Utility of the Whole Genome Sequencing based methodologies in routine European tuberculosis reference laboratory network setting.

This study aims to gather observational evidence of Whole Genome Sequencing's (WGS) impact in the pathogen identification, antimicrobial resistance profiling and transmission tracking from its users' observation within the diagnostic setting of the European reference laboratories for tuberculosis. Sixteen laboratories that have been utilising WGS in their tuberculosis diagnostic laboratory were invited and twelve (75%) responded to our online questionnaire. Key findings include its primary utilisation for drug resistance prediction and epidemiological services; Mtb surveillance and outbreak investigation. 92% reported significant improvements to the performance of TB drug resistance testing and the reduction of false clustering. Despite the public health benefits of the WGS technology was largely positive in non-tuberculous mycobacteria disease management, multidrug-resistant TB patient management, reputational aspects and turnaround times, further studies are required to review the financial impact as various regulations and service aspects have added to the complexity to disentangle this aspect.

Non-commercial phenotypic assays for the detection of Mycobacterium tuberculosis drug resistance: a systematic review.

Several rapid non-commercial culture-based methods and assays for drug susceptibility testing (DST) of Mycobacterium tuberculosis have emerged over the last decades. The aim of the current review was to summarise evidence on the performance of microscopic observation of drug susceptibility (MODS), thin-layer agar (TLA) and colorimetric redox-indicator (CRI) assays for detection of resistance to first- and second-line anti-tuberculosis (TB) drugs. Forty-three publications satisfying selection criteria were selected for data extraction. MODS and CRI assays demonstrated pooled sensitivity and specificity of > 93% for the detection of resistance to rifampicin and isoniazid and confirmed their utility for an accurate detection of multidrug-resistant TB (MDR-TB) in various settings. Sensitivity and specificity values for indirect DST for ethambutol (EMB) using CRI assays were 94.0% and 82.0%, respectively, suggesting that CRIs could be used to rule out resistance to EMB. Performance for other drugs varied more substantially across the reports. There was no sufficient evidence on the performance of the TLA assay for making any conclusion on its utility for DST. Our data suggests that non-commercial assays could be used for a rapid and accurate DST in settings where the use of commercial World Health Organization-endorsed assays could be limited due to a variety of reasons including limited resources, laboratory facilities or trained personnel. While inexpensive and easy-to-perform MODS and TLA assays can be used in low-income settings, using CRI assays for determination of minimal inhibitory concentrations may be implemented in middle- and high-income countries with high MDR-TB burden to guide clinical management of TB patients.

Novel external quality assurance scheme for drug susceptibility testing of non-tuberculous mycobacteria: a multicentre pilot study.

OBJECTIVES: Our aim was to conduct a multicentre study involving laboratories participating in the European TB Reference Laboratory Network aiming to develop a pilot external quality assessment (EQA) scheme for drug susceptibility testing (DST) of non-tuberculous mycobacteria (NTM). METHODS: The study comprised a survey using a structured questionnaire followed by a pilot EQA round using identical panels of 10 Mycobacterium avium (MAV) and Mycobacterium abscessus (MAB) isolates. EQA results were received from 16 laboratories utilizing the broth microdilution method. Consensus modal MIC values were determined, and essential and categorical agreement rates were calculated. RESULTS: Twenty-four out of 31 laboratories (77.4%) reported DST for NTM routinely. Essential agreement ranged from 78.8% (amikacin) to 96.2% (linezolid) for MAV and from 76.0% (amikacin) to 100% (doxycycline) for MAB. Categorical agreement ranged from 56.8% (moxifloxacin) to 100% (clarithromycin) for MAV and from 53.6% (linezolid) to 100% (doxycycline) for MAB. CONCLUSIONS: Our results show that interlaboratory reproducibility of DST for NTM is insufficient, highlighting the need for expanding EQA schemes. As EQAs for Mycobacterium tuberculosis complex have led to more reliable and reproducible DST, we propose to follow a similar approach for clinically relevant NTM.