Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study

BACKGROUND

Whole-genome sequencing (WGS) of Mycobacterium tuberculosis complex has become an important tool in diagnosis and management of drug-resistant tuberculosis. However, data correlating resistance genotype with quantitative phenotypic antimicrobial susceptibility testing (AST) are scarce.

METHODS

In a prospective multicentre observational study, 900 clinical M tuberculosis complex isolates were collected from adults with drug-resistant tuberculosis in five high-endemic tuberculosis settings around the world (Georgia, Moldova, Peru, South Africa, and Viet Nam) between Dec 5, 2014, and Dec 12, 2017. Minimum inhibitory concentrations (MICs) and resulting binary phenotypic AST results for up to nine antituberculosis drugs were determined and correlated with resistance-conferring mutations identified by WGS.

FINDINGS

Considering WHO-endorsed critical concentrations as reference, WGS had high accuracy for prediction of resistance to isoniazid (sensitivity 98·8% [95% CI 98·5-99·0]; specificity 96·6% [95% CI 95·2-97·9]), levofloxacin (sensitivity 94·8% [93·3-97·6]; specificity 97·1% [96·7-97·6]), kanamycin (sensitivity 96·1% [95·4-96·8]; specificity 95·0% [94·4-95·7]), amikacin (sensitivity 97·2% [96·4-98·1]; specificity 98·6% [98·3-98·9]), and capreomycin (sensitivity 93·1% [90·0-96·3]; specificity 98·3% [98·0-98·7]). For rifampicin, pyrazinamide, and ethambutol, the specificity of resistance prediction was suboptimal (64·0% [61·0-67·1], 83·8% [81·0-86·5], and 40·1% [37·4-42·9], respectively). Specificity for rifampicin increased to 83·9% when borderline mutations with MICs overlapping with the critical concentration were excluded. Consequently, we highlighted mutations in M tuberculosis complex isolates that are often falsely identified as susceptible by phenotypic AST, and we identified potential novel resistance-conferring mutations.

INTERPRETATION

The combined analysis of mutations and quantitative phenotypes shows the potential of WGS to produce a refined interpretation of resistance, which is needed for individualised therapy, and eventually could allow differential drug dosing. However, variability of MIC data for some M tuberculosis complex isolates carrying identical mutations also reveals limitations of our understanding of the genotype and phenotype relationships (eg, including epistasis and strain genetic background).

FUNDING

Bill & Melinda Gates Foundation, German Centre for Infection Research, German Research Foundation, Excellence Cluster Precision Medicine of Inflammation (EXC 2167), and Leibniz ScienceCampus EvoLUNG.

Malignant peripheral nerve sheath tumour presenting as a pneumothorax

Malignant peripheral nerve sheath tumours are rare and aggressive soft-tissue sarcomas of ectomesenchymal origin. These tumours commonly occur in patients with neurofibromatosis Type 1 with a cumulative lifetime risk of 10%. The vast majority of cases present with clinical evidence of a soft-tissue mass with or without features of nerve irritation and loss of function arising from the lesion of origin. The primary presentation of a malignant peripheral nerve sheath tumour with a pneumothorax in the absence of widespread metastatic disease in a patient with no medical or family history of neurofibromatosis has never been reported in the literature. We present a unique case of a systemically well 34-year-old male who presented with clinical evidence of a right-sided pneumothorax. The chest radiograph identified the right-sided pneumothorax and revealed an apical pleural mass that was confirmed by intravenous contrast-enhanced CT of the thorax. The patient was referred for video-assisted thorascopic surgical pleurodesis and biopsy of the lesion. Histopathology analyses confirmed the diagnosis of malignant peripheral nerve sheath tumour. To the best of our knowledge, no such case reports have been published in the literature. A diagnosis of malignant peripheral nerve sheath tumour should be considered as one of the rarer possibilities in patients presenting with pneumothoraces in association with apical pleural lesions.