Role of the first WHO mutation catalogue in the diagnosis of antibiotic resistance in Mycobacterium tuberculosis in the Valencia Region, Spain: a retrospective genomic analysis.

Data de publicació: 01/01/2024 Data Ahead of Print: 04/12/2023

Autors de IIS La Fe

Ana Gil Brusola

Autor
José Luis López Hontangas

Autor

Autors aliens a IIS La Fe

Garcia-Marin, Ana Maria
Cancino-Munoz, Irving
Torres-Puente, Manuela
Villamayor, Luis M
Borras, Rafael
Borras-Manez, Maria
Bosque, Montserrat
Camarena, Juan J
Colomer-Roig, Ester
Colomina, Javier
Escribano, Isabel
Esparcia-Rodriguez, Oscar
Gimeno, Concepcion
Gimeno-Gascon, Adelina
Gomila-Sard, Barbara
Gonzalez-Granda, Damiana
Gonzalo-Jimenez, Nieves
Guna-Serrano, Maria Remedio
Martin-Gonzalez, Coral
Moreno-Munoz, Rosario
Navarro, David
Navarro, Maria
Orta, Nieves
Perez, Elvira
Prat, Josep
Rodriguez, Juan Carlos
Ruiz-Garcia, Maria Montserrat
Vanaclocha, Hermelinda
Gonzalez-Candelas, Fernando
Furio, Victoria
Comas, Inaki
Valencia Region Tuberculosis Working Group

Grups d'Investigació

Infección Grave

Investigador Principal

María Ángeles Tormo Mas

Abstract

BACKGROUND: In June, 2021, WHO published the most complete catalogue to date of resistance-conferring mutations in Mycobacterium tuberculosis. Here, we aimed to assess the performance of genome-based antimicrobial resistance prediction using the catalogue and its potential for improving diagnostics in a real low-burden setting. METHODS: In this retrospective population-based genomic study M tuberculosis isolates were collected from 25 clinical laboratories in the low-burden setting of the Valencia Region, Spain. Culture-positive tuberculosis cases reported by regional public health authorities between Jan 1, 2014, and Dec 31, 2016, were included. The drug resistance profiles of these isolates were predicted by the genomic identification, via whole-genome sequencing (WGS), of the high-confidence resistance-causing variants included in the catalogue and compared with the phenotype. We determined the minimum inhibitory concentration (MIC) of the isolates with discordant resistance profiles using the resazurin microtitre assay. FINDINGS: WGS was performed on 785 M tuberculosis complex culture-positive isolates, and the WGS resistance prediction sensitivities were: 85·4% (95% CI 70·8-94·4) for isoniazid, 73·3% (44·9-92·2) for rifampicin, 50·0% (21·1-78·9) for ethambutol, and 57·1% (34·0-78·2) for pyrazinamide; all specificities were more than 99·6%. Sensitivity values were lower than previously reported, but the overall pan-susceptibility accuracy was 96·4%. Genotypic analysis revealed that four phenotypically susceptible isolates carried mutations (rpoB Leu430Pro and rpoB Ile491Phe for rifampicin and fabG1 Leu203Leu for isoniazid) known to give borderline resistance in standard phenotypic tests. Additionally, we identified three putative resistance-associated mutations (inhA Ser94Ala, katG Leu48Pro, and katG Gly273Arg for isoniazid) in samples with substantially higher MICs than those of susceptible isolates. Combining both genomic and phenotypic data, in accordance with the WHO diagnostic guidelines, we could detect two new multidrug-resistant cases. Additionally, we detected 11 (1·6%) of 706 isolates to be monoresistant to fluoroquinolone, which had been previously undetected. INTERPRETATION: We showed that the WHO catalogue enables the detection of resistant cases missed in phenotypic testing in a low-burden region, thus allowing for better patient-tailored treatment. We also identified mutations not included in the catalogue, relevant at the local level. Evidence from this study, together with future updates of the catalogue, will probably lead in the future to the partial replacement of culture testing with WGS-based drug susceptibility testing in our setting. FUNDING: European Research Council and the Spanish Ministerio de Ciencia.