Ngo Viet, Quynh Tram (2012) Molecular epidemiology and phenotypic and genetic characterization of Mycobacteria isolated in central Vietnam. Doctoral Thesis.
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The overall objective of this study is to determine molecular epidemiology and phenotypic and genetic characterization of mycobacteria isolated in central Vietnam.
In this study, the MODS assay was used to isolate mycobacteria and determine the proportion of drug resistant strains in 252 clinical samples. M.tuberculosis was detected in 153 samples (60.7%) and 46 (30.1%) were antibiotic resistant. One drug resistance was present in 30 strains (19.6%): 18 for RIF, 6 for INH and 3 for STR and EBM. Multidrug resistant M. tuberculosis as defined by WHO (resistant to RIF and INH) was observed in 13 strains. There were additional 14 strains showing resistance to two or more drugs.
Identification of M. tuberculosis using the 16S rDNA based PCR assay detected 258 positive in 480 clinical samples(53.8%), including 73 smear negative cases. The IS6110 PCR of positive cases could not confirm the positivity in 3 samples, probably due to the absence of the insertion sequence.
Spoligotyping produced a total of 36 different patterns for the 122 M. tuberculosis strains examined. The EAI family genotype (65.6% of isolates) dominated in our study: 15.6 % were of the EAI4-VNM genotype and 46.7 % were of EAI5. Beijing genotype was observed in 12.3 % of isolates. There were 4 isolates (3.3%) in which spoligotype pattern did not match with any of the updated international spoligotype database of the M. tuberculosis complex -SpolDB4. The remaining 22% were of other genotypes (including U, T, MANU, H and CAS).
Sequence and analysis of the whole genome of MTB_HUE_20 strain - a multidrug resistant strain with unknown spoligotype pattern - showed that it is 4,397,928 bp in length and contains 64.8% of GC. This strain harbors only one copy of IS6110 and has a mutation on katG gene.
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