Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

Abstract

BackgroundApproximately 10 % of the Mycobacterium tuberculosis genome is made up of two families of genes that are poorly characterized due to their high GC content and highly repetitive nature. The PE and PPE families are typified by their highly conserved N-terminal domains that incorporate proline-glutamate (PE) and proline-proline-glutamate (PPE) signature motifs. They are hypothesised to be important virulence factors involved with host-pathogen interactions, but their high genetic variability and complexity of analysis means they are typically disregarded in genome studies.ResultsTo elucidate the structure of these genes, 518 genomes from a diverse international collection of clinical isolates were de novo assembled. A further 21 reference M. tuberculosis complex genomes and long read sequence data were used to validate the approach. SNP analysis revealed that variation in the majority of the 168 pe/ppe genes studied was consistent with lineage. Several recombination hotspots were identified, notably pe_pgrs3 and pe_pgrs17. Evidence of positive selection was revealed in 65 pe/ppe genes, including epitopes potentially binding to major histocompatibility complex molecules.ConclusionsThis, the first comprehensive study of the pe and ppe genes, provides important insight into M. tuberculosis diversity and has significant implications for vaccine development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2467-y) contains supplementary material, which is available to authorized users.

The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs

“…For MiSeq sequence data, this drop only occurs when the GC content reaches 75% or above. Many regions in the M. tuberculosis genome, especially the pe/ppe genes [24], are high in GC content (median 69%, range 47–87%) and therefore potentially difficult to characterise. The coverage across the 36 drug-resistance candidate genes was high for MiSeq (mean ~90-fold) and exceeded the tenfold cutoff, except in the thyA gene in the three POR1 replicates (Fig.…”

“…This is critical in XDR-TB and resistance beyond XDR-TB where use of drugs like PAS may make the difference in providing a life-saving effective regimen of at least five drugs [29]. Large deletions and other structural variants may be detected by applying a combination of complementary approaches (pair-end, split-read and depth of coverage) followed by a validation process involving de novo assembly of bordering reads and re-alignment to the reference genome [10, 16, 24]. However, high genome-wide sequence coverage is necessary to perform such analyses.…”

PPE Surface Proteins Are Required for Heme Utilization by Mycobacterium tuberculosis

“…Previously, PPE proteins were thought to be involved in antigenic variation and immune evasion (54, 55). While our study identified three novel proteins involved in heme utilization by M. tuberculosis , their molecular functions and how these proteins interact with each other are unknown.…”

Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999–2009

“…M. tuberculosis exhibits very low sequence diversity compared to other bacteria, minimal evidence of horizontal gene transfer [53–55], and recombination limited to known highly variable gene families [28]. This lack of genetic diversity is pronounced in geographically restricted M. tuberculosis populations, such that locally endemic clone groups have posed a unique challenge to laboratory-based identification of TB outbreak clusters in New York City.…”

“…SNPs were called using a PHRED-scaled quality threshold of 40 (Samtools v0.1.19 [26]) and annotated using snpEff v4 [27]. We excluded from analysis all variants occuring within PE and PPE genes, a family of highly repetitive, GC-rich M.tuberculosis genes in which recombination has been observed [28]. …”