Whole-genome single nucleotide variant phylogenetic analysis of Mycobacterium tuberculosis Lineage 1 in endemic regions of Asia and Africa

Abstract

Mycobacterium tuberculosis (Mtb) lineage 1 (L1) contributes considerably to the disease morbidity. While whole genome sequencing (WGS) is increasingly used for studying Mtb, our understanding of genetic diversity of L1 remains limited. Using phylogenetic analysis of WGS data from endemic range in Asia and Africa, we provide an improved genotyping scheme for L1. Mapping deletion patterns of the 68 direct variable repeats (DVRs) in the CRISPR region of the genome onto the phylogeny provided supporting evidence that the CRISPR region evolves primarily by deletion, and hinted at a possible Southeast Asian origin of L1. Both phylogeny and DVR patterns clarified some relationships between different spoligotypes, and highlighted the limited resolution of spoligotyping. We identified a diverse repertoire of drug resistance mutations. Altogether, this study demonstrates the usefulness of WGS data for understanding the genetic diversity of L1, with implications for public health surveillance and TB control. It also highlights the need for more WGS studies in high-burden but underexplored regions.

Whole-genome sequencing of Mycobacterium tuberculosis from Cambodia

“…Within the L1.1.1 isolates, 22 isolates can be further clustered into L1.1.1.1 (6/22; 27.3%), L1.1.1.3 (4/22; 18.2%), L1.1.1.5 (7/22; 31.8%) and L1.1.1.10 (5/22; 22.7%). The distribution of the sub-lineages for L1.1 was thus found to correlate with distributions identified for Thailand and Vietnam as reported in Netikul et al 13 , including a new clade of L1.1.1.10 found only in samples from Thailand and Vietnam.…”

“…The inferred lineages of the MTB isolates were largely concordant across the 4 genotyping methods of (1) Coll et al 62-SNP barcoding 12 ; (2) Netikul et al sub-lineage 1 prediction 13 ; (3) spoligotypes from SpoTyping and (4) regions of deletions based on RD-Analyzer (Supplementary Table 1 ). Majority of the isolates belonged to Lineage 1 (Indo-Oceanic) (69/80, 86.25%), followed by Lineage 2 (East Asian) (10/80, 12.5%) and Lineage 4 (Euro-American) (1/80, 1.25%).…”

“…In this study, we identified isolates in only two of the three major Lineage 1 clades 12 , 13 , 15 , namely L1.1 and L1.2, with dominance of L1.1 (60/69, 87.0%). L1.3 was widespread in Africa, India and Thailand (specific sub-lineage of L1.3.2), while not found in Vietnam 13 .…”

“…However, the resolution provided by WGS allows finer classification of the MTB isolates into sub-lineages which have been found to correlate with that found in Thailand and Vietnam, two countries that border Cambodia. This include five isolates belonging to lineage L1.1.1.10 that are found only in Thailand (N = 2) and Vietnam (N = 8) based on a phylogenetic study of 1,761 publicly available L1 MTB isolates 13 .…”

“…The TB lineages for each isolate was predicted using 4 approaches: (1) the 62-SNP barcode as proposed by Coll et al 12 ; (2) sub-lineages 1 barcoding as proposed by Netikul et al 13 ; (3) spoligotypes using SpoTyping 30 and (4) regions of deletions identified using RD-Analzyer 31 . Given that multiple SNPs have been identified as lineage barcodes for each sub-lineage within Netikul et al, we identified an isolate to be of the particular sub-lineage if one or more lineage-barcode SNPs are found, and the isolate did not harbour any lineage-barcode SNPs for other sub-lineages.…”