 from Brazil

Introdução

Genotyping techniques, i.e., Spoligotyping and MIRU-VNTR, are still widely to evaluate the genetic diversity within Mycobacterium tuberculosis (Mtb) strains compared to whole-genome sequencing (WGS), however, genotyping are more associated to homoplasy than WGS. Homoplasy occurs when strains acquire similar traits but belong to different lineages and do not have the same common ancestral origin. In Para, Brazil, we described a new Mtb genotype by Spoligotyping, confirmed by MIRU-VNTR, belonging to Central-Asia SIT2545, the genotyping signature for Lineage 3 (L3).

Objetivo(s)

We aimed to confirm the presence of Mtb L3 in Brazil and to perform a phylogenetic assessment against a global public dataset of Mtb L3.

Material e Métodos

We performed WGS in five isolates using NextSeq Illumina platform. To create a robust dataset, obtained Mtb L3 genomic publicly available, including representative genomes from other lineages/sublineages. To confirm lineage assignment among the Brazilian genomes, we used SpoTyping v.2.1,c RD-Analyzer v.1, and TB-Profiler v.2,4. using the HPC infrastructure at Instituto Evandro Chagas (IEC). For individual and genomic cohort analysis, we used the MTBSeq-nf pipeline. High confidence variable sites, including coding and non-coding SNPs, were concatenated to generate a multi-FASTA file to construct a maximum likelihood phylogeny using RaxML with 1000 bootstrap pseudo-replicates. The figure was annotated using Itol.

Resultados e Conclusão

Of the 1691 genomes, 1350 (79.83%) passed in quality control (genomic coverage >95%). We confirmed the five Brazilian CAS belonged to L3. The Region of deletion (RD) was 750 and spoligotype 703460000000331. Strain 431 differed in >12 single nucleotide variants (SNV) against the Brazilian dataset, confirming it does not belong to the same transmission chain as previously suggested by the genotyping method. Among the global data, 8 genomes were closer to Brazilian strains and differed in >52 SNVs(4 from the United Kingdom, 1 from India, and 3 from unknown origin).
This is a pioneer study confirming the presence of L3 in Brazil and describing the complete genome of 5 samples comparing those genomes with an enormous dataset, utilising an innovative infrastructure at IEC. As a sequel to this work, phenotypic and predicted resistance will be compared, and molecular clocks will be used to estimate the historical context of the entry of L3 in Brazil.

Palavras-chave

Tuberculosis, Whole-genome sequencing, Lineage 3, Phylogenomic, Brazil.

Área

Eixo 13 | Tuberculose e outras micobactérias