Evaluation of resistance acquisition during tuberculosis treatment using whole genome sequencing

Abstract

Tuberculosis (TB) is still considered a major global public health problem in the world and there is a concern about the worldwide increase of drug-resistance (DR). This paper describes the analysis of three Mycobacterium tuberculosis isolates from a single patient collected over a long treatment period of time. DR was initially investigated through phenotypic testing, followed by line probe assays (LPAs) and whole genome sequencing (WGS). It presents an intriguing situation where a multidrug-resistant (MDR-) TB case was diagnosed and treated based only on late phenotypic drug susceptibility testing of isolate 1. During the treatment, another two isolates were cultivated: isolate 2, nine months after starting MDR-TB treatment; and isolate 3, cultivated five months later, during regular use of anti-TB drugs. These two isolates were evaluated using molecular LPA and WGS, retrospectively. All mutations detected by LPA were also detected in the WGS, including conversion from fluoroquinolones susceptibility to resistance from isolate 2 to isolate 3. WGS showed additional mutations, including some which may confer resistance to other drugs not tested (terizidone/cycloserine) and mutations with no correspondent resistance in drug susceptibility testing (streptomycin and second-line injectable drugs).

Whole-genome sequencing as a tool for studying the microevolution of drug-resistant serial Mycobacterium tuberculosis isolates

“…In conclusion, sequencing technologies can improve TB control by detecting rare and new mutations related to detection of drug resistance, as well as identifying subpopulations of DR strains allowing early clinical and therapeutic intervention. In addition, WGS can unequivocally identify diverse populations of strains, allowing the detection of exogenous reinfection cases, which is particularly important due to the high burden of TB and drug resistance [24,76,120]…”

“…Several methods have been used to evaluate the genetic diversity of M. tuberculosis strains, although for molecular epidemiology proposals Mycobacterial Interspersed Repeating Unit -Variable Number of Tandem (MIRU-VNTR) is a useful tool [15][16][17]. More recently, whole-genome sequencing (WGS), in addition to identifying the genetic relationships among strains with high accuracy [18][19][20][21][22], is an important tool to recognize the evolution of different populations of microorganisms [23,24], drug susceptibility and resistance profiles [25][26][27][28].…”