Abstract
Infections caused by non-tuberculous mycobacteria (NTM) have been a public health problem in recent decades and contribute significantly to the clinical and economic burden globally. The diagnosis of infections is difficult and time-consuming and, in addition, the conventional diagnostics tests do not have sufficient discrimination power in species identification due to cross-reactions and not fully specific probes. However, technological advances have been made and the whole genome sequencing (WGS) method has been shown to be an essential part of routine diagnostics in clinical mycobacteriology laboratories. The use of this technology has contributed to the characterization of new species of mycobacteria, as well as the identification of gene mutations encoding resistance and virulence factors. Sequencing data also allowed to track global outbreaks of nosocomial NTM infections caused by M. abscessus complex and M. chimaera. To highlight the utility of WGS, we summarize recent scientific studies on WGS as a tool suitable for the management of NTM-induced infections in clinical practice.
Highlights
Infections caused by Non-tuberculous mycobacteria (NTM) have risen rapidly in recent decades, and in many developed countries, the number of cases has exceeded the incidence of pulmonary tuberculosis [5]
whole genome sequencing (WGS) technology is currently not available in all clinical settings, the purchase price is gradually reduced, and in some reference mycobacteriological laboratories this method is implemented into routine practice for identification of mycobacteria and genotypic drug susceptibility testing of M. tuberculosis [24]. In this mini-review, we summarize the latest scientific publications focused on WGS
Accurate diagnosis of NTM is crucial in patients with structural or inflammatory lung disease such as CF, non-cystic fibrosis bronchiectasis, or chronic obstructive pulmonary disease, as these emerging pathogens cause an accelerated decline in lung function and do not respond to aggressive antibiotic treatment in up to 50% of cases [37]
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Hendrix et al combined Illumina and MinION sequencing for whole-genome assembling of M. kubicae isolates Their results have provided detailed information regarding the resistance, virulence and persistence encoded on the chromosome or plasmids of these rare, clinically important pulmonary disease-causing. Lipworth et al used sequencing data obtained from M. abscessus species for the identification of new mutations in erm and rrs genes potentially associated with macrolide antibiotic resistance These mutations are not currently included in traditional genotyping tests (such as GenoType NTM-DR; Hain Lifescience, Nehren, Germany) which may show false-negative results [76]. A recent WGS study involving a global collection of M. abscessus complex isolates revealed a 10% higher frequency of mutations in the rrl gene encoding macrolide resistance in M. massiliense compared to. Dedrick et al used WGS for a better understanding of phage resistance mechanisms of M. abscessus [81]
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