Marylette B Roa1, Francis A Tablizo1, El King D Morado1, Lovette F Cunanan1, Iris Diana C Uy1, Kamela Charmaine S Ng1, Karen G Manalastas-Cantos1, Joeriggo M Reyes1, Sharie Keanne C Ganchua2, Concepcion F Ang3, Midori Kato-Maeda4, Adithya Cattamanchi4, Ulas Karaoz5, Raul V Destura6, Arturo O Lluisma7. 1. Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines. 2. Institute of Molecular Biology and Biochemistry, National Institutes of Health, University of the Philippines-Manila, Ermita, Manila 1000, Philippines. 3. Section of Infectious Diseases, Philippine General Hospital, University of the Philippines-Manila, Ermita, Manila 1000, Philippines. 4. University of California, San Francisco, San Francisco General Hospital, Division of Pulmonary and Critical Care Medicine, 1001 Potrero Avenue, Mail Box 0841, San Francisco, CA 94110, USA. 5. Climate and Ecosystems Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. 6. Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines; Institute of Molecular Biology and Biochemistry, National Institutes of Health, University of the Philippines-Manila, Ermita, Manila 1000, Philippines. Electronic address: rvdestura@up.edu.ph. 7. Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines; Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines. Electronic address: aolluisma@up.edu.ph.
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.
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.
Authors: Jody E Phelan; Dodge R Lim; Satoshi Mitarai; Paola Florez de Sessions; Ma Angelica A Tujan; Lorenzo T Reyes; Inez Andrea P Medado; Alma G Palparan; Ahmad Nazri Mohamed Naim; Song Jie; Edelwisa Segubre-Mercado; Beatriz Simoes; Susana Campino; Julius C Hafalla; Yoshiro Murase; Yuta Morishige; Martin L Hibberd; Seiya Kato; Ma Cecilia G Ama; Taane G Clark Journal: Sci Rep Date: 2019-06-26 Impact factor: 4.379