Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases

Abstract

The 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.

FIG 1

Phylogenetic reconstruction of 410 high-confidence SNP sites from the study isolates. (A) Estimated numbers of SNPs are labeled on each branch. The clusters in which no SNP distances are shown are 0; however, due to the nature of the SNP calling algorithm, more sites are excluded as more isolates are added. We therefore reanalyzed the case isolates separately, and the resulting SNP distances were: case 1, 0; case 2, 16; case 3, 0; cases 3/4, 1; case 5, 1; and case 6, 0. Ref, reference. (B) The presence/absence of each RD region is aligned to each isolate. These regions of difference are genomic deletions that were previously reported within the M. tuberculosis complex (47). The RD105 deletion has been reported as being specific for East Asian (Beijing) strains (36).

FIG 2

An example report returned to the clinicians. Page 1 (left) summarizes the overall phenotypic and genotypic profiles of the isolates for a patient. Page 2 (right) lists more detail describing the mutations identified and their potential phenotypic consequences. The full report for case 3 is available in the supplemental material.

FIG 3

Expected time frame for receiving results for each test following sample collection.