Towards next generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics

Abstract

Tuberculosis remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel tuberculosis diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study had been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. In this work, we use large-scale comparative genomics to provide a catalog of 30 characterized loci that are unique to the MTBC.Some of these genes could be targeted to assess the physiological status of the bacilli. Remarkably, none of the conventional MTBC markers is in our catalog. In addition, we develop a qPCR assay to accurately quantify MTBC DNA in clinical samples.

Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance surveillance: an observational study

“…The shortest distance between a clinical specimen and any other sample outside its cluster was 23 SNPs (median of the shortest distance between clinical specimens and unrelated samples was 108 SNPs . This value is beyond any established threshold to identify recent transmission (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). Overall, reconstruction of the genetic networks involving the clinical specimens and the culture-based genomes resulted in a highly resolved topology.…”

“…We further enriched libraries with less than 10% M tuberculosis DNA using biotinylated RNA baits (appendix pp 2, 6). Additionally, we quantified the concentration of M tuberculosis DNA using an M tuberculosis complex-specific qPCR assay that we published this year 14 (appendix pp 2-3). The sequencing data has been deposited in the European Nucleotide Archive (accession PRJEB37609).…”