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.

doi:10.1016/j.jgar.2018.08.009

Whole-genome sequencing and single nucleotide polymorphisms in multidrug-resistant clinical isolates of Mycobacterium tuberculosis from the Philippines

Journal Article · Sat Aug 18 00:00:00 EDT 2018 · Journal of Global Antimicrobial Resistance

DOI:https://doi.org/10.1016/j.jgar.2018.08.009· OSTI ID:1567152

^[1]; Tablizo, Francis A. ^[1]; Morado, El King D. ^[1]; Cunanan, Lovette F. ^[1]; Uy, Iris Diana C. ^[1]; ^[1]; Manalastas-Cantos, Karen G. ^[1]; Reyes, Joeriggo M. ^[1]; Ganchua, Sharie Keanne C. ^[2]; Ang, Concepcion F. ^[2]; Kato-Maeda, Midori ^[3]; Cattamanchi, Adithya ^[3]; Karaoz, Ulas ^[4]; Destura, Raul V. ^[5]; Lluisma, Arturo O. ^[1]

Univ. of the Philippines, Diliman, Quezon City (Philippines)
Univ. of the Philippines, Ermita, Manila (Philippines)
Univ. of California, San Francisco, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of the Philippines, Diliman, Quezon City (Philippines); Univ. of the Philippines, Ermita, Manila (Philippines)

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. 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). 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. 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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1567152

Journal Information:: Journal of Global Antimicrobial Resistance, Journal Name: Journal of Global Antimicrobial Resistance Journal Issue: C Vol. 15; ISSN 2213-7165

Publisher:: Elsevier - The International Society of ChemotherapyCopyright Statement

Country of Publication:: United States

Language:: English

References (30)

