Molecular epidemiology of Mycobacterium tuberculosis and antibiotic resistance in Lao PDR

Abstract : Tuberculosis (TB) is still one of the top 10 leading causes of death worldwide; the emergence/re-emergence of drug resistant TB aggravates the situation globally and challenges the prospect of ending TB by 2035. Lao PDR is surrounded by TB and MDR-TB high burden countries and TB continues to be one of the priority infection diseases in this country. The prevalence of TB in 2010 was almost twice as high than previous estimates and little is known about drug resistance. Up to now, M. tuberculosis population data regarding drug resistance and genetic structure are totally absent. In this context, we aimed to study the diversity and the structure of M. tuberculosis population and the genetic determinants associated to drug resistance using clinical samples collected from the TB prevalence survey (TBPS), 2010-2011; from the Drug resistance survey (DRS), 2016-2017 and from presumptive MDR-TB cases in Lao PDR (2010-2014). Various methods and analyses were used, including drug susceptibility testing (phenotypic and genotypic), DNA sequencing and genotyping of M. tuberculosis using spoligotyping and MIRU-VNTR. The data were analyzed by statistical and phylogenetic analyses.Firstly, this work was focused on the diversity of M. tuberculosis families circulating in Lao PDR. According to the result form TBPS, EAI and Beijing family (76.7% and 14.4% respectively) were mainly observed, while Beijing family was more observed in DRS, and presumptive MDR-TB cases (35% and 41% respectively). The level of recent transmission in Lao PDR was non-negligible with a global clustering rate of 11.9% and in Beijing and EAI of 20% and 11%, respectively. Secondly, the results demonstrated the diversity of drug resistant patterns from mono-resistance to pre-extensively drug resistance (pre-XDR). A high diversity of mutations associated with drug resistance was also observed, however common mutations were mainly found (e.g: mutations in rpoB gene, katG and rpsL). The pattern was different for pncA gene, we observed a diversity of mutations without preeminent ones. Besides the number of known and unknown mutations associated with anti-TB drug resistance, deletion and insertion of bases were also observed. The sequencing showed its usefulness for drug resistance detection. Lastly, Beijing family, which is the more problematic family in the world in terms of resistance and transmissibility, was observed on a significant manner in young age group, mainly in the northern provinces, in recent transmission cases and among highly drug resistant isolates, suggesting an increasing risk of highly drug resistance TB due to highly transmissible Beijing strains in Lao PDR.In conclusion, this study provides the first genetic insights into the M. tuberculosis population in Lao PDR. The results underline the risk of increase of Beijing and drug resistant TB in the country. In order to prevent a more serious situation in the future regarding drug resistance as observed in neighboring countries, there is an urgent need of effective strategy improvement for drug resistance screening and the development of rapid molecular tests that cover a large number of drug resistance simultaneously with a feasible implementation in the limited resource countries. The results of genotyping from our study will be the baseline of families/subfamilies/genotype of M. tuberculosis population and of the mutations associated with drug resistance in Lao PDR. These data will be compared with further study/analysis to evaluate the trend of TB and drug resistant TB in the country and to determine if the drug resistance is under control after the set-up of new policies. The data of drug resistance associated mutations are used to build a regional database in collaboration with Vietnam and Cambodia in order to develop a diagnostic tool based on DNA chip technology to improve the drug resistance detection in the region.
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Silaphet Somphavong. Molecular epidemiology of Mycobacterium tuberculosis and antibiotic resistance in Lao PDR. Agricultural sciences. Université Montpellier, 2018. English. ⟨NNT : 2018MONTT097⟩. ⟨tel-02100060⟩

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