RpoB Gene-Based Characterization of Non-Tuberculous Mycobacteria in Zimbabwe
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Date
2017
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Abstract
Aims: To characterize archived nontuberculous Mycobacteria (NTM) samples previously isolated
from humans across Zimbabwe during the 2014 national tuberculosis survey. The rpoB gene of the
isolates was targeted for characterization.
Study Design: The research was an observational study where NTM samples previously isolated
from Zimbabwean population were analysed by rpoB gene sequencing and phylogeny to identify
NTM speciesPlace and Duration of Study: Department of Medical Microbiology, University of Zimbabwe
between September 2015 and July 2016.
Methodology: We obtained 99 NTM DNA samples from 963 NTM at NMRL, which we
characterised using rpoB gene analysis after PCR amplification. The amplicons were sequenced
and bioinformatics tools were used for speciation. The rpoB gene of DNA extracts from the NTM
was amplified and the sequences were analysed using bioinformatics tools to identify the NTM to
species level.
Results: From the 99 NTM isolates, 40 were sequenced and analyzed. The NTM were identified as
belonging to 13 species. The species were M. palustre (14.8%), M. aroisense (29.6%), M.
parascrofulaceum (3.7%), M. arupense (7.4%), M. asiaticum (3.7%), M. malmoense (3.7%), M.
lacus (3.7%), M. avium (7.4%), M. nonchromogenicum (3.7%), M. gordonae (3.7%), M.
aromaticivorans (3.7%), M. novocastrense (3.7%), M. bourgelatii (3.7%). One sample (3.7%)
belonged to Mtb complex species (3.7%) and another one (3.7%) was closely related to S. oryzae.
The most common species belonged to M. aroisense and M. palustre. The species showed a high
degree of rpoB sequence diversity. Sequence analysis of the rifampicin resistance determining
region (RRDR) showed the existence of only silent mutations.
Conclusion: Species of NTM from Zimbabwe showed a high degree of rpoB gene sequence
diversity. This characteristic feature can therefore be used in diagnosis and identification of NTM in
clinical specimens
Description
journal article
Keywords
rpoB gene, nontuberculous mycobacteria, sequencing, alignments, RRDR, Mutations
Citation
Manjeese, W. et al. 2017. RpoB Gene-Based Characterization of Non-Tuberculous Mycobacteria in Zimbabwe:Journal of Advances in Microbiology 6(1).