Whole-genome sequencing of presumptive MDR-TB isolates from a tertiary healthcare setting in Mumbai

• DOI: 10.1016/j.jgar.2022.10.004
• Publication Date: 2022-10-20T07:49:45Z
• Authors: Amrutraj Zade; Sanchi Shah; Nilma Hirani; Kiran Kondabagil; Ameeta Joshi; Anirvan Chatterjee
• Keywords: 0301 basic medicine; Whole-genome sequencing; Public health; 0303 health sciences; Antibiotic resistance; Tertiary Healthcare; Antitubercular Agents; Mycobacterium tuberculosis; Microbial Sensitivity Tests; Microbiology; QR1-502; 3. Good health; 03 medical and health sciences; Tuberculosis, Multidrug-Resistant; Isoniazid; Streptomycin; Humans; Rifampin; Genomic clusters; TB Diagnostics

Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB), proven to be a better alternative when compared with the combined sensitivity and specificity all other modalities for diagnosis (TB), aids epidemiological surveillance investigations by combining current research diagnostics. This study was conducted identify resolve operational challenges in performing WGS-based drug resistance testing (DRT) MTB TB culture susceptibility (DST) laboratory. Three critical, non-redundant steps DRT were tested: viz. DNA extraction, high-throughput paired-end next-generation (NGS), genomic analysis pipeline automated reporting DRT. extracted from 100 liquid isolates on mycobacterial growth indicator tube (MGIT) using DNEASY Ultraclean Microbial Kit (Qiagen, USA) as per manufacturer's instructions. Illumina performed. All custom python scripts, requiring no intervention. Variant calling performed World Health Organization (WHO) technical guide. The number cultures resistant rifampicin, isoniazid, pyrazinamide, ethambutol, streptomycin 89, 88, 35, 67, 73, respectively. Resistance amikacin, kanamycin, capreomycin found 15, 17, 15 cultures, Seventy fluoroquinolones, four ethionamide, 12 linezolid. Six only one 18 drugs tested. Seventy-five more than three anti-TB drugs. One 13 tested this study. maximum variants observed rpoB gene (n = 93, 93%), wherein Ser450Leu predominant mutation 68, 73%). Ser315Thr most common variant 86, 97%) that encoded isoniazid. Lys43Arg encodes third 65, 89%). In addition high levels dataset, we also proportion Beijing strains 63, 63%). Compared results routine diagnostics based 'Guidelines Programmatic Management Drug-Resistant (PMDT) India', none samples had DST available represents gap PMDT guidelines. WGS-DRT must considered primary method after sample is flagged rifampicin-resistant cartridge-based nucleic acid amplification (CBNAAT). With several studies currently underway globally novel associated classifiy their minimum inhibitory coefficients, presents scalable technology updates analytical pipelines, relegating need changing microbiological protocols.