Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis

Abstract

With its airborne transmission and prolonged latency period, Mycobacterium tuberculosis spreads worldwide as one of the most successful bacterial pathogens and continues to kill millions of people every year. M. tuberculosis lineage 1 is inferred to originate ancestrally based on the presence of the 52-bp TbD1 sequence and analysis of single nucleotide polymorphisms. Previously, we briefly reported the complete genome sequencing of M. tuberculosis strains 96121 and 96075, which belong to the ancient Manila family and modern Beijing family respectively. Here we present the comprehensive genomic analyses of the Manila family in lineage 1 compared to complete genomes in lineages 2–4. Principal component analysis of the presence and absence of CRISPR spacers suggests that Manila isolate 96121 is distinctly distant from lineages 2–4. We further identify a truncated whiB5 gene and a putative operon consisting of genes encoding a putative serine/threonine kinase PknH and a putative ABC transporter, which are only found in the genomes of Manila family isolates. Six single nucleotide polymorphisms are uniquely conserved in 38 Manila strains. Moreover, when compared to M. tuberculosis H37Rv, 59 proteins are under positive selection in Manila family isolate 96121 but not in Beijing family isolate 96075. The unique features further serve as biomarkers for Manila strains and may shed light on the limited transmission of this ancestral lineage outside of its Filipino host population.

Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines

“…A comparison of allele frequency differences between the Manila (N = 408) and non-Manila strains in neighbouring clades (N = 1,636) revealed 197 SNPs which were specific to the Manila clade. Of these, 180 were found in coding regions and 115 led to amino acid changes, including one premature stop codon in whiB5 , which has been described before 12 (Supplementary Data 1).…”

Whole genome SNP analysis suggests unique virulence factor differences of the Beijing and Manila families of Mycobacterium tuberculosis found in Hawaii

“…The mutant was also shown to be unable to resume growth after reactivation from chronic infection. However, as previously noted, human infections with Manila family strains do not appear to display any deficiency in reactivation [ 49 ]. Furthermore, two mutations were observed upstream of whiB5 ’s start codon (-27 and -31).…”

Genomic sequencing is required for identification of tuberculosis transmission in Hawaii

“…Our previous work illustrated that even with the full set of 24 MIRU-VNTR loci, potential Beijing and Manila family transmission clusters are poorly resolved by this method of fingerprinting [ 29 ]. Here, we identified that MIRU-VNTR’s lack of resolving ability results from the Beijing and Manila families both being characterized by a greater number of loci that are dominated by either one allele or a small set of alleles than lineage 4.…”

“…Making full use of the resulting WGS dataset, we further examined isolates from clusters that WGS identified to represent actual transmission events and investigated which genes or regions were developing mutations that differentiated individual isolates in a cluster. Our previous work has identified virulence factor mutations in the Beijing and Manila families that may be involved in virulence or latency, and this work seeks to help us further characterize these historically under-studied families [ 29 , 30 ].…”