Evaluation of pyrosequencing for extensive drug resistance-defining anti-tuberculosis drugs for use in public healthcare

• Published in: Tuberculosis (Edinburgh, Scotland) Vol. 110; pp. 86 - 90
• Main Authors: Nambiar, Remya, Shah, Daksha, Ajbani, Kanchan, Kazi, Mubin, Sadani, Meeta, Shetty, Anjali, Keskar, Padmaja, Kamble, Sanjeev, van Belkum, Alex, Rodrigues, Camilla
• Format: Journal Article
• Language: English
• Published: Scotland Elsevier Ltd 01-05-2018; Elsevier Science Ltd
• Subjects: Amikacin; Antitubercular Agents - pharmacology; Bacteria; Capreomycin; DNA, Bacterial - genetics; Drug resistance; Drug Resistance, Multiple, Bacterial - genetics; Drugs; Extensively Drug-Resistant Tuberculosis - microbiology; Feasibility Studies; Genotype; Genotypes; Health care; High-Throughput Nucleotide Sequencing - methods; Humans; Isoniazid; Kanamycin; Microbial Sensitivity Tests - methods; Moxifloxacin; Mutation; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - genetics; Ofloxacin; Phenotype; Phenotypic DST; Post-production processing; Public Health; Pyrosequencing; Resistance; Rifampin; RpoB protein; Sequence Analysis, DNA - methods; Tuberculosis; Resistance; Phenotypic DST; Mutation; Public health; Pyrosequencing
• ISSN: 1472-9792; 1873-281X
• DOI: 10.1016/j.tube.2018.03.006

MGIT 960 drug susceptibility testing (DST) for Mycobacterium tuberculosis was compared for performance and speed with pyrosequencing (PSQ). Pulmonary samples (n = 100), from GeneXpert/MTB/Rifampicin-resistant patients receiving second-line treatment for 1–3 months, were subjected to DST and PSQ for seven drugs (isoniazid, rifampicin, kanamycin, amikacin, capreomycin, moxifloxacin, and ofloxacin). The mean time-to-result was 35 and two days for DST and PSQ, respectively. Average concordancy was 92.7%. Theoretically, PSQ showed substantial incremental value over the commercial Genotype MTBDRplus/sl. Mutations not considered in commercial molecular tests were observed by PSQ. Our findings corroborated the association between S315T (katG region) and S531L (rpoB region) and phenotypic resistance. PSQ is more rapid, can be performed from the sample, provides information about all known mutations simultaneously, allows extensive post-processing analyses, and is open to the inclusion of new mutations. It indicates the exact mutation conferring resistance to the particular drug, unlike the qualitative DST.