The Relative Positioning of Genotyping and Phenotyping for Tuberculosis Resistance Screening in Two EU National Reference Laboratories in 2023.

The routine use of whole genome sequencing (WGS) as a reference typing technique for epidemiology combined with the catalogued and extensive knowledge base of resistance-associated mutations means an initial susceptibility prediction can be derived from all cultured isolates in our laboratories based on WGS data alone. Preliminary work has confirmed, in our low-burden settings, these predictions are for first-line drugs, reproducible, robust with an accuracy similar to phenotypic drug susceptibility testing (pDST) and in many cases able to also predict the level of resistance (MIC). Routine screening for drug resistance by WGS results in approximately 80% of the isolates received being predicted as fully susceptible to the first-line drugs.

WGS more accurately predicts susceptibility of Mycobacterium tuberculosis to first-line drugs than phenotypic testing.

Background: Drug-susceptibility testing (DST) of Mycobacterium tuberculosis complex (MTBC) isolates by the Mycobacteria Growth Indicator Tube (MGIT) approach is the most widely applied reference standard. However, the use of WGS is increasing in many developed countries to detect resistance and predict susceptibility. We investigated the reliability of WGS in predicting drug susceptibility, and analysed the discrepancies between WGS and MGIT against the first-line drugs rifampicin, isoniazid, ethambutol and pyrazinamide.

Cross border, highly individualised treatment of a patient with challenging extensively drug-resistant tuberculosis.

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Pyrazinamide resistance-conferring mutations in pncA and the transmission of multidrug resistant TB in Georgia.

Background: The ongoing epidemic of multidrug-resistant tuberculosis (MDR-TB) in Georgia highlights the need for more effective control strategies. A new regimen to treat MDR-TB that includes pyrazinamide (PZA) is currently being evaluated and PZA resistance status will largely influence the success of current and future treatment strategies. PZA susceptibility testing was not routinely performed at the National Reference Laboratory (NRL) in Tbilisi between 2010 and September 2015.

Utility of rpoB gene sequencing for identification of nontuberculous mycobacteria in the Netherlands.

In the Netherlands, clinical isolation of nontuberculous mycobacteria (NTM) has increased over the past decade. Proper identification of isolates is important, as NTM species differ strongly in clinical relevance. Most of the currently applied identification methods cannot distinguish between all different Mycobacterium species and complexes within species.

Combined species identification, genotyping, and drug resistance detection of Mycobacterium tuberculosis cultures by MLPA on a bead-based array.

The population structure of Mycobacterium tuberculosis is typically clonal therefore genotypic lineages can be unequivocally identified by characteristic markers such as mutations or genomic deletions. In addition, drug resistance is mainly mediated by mutations. These issues make multiplexed detection of selected mutations potentially a very powerful tool to characterise Mycobacterium tuberculosis.

Comparative study on genotypic and phenotypic second-line drug resistance testing of Mycobacterium tuberculosis complex isolates.

The mycobacterium growth indicator tube (MGIT960) automated liquid medium testing method is becoming the international gold standard for second-line drug susceptibility testing of multidrug- and extensively drug-resistant Mycobacterium tuberculosis complex isolates. We performed a comparative study of the current gold standard in the Netherlands, the Middlebrook 7H10 agar dilution method, the MGIT960 system, and the GenoType MTBDRsl genotypic method for rapid screening of aminoglycoside and fluoroquinolone resistance. We selected 28 clinical multidrug- and extensively drug-resistant M.

Clinical relevance of Mycobacterium chelonae-abscessus group isolation in 95 patients.

Objectives: To determine the clinical relevance of Mycobacterium chelonae-abscessus group isolation from clinical samples.

Methods: We retrospectively reviewed medical files of all patients from whom these mycobacteria were isolated between January 1999 and January 2005 and re-identified the isolates by rpoB sequencing. We applied the American Thoracic Society (ATS) diagnostic criteria to establish clinical relevance.

Mycobacterium mantenii sp. nov., a pathogenic, slowly growing, scotochromogenic species.

Slowly growing, scotochromogenic bacteria of a novel Mycobacterium species were isolated from lymph node samples in two children and pulmonary samples in two elderly patients from different regions in the Netherlands as well as from a surface water sample in Zambia. Its 16S rRNA gene, 16S-23S internal transcribed spacer (ITS), hsp65 and rpoB gene sequences are unique in comparison with other mycobacteria. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that these micro-organisms are most closely related to Mycobacterium scrofulaceum ATCC 19981(T) (8 differences; 0.

Region of difference 1 in nontuberculous Mycobacterium species adds a phylogenetic and taxonomical character.

The esat-6 and cfp-10 genes are essential for virulence in Mycobacterium tuberculosis. Among nontuberculous mycobacteria, we found these genes only in M. kansasii, M.

Mycobacterium riyadhense sp. nov., a non-tuberculous species identified as Mycobacterium tuberculosis complex by a commercial line-probe assay.

A non-chromogenic, slowly growing Mycobacterium strain was isolated from a maxillary sinus lavage from a symptomatic patient in Riyadh, Saudi Arabia. It was initially identified as a member of the Mycobacterium tuberculosis complex by a commercial line-probe assay. Its 16S rRNA, hsp65 and rpoB gene and 16S-23S internal transcribed spacer sequences were unique; phylogenetic analysis based on the 16S rRNA gene sequence groups this organism close to Mycobacterium szulgai and Mycobacterium malmoense.