The Future of TB Resistance Diagnosis: The Essentials on Whole Genome Sequencing and Rapid Testing Methods

Abstract

Tuberculosis resistance diagnostics have vastly improved in recent years thanks to the development of standardised phenotypic and molecular testing methods. However, these methods are either slow or limited in the number of resistant genotypes they can detect. With the advent of next-generation sequencing (NGS) we can sidestep all those problems, as we can sequence whole tuberculosis genomes at increasingly smaller costs and requiring less and less DNA. In this review, we explain how accumulated knowledge in the field has allowed us to go from phenotypic testing to molecular methods to Whole Genome Sequencing (WGS) for resistance diagnostics. We compare current diagnostic methods with WGS as to their efficacy in detecting resistant cases, and show how forthcoming advances in NGS technologies will be crucial in widespread implementation of WGS as a diagnostic tool. ResumenEl diagnóstico de la tuberculosis resistente ha mejorado ampliamente en los últimos años gracias al desarrollo de pruebas estandarizadas de diagnóstico tanto fenotípicas como moleculares. Sin embargo, estas pruebas son o bien lentas o limitadas en el número de genotipos resistentes que son capaces de detectar. Con el auge de las nuevas tecnologías de secuenciación masiva podemos evitar esos problemas secuenciando el genoma completo cada vez a un coste más bajo y requiriendo cantidades menores de ADN. En esta revisión, explicamos cómo se ha podido progresar desde las pruebas fenotípicas a los métodos moleculares hasta la secuenciación de genoma completo para el diagnóstico de resistencias gracias a sucesivos descubrimientos en el campo. Comparamos la eficacia de la secuenciación de genoma completo para detectar casos resistentes con respecto a la de los métodos diagnósticos actuales , y mostramos cómo los avances futuros en esta tecnología serán cruciales para la implementación generalizada de esta herramienta diagnóstica.

An evolutionary functional genomics approach identifies novel candidate regions involved in isoniazid resistance in Mycobacterium tuberculosis

“…Most of what we know of tuberculosis drug resistance comes from genetic association studies in which a particular mutation is associated with a specific resistance phenotype 4 . We now have large databases of diagnostic mutations with which we can reliably predict the resistance phenotype of our strain when we determine its genomic sequence 5 . For instance, we can detect rifampicin resistance with a 92% sensitivity, but the figure drops to 87% for isoniazid and 58% for ethambutol 6 .…”

Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Drug Resistance: A Retrospective Observational Study in Eastern China

“…It covers the most common anti-TB drugs and provides timely detection results. Therefore, WGS has the potential for the rapid detection of drug-resistant MTB strains, leading to more anti-TB drugs and supporting TB treatment [ 20 ]. Based on the progress in WGS, the WHO has selected a series of genetic mutations to predict drug resistance.…”

Evaluation of whole-genome sequence to predict drug resistance of nine anti-tuberculosis drugs and characterize resistance genes in clinical rifampicin-resistant Mycobacterium tuberculosis isolates from Ningbo, China

“…It is well known that the inh A c-15t mutation is associated with PTO resistance ( 37 ). We found that fab G1 t-8c and eth A genes mutation were most prevalent, and that no isolates harbored an inh A mutation in our study.…”