Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics and beyond
Authors: Caroline Colijn, Ted Cohen
Journal: The Lancet Respiratory Medicine (2015)

In The Lancet Respiratory Medicine, Louise Pankhurst and colleagues1Pankhurst LJ del Ojo Elias C Votintseva AA et al.for the COMPASS-TB Study GroupRapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective study.Lancet Respir Med. 2015; (published online Dec 3.)http://dx.doi.org/10.1016/S2213-2600(15)00466-XPubMed Google Scholar establish the feasibility of adoption of whole-genome-sequencing (WGS) for routine diagnosis of and drug susceptibility testing for Mycobacterium tuberculosis in well resourced settings with a low tuberculosis burden. Within the context of this impressive study, this international team of researchers show the favourable performance and costs of WGS-based species identification and prediction of drug susceptibility. The availability of WGS led to earlier diagnosis of multidrug resistance than with routine laboratory diagnostics for one patient, and WGS also led to the identification of a new suspect transmission cluster. This effort needed substantial coordination across eight participating international centres and development of new data and bioinformatics infrastructure. As such, the findings provide an important proof of principle that WGS methods can provide an attractive alternative to conventional approaches for routine diagnosis and drug susceptibility testing and that the information made available by routine WGS can improve understanding of transmission beyond what might be possible with molecular genetic tests. Although Pankhurst and colleagues map a way forward for expanded use of WGS as a routine method for diagnosis of tuberculosis, several important challenges exist that limit the effect of WGS used in the manner described in the study. First, although early identification of drug resistance by WGS could have an important effect on the treatment outcome for individual patients2Cegielski JP Kurbatova E van der Walt M et al.for the Global PETTS InvestigatorsMultidrug-resistant tuberculosis treatment outcomes in relation to treatment, initial and acquired second-line drug resistance.Clin Infect Dis. 2015; (published online Oct 27.)https://doi.org/10.1093/cid/civ910Crossref Scopus (76) Google Scholar and on reduction of onward transmission of resistant strains, the approach described by Pankhurst and colleagues needs a positive culture to be obtained before DNA isolation and WGS. This approach is appealing because attempting to do WGS for detection of M tuberculosis and identification of drug resistance-associated mutations directly from sputum is challenging,3Brown AC Bryant JM Einer-Jensen K et al.Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples.J Clin Microbiol. 2015; 53: 2230-2237Crossref PubMed Scopus (167) Google Scholar and doing these tests on all sputum samples collected from patients who might have tuberculosis (not just those that exhibit growth in selective culture) would inflate WGS costs tremendously. However, a need for culture before WGS adds substantial delay to detection of resistance compared with commercially available tests done directly on sputum in a matter of hours, such as cartridge-based nucleic acid amplification tests like Cepheid Xpert MTB/RIF (Cepheid, Sunnyvale, CA, USA).4Boehme CC Nabeta P Hillemann D et al.Rapid molecular detection of tuberculosis and rifampin resistance.N Engl J Med. 2010; 363: 1005-1015Crossref PubMed Scopus (1726) Google Scholar In some settings, GeneXpert could be used for early identification of rifampin resistance, with WGS (as was done by Pankhurst and colleagues) providing a comprehensive picture of susceptibility, allowing individualisation of second-line treatment. Second, although WGS can play a part in identification or exclusion of transmission between individuals and can, in some circumstances, suggest directionality of transmission, little evidence exists that routine use of genotyping has helped to curb transmission,5Mears J Vynnycky E Lord J et al.The prospective evaluation of the TB strain typing service in England: a mixed methods study.Thorax. 2015; (published online April 16.)https://doi.org/10.1136/thoraxjnl-2014-206480Crossref PubMed Scopus (18) Google Scholar although ruling out of transmission has probably averted unnecessary contact tracing efforts. Although we are optimistic that improved characterisation of transmission patterns will ultimately result from incorporation of WGS data into transmission studies, whether this information can be effectively used to avert transmission events that would have occurred in the absence of such information remains to be seen. Third, we note that Pankhurst and colleagues included eight international study sites with state-of-the-art facilities and low throughput of samples; across these sites, 171 M tuberculosis-positive samples were identified