Next-generation sequencing to characterise pyrazinamide resistance in Mycobacterium tuberculosis isolates from two Balkan countries

Objectives: Next-generation sequencing (NGS) can provide a comprehensive analysis of the genetic al -terations most commonly linked with pyrazinamide (PZA) resistance. However, there are no studies re-porting the molecular background of PZA resistance in Mycobacterium tuberculosis (TB) isolates from the Balkan Peninsula. We aimed to examine the feasibility of full-length analysis of a gene linked with PZA resistance (pncA) using Ion Torrent technology compared with phenotypic BACTEC MGIT 960 drug sus-ceptibility testing (DST) in clinical TB isolates from two countries of the Balkan Peninsula.Methods: Between 1996 and 2017, we retrospectively selected 61 TB isolates. To identify gene variants related to drug resistance in genomic DNA extracted from TB isolates, AmpliSeq libraries were generated automatically using an AmpliSeqTM Kit for Chef DL8 and Ion AmpliSeq TB Research Panel.Results: Of the 61 TB isolates, 56 were phenotypically resistant to any antibiotic. Among them, 38/56 iso-lates (67.9%) were phenotypically resistant to pyrazinamide, and pncA mutations were detected in 34/38 cases (89.5%). A mutation in the pncA promoter region was the most prevalent genetic alteration, de-tected in eight TB isolates. Comparison of NGS data with conventional BACTEC MGIT 960 DST revealed very strong agreement (91.8%) between the two methods in identifying PZA resistance, with high sensi-tivity (89.5%) and specificity (95.7%) for NGS. Conclusion: Detection of PZA resistance using NGS appears to be a valuable tool for surveillance of TB drug resistance in the Balkan Peninsula, with great potential to provide useful information at least 1 weak earlier than is possible with phenotypic DST.(c) 2021 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )

Automated summary

This study investigated the feasibility of full-length analysis of a gene linked with pyrazinamide (PZA) resistance using Ion Torrent technology and its comparison with phenotypic drug susceptibility testing (DST) in clinical tuberculosis (TB) isolates from the Balkan Peninsula. The results showed high agreement and sensitivity between NGS and conventional DST methods in detecting PZA resistance.