Nontuberculous mycobacteria (NTM) are ubiquitous organisms in all natural ecosystems, including water environments. Several of these species are potential pathogens which affect human health. NTM most commonly cause pulmonary, skin or soft tissue infections. Primary sludge obtained from the water treatment plants of four drinking water reservoirs were subjected to analysis for mycobacteria. Five decontamination methods (5% oxalic acid, modified Petroff, HCl-NaOH, N-acetyl-L-cysteine-sodium hydroxide and 0.05% cetylpyridinium chloride), three growth media (Herrold's egg yolk medium with and without the antibiotic cocktail PANTA and Löwenstein-Jensen medium with sodium pyruvate) and three incubation temperatures (25, 30 and 37 °C) for isolation of mycobacteria were compared in the analysis of 18 sludge samples. To evaluate examined methods, the overall positive, negative, and contamination rate, and these rates in respect to localities are taken into account. Statistical analysis demonstrated that the best combination for the recovery of mycobacteria with the minimum number of contaminating microorganisms is 5% oxalic acid decontamination cultured on Herrold's egg yolk medium with the antibiotic cocktail PANTA at 25 °C. The least suitable is N-acetyl-L-cysteine-sodium hydroxide decontamination cultured on Löwenstein-Jensen medium with sodium pyruvate at 25 °C. From 18 sludge samples we isolated 27 mycobacterial species or groups; Mycobacterium algericum, M. arabiense, M. heraklionense, M. minnesotense, M. moriokaense, M. salmoniphilum and M. vulneris were isolated from the natural water environment for the first time. Because the natural water environment is the main source of potentially pathogenic mycobacteria for humans, it is important to direct particular focus to newly described mycobacterial species.

• MeSH
• bakteriologické techniky metody   MeSH
• čištění vody přístrojové vybavení   metody   MeSH
• dekontaminace metody   MeSH
• kultivační média analýza   metabolismus   MeSH
• Mycobacterium genetika   růst a vývoj   izolace a purifikace   MeSH
• odpadní vody mikrobiologie   MeSH
• sladká voda mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• kultivační média MeSH
• odpadní vody MeSH

Small RNAs (sRNAs) are molecules essential for a number of regulatory processes in the bacterial cell. Here we characterize Ms1, a sRNA that is highly expressed in Mycobacterium smegmatis during stationary phase of growth. By glycerol gradient ultracentrifugation, RNA binding assay, and RNA co-immunoprecipitation, we show that Ms1 interacts with the RNA polymerase (RNAP) core that is free of the primary sigma factor (σA) or any other σ factor. This contrasts with the situation in most other species where it is 6S RNA that interacts with RNAP and this interaction requires the presence of σA. The difference in the interaction of the two types of sRNAs (Ms1 or 6S RNA) with RNAP possibly reflects the difference in the composition of the transcriptional machinery between mycobacteria and other species. Unlike Escherichia coli, stationary phase M. smegmatis cells contain relatively few RNAP molecules in complex with σA. Thus, Ms1 represents a novel type of small RNAs interacting with RNAP.

• MeSH
• bakteriální chromozomy MeSH
• DNA řízené RNA-polymerasy metabolismus   MeSH
• konformace nukleové kyseliny MeSH
• malá nekódující RNA chemie   genetika   metabolismus   MeSH
• Mycobacterium smegmatis enzymologie   genetika   růst a vývoj   MeSH
• Mycobacterium genetika   MeSH
• sigma faktor metabolismus   MeSH
• syntenie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA řízené RNA-polymerasy MeSH
• malá nekódující RNA MeSH
• sigma faktor MeSH

STUDY OBJECTIVE: Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has recently been widely used in diagnostic microbiological laboratories. It is a cheap and rapid method for the identification of bacteria and micromycetes. Apart from this purpose, it is also used for the detection of antibiotic resistance mechanisms. It has the potential to be extended for other purposes in microbiology. The aim of this study was to validate MALDI-TOF MS for the identification of mycobacteria. MATERIAL AND METHODS: Thirty isolates of Mycobacterium spp. isolated in the Laboratory of Mycobacteriology of the Plzeň University Hospital were included in the study. The isolates were identified to the species level using biochemical tests, gene probes, and sequencing of the gene encoding 16S rRNA. The identification by MALDI-TOF MS was performed with the use of silica beads. Strain identification by sequencing the gene encoding 16S rRNA was considered as the reference method. RESULTS: MALDI-TOF MS correctly identified all isolates of Mycobacterium spp. (score range 1.461 - 2.168). The species identified were Mycobacterium tuberculosis (n= 5), Mycobacterium kansasii (n=5), Mycobacterium avium (n=6), Mycobacterium intracelullare (n=3), Mycobacterium xenopi (n=3), Mycobacterium gordonae (n=1), Mycobacterium abscessus (n=1), Mycobacterium kumamotonense (n=2), Mycobacterium mantenii (n=1), Mycobacterium lentiflavum (n=1), Mycobacterium fortuitum (n=1), and Mycobacterium scrofulaceum (n=1). CONCLUSION: MALDI-TOF MS is a suitable tool for the routine identification of Mycobacterium spp. in laboratories using this method for the conventional identification of microbes.

