Analysis and application of evolutionary markers in the epidemiology of Mycobacterium tuberculosis

[摘要] This series of studies includes both methodological analyses, aimed at furthering our understanding of, and improving the tools used in molecular epidemiology, and investigative projects which have used these tools to add to our knowledge of the M. tuberculosis epidemic.Using serial isolates from tuberculosis patients, we have investigated the evolutionary rate of theIS6110 RFLP pattern. In accordance with other studies, we determined a ½-life for thisepidemiological marker of 10.69 years, confirming its appropriateness for this purpose. We alsoidentified an initial, much higher apparent rate which we proposed was the result of pre-diagnosticevolution. In support of this, our investigations in the context of household transmission of M.tuberculosis revealed that IS6110-based evolution is closely associated with transmission of theorganism, resulting in a strain population rate of change of 2.9% per annum.To accommodate evolution within estimates of transmission, we proposed that calculationsincorporate the concept of Nearest Genetic Distance (cases most similar in RFLP pattern and most closely associated in time). We used this to create transmission chains which allowed for limited evolution of the IS6110 marker. As a result, in our study community, the estimated level of disease attributable to ongoing transmission was increased to between 73 and 88% depending on the Genetic Distance allowed.We identified the duration of a study as a further source of under-estimation of transmission. This results from the artefactual abridgement of transmission chains caused by the loss of cases at the temporal boundaries of a study. Using both real and simulated data, we showed that viewing a 12-year study through shorter window periods dramatically lowered estimates of transmission. This effectwas negatively correlated with the size of a cluster.Various combinations of MIRU-VNTR loci have been proposed as an alternative epidemiologicalmarker. Our investigations showed that, while this method yielded estimates of transmission similar to those of IS6110, there was discordance between the two markers in the epidemiological linking of cases as a result of their independent evolution. Attempting to compensate for this by allowing for evolution during transmission improved the performance of IS6110, but generally had a deleterious effect of that of MIRU-VNTR. However, this marker remains a valuable tool for higher phylogenetic analysis and we used it to demonstrate a correlation between sublineages of the Beijing clade and the regions in which they are found. We proposed that, either the host population had selected for a particular sublineage, or that specific sublineages had adapted to be more successful in particularhuman populations.We further explored the dynamics of the epidemic over a 12-year period in terms of the fivepredominant M. tuberculosis clades. We found that, while four of these clades remained relatively stable, the incidence of cases from the Beijing clade increased exponentially. This growth was attributed to drug-sensitive cases although drug-resistant Beijing cases also appeared to be more successful than their non-Beijing counterparts. Possible factors contributing to this clade's success were a greater proportion of positive sputum smears and a lower rate of successful treatment.

[发布机构] Stellenbosch University