Genomic Epidemiology of Tuberculosis
The application of next generation sequencing technologies has opened the door to a new molecular epidemiology of tuberculosis, in which we can now look at transmission at a resolution not possible before. At the same time, new technical and analytical challenges have appeared, and we are still exploring the wider potential of this new technology. Whole genome sequencing in tuberculosis still requires bacterial cultures. Thus, although whole genome sequencing has revolutionized the interpretation of transmission patterns, it is not yet ready to be applied at the point-of-care. In this chapter, I will review the promises and challenges of genomic epidemiology, as well as some of the new questions that have arisen from the use of this new technology. In addition, I will examine the role of molecular epidemiology within the general frame of global tuberculosis control and how genomic epidemiology can contribute towards the elimination of the disease.
KeywordsTransmission, genome sequencing, outbreak, mutation rate
I thank the members of my group for stimulating discussions. Work in my laboratory is supported by the Spanish National Foundation (MINECO SAF2013-43521-R) and the European Research Council (638553-TB-ACCELERATE).
- Coscolla M, Barry PM, Oeltmann JE et al (2015) Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread. J Infect Dis 15:383–388Google Scholar
- Guerra-Assunção JA, Houben RMGJ, Crampin AC et al (2015b) Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up. J Infect Dis 211:1154–1163CrossRefPubMedGoogle Scholar
- Loman NJ, Pallen MJ (2015) Twenty years of bacterial genome sequencing. Nat Rev Microbiol:1–9Google Scholar
- Pérez-Lago L, Comas I, Navarro Y et al (2013) Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission. J Infect Dis:1–11Google Scholar
- Stucki D, Ballif M, Egger M et al (2015b) Standard genotyping overestimates transmission of Mycobacterium tuberculosis among immigrants in a low-incidence country. J Clin Microbiol 7:1862–1870Google Scholar
- Tameris MD, Hatherill M, Landry BS et al (2013) Safety and efficacy of MVA85A, a new tuberculosis vaccine, in infants previously vaccinated with BCG: a randomised, placebo-controlled phase 2b trial. Lancet 6736:1–8Google Scholar
- Votintseva AA, Bradley P, Pankhurst L, Del Ojo Elias C, Loose M, Nilgiriwala K, Chatterjee A, Smith EG, Sanderson N, Walker TM, Morgan MR, Wyllie DH, Walker AS, Peto TEA, Crook DW, Iqbal Z (2017) Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples. J Clin Microbiol 55(5):1285–1298Google Scholar
- World Health Organization (2015). Global tuberculosis reportGoogle Scholar