Best drug treatment for multidrug-resistant and extensively drug-resistant tuberculosis Caminero, José A.; Sotgiu, Giovanni; Zumla, Alimuddin The Lancet Infectious Diseases, Vol. 10, Issue 9 https://doi.org/10.1016/S1473-3099(10)70139-0	journal	September 2010
Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study Zignol, Matteo; Cabibbe, Andrea Maurizio; Dean, Anna S. The Lancet Infectious Diseases, Vol. 18, Issue 6 https://doi.org/10.1016/S1473-3099(18)30073-2	journal	June 2018
Population Genomics of Mycobacterium tuberculosis in Ethiopia Contradicts the Virgin Soil Hypothesis for Human Tuberculosis in Sub-Saharan Africa Comas, Iñaki; Hailu, Elena; Kiros, Teklu Current Biology, Vol. 25, Issue 24 https://doi.org/10.1016/j.cub.2015.10.061	journal	December 2015
Does M. tuberculosis genomic diversity explain disease diversity? Coscolla, Mireilla; Gagneux, Sebastien Drug Discovery Today: Disease Mechanisms, Vol. 7, Issue 1 https://doi.org/10.1016/j.ddmec.2010.09.004	journal	March 2010
Gene expression analysis of two extensively drug-resistant tuberculosis isolates show that two-component response systems enhance drug resistance Yu, Guohua; Cui, Zhenling; Sun, Xian Tuberculosis, Vol. 95, Issue 3 https://doi.org/10.1016/j.tube.2015.03.008	journal	May 2015
A robust SNP barcode for typing Mycobacterium tuberculosis complex strains Coll, Francesc; McNerney, Ruth; Guerra-Assunção, José Afonso Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5812	journal	September 2014
Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance Zhang, Hongtai; Li, Dongfang; Zhao, Lili Nature Genetics, Vol. 45, Issue 10 https://doi.org/10.1038/ng.2735	journal	September 2013
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans Comas, Iñaki; Coscolla, Mireia; Luo, Tao Nature Genetics, Vol. 45, Issue 10 https://doi.org/10.1038/ng.2744	journal	September 2013
Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools Schleusener, Viola; Köser, Claudio U.; Beckert, Patrick Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep46327	journal	April 2017
Variable host-pathogen compatibility in Mycobacterium tuberculosis Gagneux, S.; DeRiemer, K.; Van, T. Proceedings of the National Academy of Sciences, Vol. 103, Issue 8 https://doi.org/10.1073/pnas.0511240103	journal	February 2006
A new evolutionary scenario for the Mycobacterium tuberculosis complex Brosch, R.; Gordon, S. V.; Marmiesse, M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 6 https://doi.org/10.1073/pnas.052548299	journal	March 2002
Mycobacterium tuberculosis Lineage—What’s in Your Lungs? Kato-Maeda, Midori; Nahid, Payam Clinical Infectious Diseases, Vol. 54, Issue 2 https://doi.org/10.1093/cid/cir795	journal	January 2012
Totally Drug-Resistant Tuberculosis in India Udwadia, Z. F.; Amale, R. A.; Ajbani, K. K. Clinical Infectious Diseases, Vol. 54, Issue 4 https://doi.org/10.1093/cid/cir889	journal	December 2011
embCAB sequence variation among ethambutol-resistant Mycobacterium tuberculosis isolates without embB306 mutation Plinke, C.; Cox, H. S.; Zarkua, N. Journal of Antimicrobial Chemotherapy, Vol. 65, Issue 7 https://doi.org/10.1093/jac/dkq120	journal	April 2010
Phylogenetic polymorphisms in antibiotic resistance genes of the Mycobacterium tuberculosis complex Feuerriegel, S.; Koser, C. U.; Niemann, S. Journal of Antimicrobial Chemotherapy, Vol. 69, Issue 5 https://doi.org/10.1093/jac/dkt535	journal	January 2014
Pyrazinamide Susceptibility Testing in Mycobacterium tuberculosis: a Systematic Review with Meta-Analyses Chang, Kwok Chiu; Yew, Wing Wai; Zhang, Ying Antimicrobial Agents and Chemotherapy, Vol. 55, Issue 10 https://doi.org/10.1128/AAC.00630-11	journal	July 2011
Characterization of the Manila Family of Mycobacterium tuberculosis Douglas, James T.; Qian, Lishi; Montoya, Jaime C. Journal of Clinical Microbiology, Vol. 41, Issue 6 https://doi.org/10.1128/JCM.41.6.2723-2726.2003	journal	June 2003
Mycobacterium tuberculosis Pyrazinamide Resistance Determinants: a Multicenter Study Miotto, Paolo; Cabibbe, Andrea M.; Feuerriegel, Silke mBio, Vol. 5, Issue 5 https://doi.org/10.1128/mBio.01819-14	journal	October 2014
Low prevalence of fluoroquinolone resistance among patients with tuberculosis in the Philippines: results of a national survey Lim, Dodge R.; Dean, Anna S.; Taguinod-Santiago, Mary Rosary European Respiratory Journal, Vol. 51, Issue 3 https://doi.org/10.1183/13993003.02571-2017	journal	March 2018
Sequence analysis for detection of first-line drug resistance in Mycobacterium tuberculosis strains from a high-incidence setting Feuerriegel, Silke; Oberhauser, Barbara; George, Abu BMC Microbiology, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2180-12-90	journal	January 2012
Genotypic characteristics of Mycobacterium tuberculosis isolated from household contacts of tuberculosis patients in the Philippines Sia, Irene G.; Buckwalter, Seanne P.; Doerr, Kelly A. BMC Infectious Diseases, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2334-13-571	journal	December 2013
High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography Hershberg, Ruth; Lipatov, Mikhail; Small, Peter M. PLoS Biology, Vol. 6, Issue 12 https://doi.org/10.1371/journal.pbio.0060311	journal	December 2008
Tuberculosis Drug Resistance Mutation Database Sandgren, Andreas; Strong, Michael; Muthukrishnan, Preetika PLoS Medicine, Vol. 6, Issue 2 https://doi.org/10.1371/journal.pmed.1000002	journal	February 2009
High Resolution Discrimination of Clinical Mycobacterium tuberculosis Complex Strains Based on Single Nucleotide Polymorphisms Homolka, Susanne; Projahn, Michaela; Feuerriegel, Silke PLoS ONE, Vol. 7, Issue 7 https://doi.org/10.1371/journal.pone.0039855	journal	July 2012
TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing Sekizuka, Tsuyoshi; Yamashita, Akifumi; Murase, Yoshiro PLOS ONE, Vol. 10, Issue 11 https://doi.org/10.1371/journal.pone.0142951	journal	November 2015
Discordance across Phenotypic and Molecular Methods for Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates in a Low TB Incidence Country Ahmad, Suhail; Mokaddas, Eiman; Al-Mutairi, Noura PLOS ONE, Vol. 11, Issue 4 https://doi.org/10.1371/journal.pone.0153563	journal	April 2016
Emergence of New Forms of Totally Drug-Resistant Tuberculosis Bacilli Velayati, Ali Akbar; Masjedi, Mohammad Reza; Farnia, Parissa Chest, Vol. 136, Issue 2 https://doi.org/10.1378/chest.08-2427	journal	August 2009
Emergence and Spread of Extensively and Totally Drug-Resistant Tuberculosis, South Africa Klopper, Marisa; Warren, Robin Mark; Hayes, Cindy Emerging Infectious Diseases, Vol. 19, Issue 3 https://doi.org/10.3201/eid1903.120246	journal	March 2013
Mycobacterial Lineages Causing Pulmonary and Extrapulmonary Tuberculosis, Ethiopia Firdessa, Rebuma; Berg, Stefan; Hailu, Elena Emerging Infectious Diseases, Vol. 19, Issue 3 https://doi.org/10.3201/eid1903.120256	journal	March 2013
Mechanisms of drug resistance in Mycobacterium tuberculosis: update 2015 Zhang, Y.; Yew, W-W. The International Journal of Tuberculosis and Lung Disease, Vol. 19, Issue 11 https://doi.org/10.5588/ijtld.15.0389	journal	November 2015

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60 APPLIED LIFE SCIENCES
Bioinformatics
Drug resistance
Mycobacterium tuberculosis
Single nucleotide polymorphism
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Whole-genome sequencing and single nucleotide polymorphisms in multidrug-resistant clinical isolates of Mycobacterium tuberculosis from the Philippines

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