• MeSH
• lidé MeSH
• Mycobacterium chemie   klasifikace   genetika   izolace a purifikace   MeSH
• mykobakteriózy mikrobiologie   MeSH
• RNA ribozomální 16S genetika   MeSH
• spektrometrie hmotnostní - ionizace laserem za účasti matrice metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• Názvy látek
• RNA ribozomální 16S MeSH

The environment is a reservoir of nontuberculous mycobacteria and is considered a source of infection for animals and humans. Mycobacteria can persist in different types of environments for a relatively long time. We have studied their possible internalization into plant tissue through intact, as well as damaged, root systems of different types of plants grown in vitro and under field conditions. The substrate into which plants were seeded was previously contaminated with different strains of Mycobacterium avium (10(8) to 10(10) cells/g of soil) and feces from animals with paratuberculosis. We detected M. avium subsp. avium, hominissuis, and paratuberculosis in the stems and leaves of the plants by both culture and real-time quantitative PCR. The presence of mycobacteria in the plant tissues was confirmed by microscopy. The concentration of mycobacteria found inside plant tissue was several orders of magnitude lower (up to 10(4) cells/g of tissue) than the initial concentration of mycobacteria present in the culture medium or substrate. These findings led us to the hypothesis that plants may play a role in the spread and transmission of mycobacteria to other organisms in the environment.

• MeSH
• bakteriologické techniky MeSH
• endocytóza * MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• listy rostlin mikrobiologie   MeSH
• mikroskopie MeSH
• Mycobacterium genetika   růst a vývoj   fyziologie   MeSH
• rostliny mikrobiologie   MeSH
• stonky rostlin mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Nontuberculous mycobacteria (NTM) are ubiquitous organisms of a wide variety of environmental reservoirs, including natural and municipal water, soil, aerosols, protozoans, animals and humans. Several of these species are potential pathogens which affect human health. The aim of this study was to determine the occurrence of NTM in the water environment. Samples were taken from 13 water-related facilities including fish ponds, storage ponds, drinking water reservoirs and an experimental recirculation system. Altogether, 396 samples of water, sediment and aquatic plants were collected and analysed. All samples were examined using conventional culture methods. Suspected microbial isolates were subjected to polymerase chain reaction analysis and identified using partial sequence analysis of the 16S rDNA gene. The culture revealed 94/396 samples (23.7%) that contained mycobacteria. Among known NTM we identified potentially pathogenic mycobacteria isolated from the fresh water environment for the first time: Mycobacterium asiaticum, M. chimaera, M. interjectum, M. kumamotonense, M. lentiflavum, M. montefiorense, M. nebraskense, M. paraffinicum and M. simiae. Epidemiologic studies suggest that the natural water environment is the principal source of human exposure. Our results indicate that besides the well-known potentially pathogenic mycobacteria it is important to observe occurrence, proliferation and persistence of newly discovered mycobacterial species.

• MeSH
• mikrobiota MeSH
• Mycobacterium genetika   izolace a purifikace   MeSH
• pitná voda mikrobiologie   MeSH
• polymerázová řetězová reakce MeSH
• RNA ribozomální 16S genetika   metabolismus   MeSH
• roční období MeSH
• sekvenční analýza DNA MeSH
• sladká voda mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• pitná voda MeSH
• RNA ribozomální 16S MeSH

A survey of the occurrence of mycobacteria was conducted from 717 freshwater fish (25 species) in two water reservoirs, five ponds and two farms in the Czech Republic. A total of 2182 tissue samples from these fish were examined using the conventional culture method. Thirteen mycobacterial isolates were obtained from 12 (1.7%) fish belonging to nine species. Isolates were identified using sequence analysis of the 16SrRNA gene as: Mycobacterium algericum, M. fortuitum, M. gordonae, M. insubricum, M. kumamotonense, M. nonchromogenicum, two isolates of M. peregrinum, M. terrae and M. triplex. Mycobacteria were isolated more frequently from fish skin and gills than from internal organs or muscles.

• MeSH
• Mycobacterium * genetika   izolace a purifikace   MeSH
• mykobakteriózy epidemiologie   veterinární   MeSH
• nemoci ryb epidemiologie   mikrobiologie   MeSH
• prevalence MeSH
• RNA ribozomální 16S genetika   MeSH
• rybníky MeSH
• ryby MeSH
• sladká voda * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• RNA ribozomální 16S MeSH

The isolation of potentially pathogenic mycobacteria (PPM) from clinical specimens has become very frequent in the last years. Such organisms are typically environmental and occasionally pathogenic for humans. Standard diagnosis of mycobacterial infections relies on direct examination and culture. Nowadays, molecular tools are available, allowing quicker accurate diagnosis. Detection of PPM can be performed directly from clinical samples, although in most cases identification is carried out after isolation. Sequencing of genomic targets (such as 16S rRNA, rpoB or hsp65) allows accurate and quick identifications but has some technical limitations. Problems concerning sequencing analysis used for PPM identification together with description of available algorithms for PPM identification are the major objectives of this review.

