Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Abstract

To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.

Predicting Antimicrobial Resistance Using Conserved Genes

“…The PATRIC command line interface was used for all other annotation and metadata acquisition tasks 32 . In the case of M. tuberculosis, we also used data from a study that had not yet been integrated into the PATRIC collection 33 . The reads for these genomes were downloaded from the European Nucleotide Archive 34 , assembled using the full spades pipeline at PATRIC 32,35,36 , and annotated using the PATRIC annotation service, which is a variant of RAST 37 .…”

Genome wide association with quantitative resistance phenotypes in Mycobacterium tuberculosis reveals novel resistance genes and regulatory regions

“…The knowledge of genetic mechanisms of antibiotic resistance has formed the basis of several commercial molecular diagnostics for TB that have had remarkable global uptake, despite the fact that they only reliably test for a subset of TB drugs and hence have not yet been able to replace the traditional more costly and slow process of mycobacterial culture and drug susceptibility testing (DST) 1,5-7 . Understanding antibiotic resistance mechanisms and methods that compensate for lost bacterial fitness in the context of antibiotic resistance can also pave the way for the development of companion drugs that restore antibiotic susceptibility 8,9 and can open the possibility of 'evolutionarily directed' therapies that can aid in primary prevention of resistance acquisition 10 .To date, attempts at genome wide association for antibiotic resistance in Mycobacterium tuberculosis (MTB) have been limited by the relatively low number of isolates phenotypically resistant to antibiotics, and have exclusively relied on phenotypes defined by drug susceptibility testing (DST) performed at a single 'critical concentration', likely a result of convenience sampling from clinical isolate archives in clinical mycobacterial laboratories [11][12][13] . Although such 'binary' DST is currently the standard to guide patient care, MTB critical concentrations are largely based on consensus and lack solid scientific support.…”

“…To date, attempts at genome wide association for antibiotic resistance in Mycobacterium tuberculosis (MTB) have been limited by the relatively low number of isolates phenotypically resistant to antibiotics, and have exclusively relied on phenotypes defined by drug susceptibility testing (DST) performed at a single 'critical concentration', likely a result of convenience sampling from clinical isolate archives in clinical mycobacterial laboratories [11][12][13] . Although such 'binary' DST is currently the standard to guide patient care, MTB critical concentrations are largely based on consensus and lack solid scientific support.…”

Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis

“…To this end, we determined the sensitivity of 15 of the 18 MTBC strains to para-aminosalicylic acid (PAS), an inhibitor of tetrahydrofolate (THF) biosynthesis and one of the antimycobacterial drugs currently used for multi-drug-resistant TB 47,48 . Although no strain carried the genetic determinants of PAS resistance 49 , strains from lineages 1-4 were significantly more susceptible to PAS than strains from lineages 5 and 6 (t-test, p = 4.5 × 10 −13 , n = 55) ( Fig. 4b).…”