Functional and evolutionary genomics of Mycobacterium tuberculosis : Insights from genomic deletions in 100 strains

Abstract

To better understand genome function and evolution in Mycobacterium tuberculosis, the genomes of 100 epidemiologically well characterized clinical isolates were interrogated by DNA microarrays and sequencing. We identified 68 different large-sequence polymorphisms (comprising 186,137 bp, or 4.2% of the genome) that are present in H37Rv, but absent from one or more clinical isolates. A total of 224 genes (5.5%), including genes in all major functional categories, were found to be partially or completely deleted. Deletions are not distributed randomly throughout the genome but instead tend to be aggregated. The distinct deletions in some aggregations appear in closely related isolates, suggesting a genomically disruptive process specific to an individual mycobacterial lineage. Other genomic aggregations include distinct deletions that appear in phylogenetically unrelated isolates, suggesting that a genomic region is vulnerable throughout the species. Although the deletions identified here are evidently inessential to the causation of disease (they are found in active clinical cases), their frequency spectrum suggests that most are weakly deleterious to the pathogen. For some deletions, short-term evolutionary pressure due to the host immune system or antibiotics may favor the elimination of genes, whereas longer-term physiological requirements maintain the genes in the population.

Genomic interrogation of ancestral Mycobacterium tuberculosis from south India

“…We used previously published studies of genomic deletions (Tsolaki et al, 2004) to identify phylogenetically important genomic deletions and screen for them using PCR. For the detection of LSPs by multiplex real-time PCR, we designed a series of assays based on different TaqMan primer/probe combinations.…”

“…This involves the interrogation of unsequenced genomes by DNA-microarray to identify sequences present in a fully sequenced isolate but absent from interrogated isolate (KatoMaeda et al, 2001, Tsolaki et al, 2004. Nucleotide sequences provide robust, portable and comparable data for studying population variation.…”

Defining mycobacteria: Shared and specific genome features for different lifestyles

“…• The work of Maeda et al [63] and Tsolaki et al [64] attempted to study the genomes of clinical isolates (in an array hybridization format) and to relate the genotypes to transmission phenotypes. They included strains with well characterized clinical and epidemiological datasets.…”

“…LOSs are considered to be 'avirulence' factors absent in most clinical strains of M. tuberculosis. From the above San Francisco M. tuberculosis strain bank, Tsolaki et al [64] further studied 100 strains to look for lineage specifi c and non-lineage specifi c genetic variations (50 that were involved in transmission clusters, and 50 that were unique or non-clustered). They identifi ed ~250 regions of difference (RD) [64].…”

“…From the above San Francisco M. tuberculosis strain bank, Tsolaki et al [64] further studied 100 strains to look for lineage specifi c and non-lineage specifi c genetic variations (50 that were involved in transmission clusters, and 50 that were unique or non-clustered). They identifi ed ~250 regions of difference (RD) [64]. Theoretically, these 'RD' genes are non-essential for human disease, or may have altered levels of virulence and host specifi city.…”