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Whole-genome sequencing and single nucleotide polymorphisms in multidrug-resistant clinical isolates of Mycobacterium tuberculosis from the Philippines
- Roa, Marylette B;
- Tablizo, Francis A;
- Morado, El King D;
- Cunanan, Lovette F;
- Uy, Iris Diana C;
- Ng, Kamela Charmaine S;
- Manalastas-Cantos, Karen G;
- Reyes, Joeriggo M;
- Ganchua, Sharie Keanne C;
- Ang, Concepcion F;
- Kato-Maeda, Midori;
- Cattamanchi, Adithya;
- Karaoz, Ulas;
- Destura, Raul V;
- Lluisma, Arturo O
- et al.
Published Web Location
http://dx.doi.org/10.1016/j.jgar.2018.08.009No data is associated with this publication.
Abstract
Objectives
Thousands of cases of multidrug-resistant tuberculosis (TB) have been observed in the Philippines, but studies on the Mycobacterium tuberculosis (MTB) genotypes that underlie the observed drug resistance profiles are lacking. This study aimed to analyse the whole genomes of clinical MTB isolates representing various resistance profiles to identify single nucleotide polymorphisms (SNPs) in resistance-associated genes.Methods
The genomes of ten MTB isolates cultured from banked sputum sources were sequenced. Bioinformatics analysis consisted of assembly, annotation and SNP identification in genes reported to be associated with resistance to isoniazid (INH), rifampicin (RIF), ethambutol (ETH), streptomycin, pyrazinamide (PZA) and fluoroquinolones (FQs).Results
The draft assemblies covered an average of 97.08% of the expected genome size. Seven of the ten isolates belonged to the Indo-Oceanic lineage/EA12-Manila clade. Two isolates were classified into the Euro-American lineage, whilst the pre-XDR (pre-extensively drug-resistant) isolate was classified under the East Asian/Beijing clade. The SNPs katG Ser315Thr, rpoB Ser450Leu and embB Met306Val were found in INH- (4/7), RIF- (3/6) and ETH-resistant (2/6) isolates, respectively, but not in susceptible isolates. Mutations in the inhA promoter and in the pncA and gyrA genes known to be involved in resistance to INH, PZA and FQs, respectively, were also identified.Conclusions
This study represents the first effort to investigate the whole genomes of Philippine clinical strains of MTB exhibiting various multidrug resistance profiles. Whole-genome data can provide valuable insights to the mechanistic and epidemiological qualities of TB in a high-burden setting such as the Philippines.Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.