Whole-genome sequence analysis of Mycobacteria tuberculosis bacteria to identify the genetic determinants and mechanisms of anti-tuberculosis drug

点击翻译按钮获取中文摘要

resistance.Tuberculosis disease (TB) is a major public health problem. The emergence of Mycobacteriumtuberculosis strains resistant to the drugs used to treat the disease threatens to derail efforts tocontrol TB. Resistance to at least two of the first line drugs is denoted as multidrug-resistanttuberculosis (MDR-TB), whilst additional resistance to any drug used to treat MDR-TB is known asextensively drug-resistant tuberculosis (XDR-TB). The appearance of these strains has complicatedclinical drug selection, which along with the considerable toxicity and side effects of the drugs resultin poor outcomes, less compliance and ultimately can amplify resistance. For this reason, earlydetection of resistant strains is crucial. Susceptibility tests of clinical samples have been traditionallycarried out by phenotypic methods, which are costly and can take weeks since they involve cultureand manipulation of highly infectious bacteria. For some first-line drugs there are also molecularbasedtests, but most have low sensitivity.Drug resistance is conferred almost exclusively by accumulation of point mutations and insertionsand deletions in genes encoding targets or drug-activating enzymes. The study of genotypephenotypeassociations has enabled the creation of a mutation library for drug resistance markers.Therefore, the use of whole-genome sequence analysis of clinical samples in combination with amutation library can inform clinical drug management, in a more timely fashion than phenotypicmethods. Nevertheless, one of the challenges is implement the direct analysis of sputum samples,for which culture of the bacteria prior to sequence is still necessary. A method known as selectivewhole-genome amplification (SWGA) is a potential solution, and enables the amplification of the M.tuberculosis target genome from a complex sample by using specific primers that do not anneal tonon- M. tuberculosis meta genomes in the sputum.On this basis, the aims of this project are: (i) to identify novel resistance mutations and mechanismsof anti-tuberculosis drug resistance from whole-genome sequence data by applying regression-2based models; (ii) to characterise the effects of mutations on protein stability and drug docking byusing protein structure models; (iii) to develop quantitative methods to rapidly predict drugresistance from whole genome sequence data. In order to accomplish these aims, strongbioinformatics and big data analysis skills will be gained and applied in the field of genomics.Interdisciplinary skills will be gained including training in culture of M. tuberculosis and developmentof the SWGA approach. Finally, the results of this project could lead to new diagnostic tools, assistwith the management of the TB, and eventually benefit public health. The participation of St.George's Hospital and University will assist with the roll-out in a clinical setting of any sequencingor laboratory-based tools developed..