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Roa MB, Tablizo FA, Morado EKD, Cunanan LF, Uy IDC, Ng KCS, Manalastas-Cantos KG, Reyes JM, Ganchua SKC, Ang CF, Kato-Maeda M, Cattamanchi A, Karaoz U, Destura RV, Lluisma AO. Whole-genome sequencing and single nucleotide polymorphisms in multidrug-resistant clinical isolates of Mycobacterium tuberculosis from the Philippines. J Glob Antimicrob Resist 2018; 15:239-245. [PMID: 30130640 DOI: 10.1016/j.jgar.2018.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/06/2018] [Accepted: 08/11/2018] [Indexed: 11/16/2022] Open
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.
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Affiliation(s)
- Marylette B Roa
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Francis A Tablizo
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - El King D Morado
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Lovette F Cunanan
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Iris Diana C Uy
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Kamela Charmaine S Ng
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | | | - Joeriggo M Reyes
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Sharie Keanne C Ganchua
- Institute of Molecular Biology and Biochemistry, National Institutes of Health, University of the Philippines-Manila, Ermita, Manila 1000, Philippines
| | - Concepcion F Ang
- Section of Infectious Diseases, Philippine General Hospital, University of the Philippines-Manila, Ermita, Manila 1000, Philippines
| | - Midori Kato-Maeda
- 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
| | - Adithya Cattamanchi
- 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
| | - Ulas Karaoz
- Climate and Ecosystems Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Raul V Destura
- 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.
| | - Arturo O Lluisma
- Philippine Genome Center, University of the Philippines, Diliman, Quezon City 1101, Philippines; Marine Science Institute, University of the Philippines, Diliman, Quezon City 1101, Philippines.
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Narciso JET, Uy IDC, Cabang AB, Chavez JFC, Pablo JLB, Padilla-Concepcion GP, Padlan EA. Analysis of the antibody structure based on high-resolution crystallographic studies. N Biotechnol 2011; 28:435-47. [PMID: 21477671 DOI: 10.1016/j.nbt.2011.03.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
High-resolution structures of liganded and unliganded antibody molecules were analyzed in terms of the interaction between the antibody with ligand, between the residues in the contact between the variable domains, and between the framework and the complementarity-determining regions of the antibody. The solvent accessibilities of the residues in the variable domains were also analyzed. The structural information is useful in the engineering of antibodies for therapeutic and other purposes.
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Affiliation(s)
- Jo Erika T Narciso
- The Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines
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