Whole-genome sequencing in drug susceptibility testing of Mycobacterium tuberculosis in routine practice in Lyon, France

• Published in: International journal of antimicrobial agents Vol. 55; no. 4; p. 105912
• Main Authors: Genestet, Charlotte, Hodille, Elisabeth, Berland, Jean-Luc, Ginevra, Christophe, Bryant, Juliet E., Ader, Florence, Lina, Gérard, Dumitrescu, Oana
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.04.2020
• Subjects: Antitubercular Agents - pharmacology; Bacterial Proteins - genetics; DNA-Directed RNA Polymerases - genetics; Drug resistance; Drug Resistance, Multiple, Bacterial - genetics; Drug susceptibility testing; Ethambutol - pharmacology; France; Humans; Isoniazid - pharmacology; Life Sciences; Line probe assay; Microbial Sensitivity Tests; Mycobacterium tuberculosis; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - isolation & purification; Pentosyltransferases - genetics; Pyrazinamide - pharmacology; Rifampin - pharmacology; Tuberculosis, Multidrug-Resistant - drug therapy; Tuberculosis, Multidrug-Resistant - microbiology; Tuberculosis, Pulmonary - drug therapy; Tuberculosis, Pulmonary - microbiology; Whole Genome Sequencing; France; Line probe assay; Mycobacterium tuberculosis; Drug susceptibility testing; Drug resistance; Whole-genome sequencing
• ISSN: 0924-8579; 1872-7913; 0924-8579
• DOI: 10.1016/j.ijantimicag.2020.105912

•M. tuberculosis (MTB) whole-genome sequencing (WGS) accurately predicts susceptibility for first-line anti-TB drugs.•WGS performs better than drug susceptibility testing (DST) for rifampicin and ethambutol low-level resistance.•Line probe assay is less accurate than WGS for anti-TB drug susceptibility prediction.•WGS could replace phenotypic DST in a country with a low prevalence of resistant MTB. Rapid and correct determination of Mycobacterium tuberculosis (MTB) drug susceptibility is a challenge for tuberculosis (TB) management. Phenotypic drug susceptibility testing (DST) remains the reference method but is time consuming. In this study, genotypic prediction of the first-line drug susceptibility profile obtained by whole-genome sequencing (WGS) was compared with that obtained by phenotypic DST and the line probe assay (LPA). All MTB strains isolated from patients during routine practice at the mycobacteria laboratory of Lyon University Hospital, France, between November 2016 and July 2019 were included (n = 274). Isolates were tested for the first-line drugs using phenotypic DST (Mycobacteria Growth Indicator Tube) and for genotypic prediction of the susceptibility profile with LPA and WGS. Considering phenotypic DST as the reference, WGS predicted resistance to rifampicin, isoniazid, ethambutol and pyrazinamide with sensitivities of 100%, 100%, 100% and 93.8%, respectively, and susceptibility to these drugs with specificities of 99.6%, 100%, 98.5% and 100%, respectively. Performance of the LPA was poorer, with sensitivity of 83.3% for rifampicin and 85.7% for isoniazid resistance. Five isolates were classified as susceptible according to phenotypic DST (1 for rifampicin, 4 for ethambutol) while WGS detected resistance mutations in rpoB and embB genes. WGS, used under appropriate quality-control conditions, has good performance to predict the resistance profile for the four first-line drugs and can correct phenotypic DST results. This study highlights the need for future guidelines recommending WGS as the initial tool in routine practice in areas where the prevalences of TB and drug-resistant MTB are low.