Clinical Application of Whole-Genome Sequencing To Inform Treatment for Multidrug-Resistant Tuberculosis Cases

Abstract

cThe treatment of drug-resistant tuberculosis cases is challenging, as drug options are limited, and the existing diagnostics are inadequate. Whole-genome sequencing (WGS) has been used in a clinical setting to investigate six cases of suspected extensively drug-resistant Mycobacterium tuberculosis (XDR-TB) encountered at a London teaching hospital between 2008 and 2014. Sixteen isolates from six suspected XDR-TB cases were sequenced; five cases were analyzed in a clinically relevant time frame, with one case sequenced retrospectively. WGS identified mutations in the M. tuberculosis genes associated with antibiotic resistance that are likely to be responsible for the phenotypic resistance. Thus, an evidence base was developed to inform the clinical decisions made around antibiotic treatment over prolonged periods. All strains in this study belonged to the East Asian (Beijing) lineage, and the strain relatedness was consistent with the expectations from the case histories, confirming one contact transmission event. We demonstrate that WGS data can be produced in a clinically relevant time scale some weeks before drug sensitivity testing (DST) data are available, and they actively help clinical decision-making through the assessment of whether an isolate (i) has a particular resistance mutation where there are absent or contradictory DST results, (ii) has no further resistance markers and therefore is unlikely to be XDR, or (iii) is identical to an isolate of known resistance (i.e., a likely transmission event). A small number of discrepancies between the genotypic predictions and phenotypic DST results are discussed in the wider context of the interpretation and reporting of WGS results. In 2013, of the 6.1 million new tuberculosis (TB) cases reported worldwide, 480,000 were defined as multidrug resistant (MDR) (1). MDR strains of Mycobacterium tuberculosis are defined as those that are resistant to the key first-line drugs, rifampin (RIF) and isoniazid (INH). Such cases need to be treated using a more complex and flexible drug selection algorithm than the standard, with a combination of at least four drugs from an available panel classified according to their mode of action, efficacy, and clinical experience, and should be further modified if other resistances become apparent (2).Extensively drug-resistant (XDR) strains of M. tuberculosis are defined as MDR strains that in addition to being RIF and INH resistant are also resistant to the two most effective remaining bactericidal drug classes, at least one fluoroquinolone (FLQ), and one second-line injectable agent (amikacin [AMI] or kanamycin [KAN], or capreomycin [CAP]). The XDR designation reflects the concern that these are even more difficult to treat. Globally, in 2014, 9.0% of MDR cases were reported as being XDR (1); these figures are likely to be underestimates, because testing and reporting practices are not universal.The overall rates of TB in the United Kingdom have been stable, at ϳ14 per 100,000 since 2005, with London having the highest regional ...

Role of gyrB Mutations in Pre-extensively and Extensively Drug-Resistant Tuberculosis in Thai Clinical Isolates

“…Currently, the clinical applications of whole-genome sequencing are being expanded to produce genotypic drug susceptibility profiles faster than phenotypic susceptibility results can be obtained (50,51). The construction of a database of resistance-related mutations is required for the reliable genotypic prediction of drug resistance.…”

Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State

“…Recent publications have described the potential of implementing WGS in a clinical setting for rapid resistance profiling of M. tuberculosis. Witney et al demonstrated the clinical utility of WGS for drug resistance profiling of suspected XDR-TB cases and found that WGS could predict resistance weeks earlier than complete culture-based DST (23). However, as their approach used WGS as a second-tier tool to supplement the information provided by DST for drug-resistant strains, the TAT was not optimal and could not provide information for susceptibility to first-line drugs prior to culture-based DST results.…”

New Diagnostics for Childhood Tuberculosis

“…To date, the clinical utility of WGS has been described in only a few cases in which WGS allowed faster diagnosis of extensive drug resistance compared with conventional DST. 120,121 The high cost of sequencing and the advanced expertise required preclude its use in most TB-prevalent settings. Future studies should further characterize the clinical utility of sequencing methods-including in children-and explore ways to make these techniques accessible for resource-limited countries.…”