Phylogenomic and genomic analysis reveals unique and shared genetic signatures of complex species.

Species belonging to the complex (MKC) are frequently isolated from humans and the environment and can cause serious diseases. The most common MKC infections are caused by the species (), leading to tuberculosis-like disease. However, a broad spectrum of virulence, antimicrobial resistance and pathogenicity of these non-tuberculous mycobacteria (NTM) are observed across the MKC.

Drug-Resistant Tuberculosis on the Balkan Peninsula: Determination of Drug Resistance Mechanisms with Xpert MTB/XDR and Whole-Genome Sequencing Analysis.

The new molecular assay Xpert MTB/XDR (Cepheid, Sunnyvale, CA, USA) was launched in 2021 to detect Mycobacterium tuberculosis (MT) complex with mutations conferring resistance to isoniazid (INH), ethionamide (ETH), fluoroquinolone (FQ), and second-line injectable drugs (SLIDs). The aim of our study was to evaluate the performance of the Xpert MTB/XDR rapid molecular assay on rifampicin-resistant, multidrug-resistant, and pre-extensively resistant tuberculosis (TB) isolates in a clinical laboratory in the Balkan Peninsula compared to a phenotypic drug susceptibility test (pDST). Xpert MTB/XDR was used to test positive Bactec MGIT 960 (Becton, Dickinson and Co.

Next-generation sequencing to characterise pyrazinamide resistance in Mycobacterium tuberculosis isolates from two Balkan countries.

Objectives: Next-generation sequencing (NGS) can provide a comprehensive analysis of the genetic alterations most commonly linked with pyrazinamide (PZA) resistance. However, there are no studies reporting the molecular background of PZA resistance in Mycobacterium tuberculosis (TB) isolates from the Balkan Peninsula. We aimed to examine the feasibility of full-length analysis of a gene linked with PZA resistance (pncA) using Ion Torrent technology compared with phenotypic BACTEC MGIT 960 drug susceptibility testing (DST) in clinical TB isolates from two countries of the Balkan Peninsula.

Subspecies-specific sequence detection for differentiation of Mycobacterium abscessus complex.

Mycobacterium abscessus complex (MABC) is a taxonomic group of rapidly growing, nontuberculous mycobacteria that are found as etiologic agents of various types of infections. They are considered as emerging human pathogens. MABC consists of 3 subspecies-M.

Nationwide analysis of Mycobacterium chimaera and Mycobacterium intracellulare isolates: Frequency, clinical importance, and molecular and phenotypic resistance profiles.

The burden of tuberculosis (TB) in Slovenia is low due to good ongoing preventive measures. However, analysis of data obtained from the Registry for Tuberculosis and National Reference Laboratory for Mycobacteria at University Clinic of Respiratory and Allergic Diseases Golnik from January 2000 to December 2017 revealed that the number of nontuberculous mycobacterial (NTM) isolates is increasing. A group of slowly growing NTM and a common cause of NTM disease among humans is the Mycobacterium avium complex, the taxonomy of which is rapidly changing.

Genomic Insights Into the Complex: An Update.

Only very recently, has it been proposed that the hitherto existing subtypes (I-VI) should be elevated, each, to a species rank. Consequently, the former subtypes have been denominated as (former type I), (II), (III), (V), and (VI). The present work extends the recently published findings by using a three-pronged computational strategy, based on the alignment fraction-average nucleotide identity, genome-to-genome distance, and core-genome phylogeny, yet essentially independent and much larger sample, and thus delivers a more refined and complete picture of the complex.

Prospective genotyping of Mycobacterium tuberculosis from fresh clinical samples.

Shorter time-to-result is key for improving molecular-guided epidemiological investigation of tuberculosis (TB) cases. We performed a prospective study to evaluate the use of standardized MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat) typing of Mycobacterium tuberculosis directly on 79 fresh clinical samples from 26 TB patients consecutively enrolled over a 17-month period. Overall, complete 24-locus types were obtained for 18 out of the 26 (69.

Inventory study of non-tuberculous mycobacteria in the European Union.

Background: Since non-tuberculous mycobacteria (NTM) disease is not notifiable in most European Union (EU) and European Economic Area (EEA) countries, the epidemiological situation of the >150 NTM species is largely unknown. We aimed to collect data on the frequency of NTM detection and NTM species types in EU/EEA countries.

Methods: Officially nominated national tuberculosis reference laboratories of all EU/EEA countries were asked to provide information on: laboratory routines for detection and identification of NTM, including drug sensitivity testing (DST) methods; data on the number and type of NTM species identified; coverage and completeness of the provided data on NTM; type and number of human specimens tested for NTM; and number of specimens tested for Mycobacterium tuberculosis complex and NTM.

One year nationwide evaluation of 24-locus MIRU-VNTR genotyping on Slovenian Mycobacterium tuberculosis isolates.

Background: Slovenia is one of the few countries where IS6110 RFLP is applied for genotyping M. tuberculosis at a nationwide level, which has been in effect since 2000. Based on S6110 RFLP clustering, typical risk factors and routes of M.

The First Report of Mycobacterium celatum Isolation from Domestic Pig (Sus scrofa domestica) and Roe Deer (Capreolus capreolus) and an Overview of Human Infections in Slovenia.

Mycobacterium celatum, a slowly growing potentially pathogenic mycobacterium first described in humans, is regarded as an uncommon cause of human infection, though capable of inducing invasive disease in immunocompromised hosts. According to some reports, a serious disease due to M. celatum may also occur in individuals with no apparent immunodeficiency.

Delayed diagnosis of Mycobacterium marinum infection: A case report and review of the literature.

Mycobacterium marinum infection is the most common atypical skin mycobacterial infection of increasing importance. It results from skin injury and contact with contaminated aquarium water, fish, or shellfish; it is only rarely related to swimming pool sources nowadays. Diagnosis should be confirmed by isolation and identification of the organism; however, this gold standard is difficult to achieve in practice.

IS1245 RFLP-based genotyping study of Mycobacterium avium subsp. hominissuis isolates from pigs and humans.

Mycobacterium avium subsp. hominissuis, ubiquitous environmental mycobacterium, is an opportunistic pathogen that is regularly isolated from pigs and humans in Slovenia. Genetic diversity of 114 isolates from pigs (n = 57) and humans (n = 57), identified by means of bacteriology, DNA-RNA hybridization techniques, IS901 PCR and IS1245 PCR, was investigated in this study, using IS1245 restriction fragment length polymorphism (RFLP) analysis.

Transmission of Mycobacterium tuberculosis from human to cattle.

We describe the first transmission of Mycobacterium tuberculosis from human to cattle confirmed by molecular typing of isolates involved in the transmission. IS6110-based restriction fragment length polymorphism analysis showed that the isolates from the cattle and farm worker who suffered from pulmonary tuberculosis 1 year prior to this case were the same strains.

Molecular fingerprinting of Mycobacterium bovis subsp. caprae isolates from central Europe.

To study the dissemination of Mycobacterium bovis subsp. caprae, 79 European isolates from cattle, humans, and other hosts were examined by spoligotyping and IS6110 restriction fragment length polymorphism (RFLP) analysis. Among a total of 11 different spoligotypes identified, type C1 proved to be predominant (n = 62).

Molecular epidemiology of tuberculosis in Slovenia: results of a one-year (2001) nation-wide study.

Slovenia is a small Central European country with a population of 1.99 million and an incidence of tuberculosis (TB) of 18.6 per 100,000 inhabitants in 2001.