title: Whole-Genome Sequencing Analysis of Serially Isolated Multi-Drug and Extensively Drug Resistant Mycobacterium tuberculosis from Thai Patients.
abstract: Multi-drug and extensively drug-resistant tuberculosis (MDR and XDR-TB) are problems that threaten public health worldwide. Only some genetic markers associated with drug-resistant TB are known. Whole-genome sequencing (WGS) is a promising tool for distinguishing between re-infection and persistent infection in isolates taken at different times from a single patient, but has not yet been applied in MDR and XDR-TB. We aim to detect genetic markers associated with drug resistance and distinguish between reinfection and persistent infection from MDR and XDR-TB patients based on WGS analysis. Samples of Mycobacterium tuberculosis (n = 7), serially isolated from 2 MDR cases and 1 XDR-TB case, were retrieved from Siriraj Hospital, Bangkok. The WGS analysis used an Illumina Miseq sequencer. In cases of persistent infection, MDR-TB isolates differed at an average of 2 SNPs across the span of 2-9 months whereas in the case of reinfection, isolates differed at 61 SNPs across 2 years. Known genetic markers associated with resistance were detected from strains susceptible to streptomycin (2/7 isolates), p-aminosalicylic acid (3/7 isolates) and fluoroquinolone drugs. Among fluoroquinolone drugs, ofloxacin had the highest phenotype-genotype concordance (6/7 isolates), whereas gatifloxcain had the lowest (3/7 isolates). A putative candidate SNP in Rv2477c associated with kanamycin and amikacin resistance was suggested for further validation. WGS provided comprehensive results regarding molecular epidemiology, distinguishing between persistent infection and reinfection in M/XDR-TB and potentially can be used for detection of novel mutations associated with drug resistance.
authors: Department of Microbiology Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.|Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
authors: Kiatichai
authors: K
authors: Faksri
authors: Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
authors: Jun Hao
authors: JH
authors: Tan
authors: Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
authors: Areeya
authors: A
authors: Disratthakit
authors: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.
authors: Eryu
authors: E
authors: Xia
authors: National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Ministry of Science and Technology, Pathum Thani, Thailand.
authors: Therdsak
authors: T
authors: Prammananan
authors: Bioinformatics and Data Management for Research Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
authors: Prapat
authors: P
authors: Suriyaphol
authors: Genome Institute of Singapore, Singapore.
authors: Chiea Chuen
authors: CC
authors: Khor
authors: Saw Swee Hock School of Public Health, National University of Singapore, Singapore.|NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.|Genome Institute of Singapore, Singapore.|Department of Statistics and Applied Probability, National University of Singapore, Singapore.|Life Sciences Institute, National University of Singapore, Singapore.
authors: Yik-Ying
authors: YY
authors: Teo
authors: Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
authors: Rick Twee-Hee
authors: RT
authors: Ong
authors: Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
authors: Angkana
authors: A
authors: Chaiprasert
mesh_terms: D003198:Computer Simulation; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D054908:Extensively Drug-Resistant Tuberculosis / Q000382:microbiology*; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics; D005838:Genotype; D006801:Humans; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification* / Q000502:physiology; D017421:Sequence Analysis; D013785:Thailand
chemical_list: D005819:Genetic Markers