with WGS. As Pankhurst and colleagues note, scaling up of WGS technologies to much larger numbers of samples within centres with less advanced infrastructure than those in this study is challenging because of the need for sequencing and data infrastructure along with bioinformatics expertise. We believe that this study represents a major step forward in the effort to use WGS as a method for routine diagnosis and are optimistic that WGS infrastructure will have positive effects beyond diagnosis. Methods to infer patterns of transmission from sequence data are being improved, but use of these methods to inform realtime tuberculosis control will need more robust analytical methods than those at present and systems allowing rapid dissemination of WGS data and associated metadata to public health authorities.6Walker TM Ip CL Harrell RH et al.Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.Lancet Infect Dis. 2013; 13: 137-146Summary Full Text Full Text PDF PubMed Scopus (602) Google Scholar, 7Roetzer A Diel R Kohl TA et al.Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.PLoS Med. 2013; 10: e1001387Crossref PubMed Scopus (357) Google Scholar, 8Didelot X Gardy J Colijn C Bayesian inference of infectious disease transmission from whole-genome sequence data.Mol Biol Evol. 2014; 31: 1869-1879Crossref PubMed Scopus (141) Google Scholar, 9Kohl TA Diel R Harmsen D et al.Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach.J Clin Microbiol. 2014; 52: 2479-2486Crossref PubMed Scopus (141) Google Scholar If efforts to link WGS data to de-identified metadata and make these available are successful,10Theron G Jenkins HE Cobelens F et al.Data for action: collection and use of local data to end tuberculosis.Lancet. 2015; (published online Oct 23.)http://dx.doi.org/10.1016/S0140-6736(15)00321-9Google Scholar, 11Chernyaeva EN Shulgina MV Rotkevich MS et al.Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology.BMC Genomics. 2014; 15: 308Crossref PubMed Scopus (55) Google Scholar the scientific community will be able to expand the already growing database relating sequences to resistance profiles and continue to improve prediction of resistance from sequences.12Bradley P Gordon NC Walker TM et al.Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis.bioRxiv. 2015; (published online April 26.)https://doi.org/10.1101/018564Crossref Google Scholar, 13Coll F McNerney R Preston MD et al.Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences.Genome Med. 2015; 7: 51Crossref PubMed Scopus (240) Google Scholar, 14Starks AM Avilés E Cirillo DM et al.Collaborative effort for a centralized worldwide tuberculosis relational sequencing data platform.Clin Infect Dis. 2015; 61: S141-S146Crossref PubMed Scopus (58) Google Scholar The costs of sequencing are likely to continue to decrease, and the capabilities of sequencing-based technologies will probably continue to improve. Both of these factors make adoption of WGS infrastructure appealing beyond the slight cost benefit reported in this study. Exciting approaches to the challenge of sequencing directly from sputum (without waiting for culture) have already yielded promising results.3Brown AC Bryant JM Einer-Jensen K et al.Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples.J Clin Microbiol. 2015; 53: 2230-2237Crossref PubMed Scopus (167) Google Scholar, 15Colman RE Schupp JM Hicks ND et al.Detection of low-level mixed-population drug resistance in Mycobacterium tuberculosis using high fidelity amplicon sequencing.PLoS One. 2015; 10: e0126626Crossref Scopus (60) Google Scholar These approaches, together with deep sequencing, could improve detection of minority variants in sputum, further improving characterisation and understanding of both transmission and resistance and needing essentially the same WGS infrastructure. In principle, WGS methods offer the ability to customise treatment regimens on the basis of rapidly obtained knowledge of individual resistance profiles to understand when and where transmission is taking place and characterise the acquisition and transmission of drug resistance in real time. Pankhurst and colleagues have shown a proof of principle that a move to WGS technologies is feasible in high-income settings; ultimately, expanded adoption of WGS, if effectively combined with data deposition and sharing, could be a major step towards realisation of the promised benefits of sequencing technologies for improvement of understanding and control of tuberculosis. We declare no competing interests. Rapid, comprehensive, and affordable mycobacterial diagnosis with whole-genome sequencing: a prospective studyWe have shown that WGS has a scalable, rapid turnaround, and is a financially feasible method for full MTBC diagnostics. Continued improvements to mycobacterial processing, bioinformatics, and analysis will improve the accuracy, speed, and scope of WGS-based diagnosis. Full-Text PDF Open Access