• MeSH
• lidé MeSH
• Mycobacterium klasifikace   genetika   MeSH
• mykobakteriózy mikrobiologie   MeSH
• sekvenční analýza * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• anglický abstrakt MeSH
• časopisecké články MeSH
• přehledy MeSH

The low frequency of nontuberculous mycobacterial infections, nonspecific symptoms for individual mycobacteria, and the lack of specific identification methods could alter correct diagnosis. This study presents a combined microbiology and molecular-based approach for Mycobacterium marinum detection in four aquarists with cutaneous mycobacterial infection. Simultaneously, ecology screening for M. marinum presence in the aquarists' fish tanks was performed. A total of 38 mycobacterial isolates originated from four human patients (n = 20), aquarium animals (n = 8), and an aquarium environment (n = 10). Isolate identification was carried out using 16S rRNA sequence analysis. A microbiology-based approach, followed by 16S rRNA sequence analysis, was successfully used for detection of M. marinum in all four patients. Animal and environmental samples were simultaneously examined, and a total of seven mycobacterial species were isolated: Mycobacterium chelonae , Mycobacterium fortuitum , Mycobacterium gordonae , Mycobacterium kansasii , Mycobacterium mantenii , Mycobacterium marinum , and Mycobacterium peregrinum . The presence of M. marinum was proven in the aquarium environments of two patients. Although M. marinum is described as being present in water, it was detected only in fish.

• MeSH
• antibakteriální látky farmakologie   terapeutické užití   MeSH
• atypické mykobakteriální infekce diagnóza   farmakoterapie   mikrobiologie   patologie   MeSH
• klarithromycin farmakologie   terapeutické užití   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• mikrobiologie životního prostředí MeSH
• Mycobacterium marinum klasifikace   účinky léků   genetika   izolace a purifikace   MeSH
• Mycobacterium klasifikace   genetika   izolace a purifikace   MeSH
• RNA ribozomální 16S genetika   MeSH
• ryby mikrobiologie   MeSH
• výsledek terapie MeSH
• zvířata MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH
• práce podpořená grantem MeSH
• Názvy látek
• antibakteriální látky MeSH
• klarithromycin MeSH
• RNA ribozomální 16S MeSH

Non-coding RNAs (ncRNAs) are regulatory molecules encoded in the intergenic or intragenic regions of the genome. In prokaryotes, biocomputational identification of homologs of known ncRNAs in other species often fails due to weakly evolutionarily conserved sequences, structures, synteny and genome localization, except in the case of evolutionarily closely related species. To eliminate results from weak conservation, we focused on RNA structure, which is the most conserved ncRNA property. Analysis of the structure of one of the few well-studied bacterial ncRNAs, 6S RNA, demonstrated that unlike optimal and consensus structures, suboptimal structures are capable of capturing RNA homology even in divergent bacterial species. A computational procedure for the identification of homologous ncRNAs using suboptimal structures was created. The suggested procedure was applied to strongly divergent bacterial species and was capable of identifying homologous ncRNAs.

• MeSH
• bakteriální RNA chemie   MeSH
• konformace nukleové kyseliny MeSH
• molekulární sekvence - údaje MeSH
• Mycobacterium genetika   MeSH
• nekódující RNA chemie   MeSH
• sekvence nukleotidů MeSH
• sekvenční homologie nukleových kyselin MeSH
• Streptomyces genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 6S RNA MeSH Prohlížeč
• bakteriální RNA MeSH
• nekódující RNA MeSH

From Mycobacterium avium species Mycobacterium avium subsp. paratuberculosis (n=961), Mycobacterium a. avium (n=677), Mycobacterium a. silvaticum (n=5), and Mycobacterium a. hominissuis (n=1566) were examined, and from Mycobacterium tuberculosis complex M. tuberculosis (n=2), Mycobacterium bovis (n=13), M. bovis BCG (n=4), and Mycobacterium caprae (n=10) were examined. From other mycobacterial species Mycobacterium intracellulare (n=60) and atypical mycobacteria (n=256) including Mycobacterium fortuitum, Mycobacterium chelonae, Mycobacterium scrofulaceum, Mycobacterium gastri and other species of conditionally pathogenic mycobacteria were analysed. The internal standard molecules corresponding to insertion sequences IS900, IS901, IS1245, and flanking region (FR300) of IS901 were produced by PCR of alfalfa genome segment and inserted into plasmid vector. The resulting recombinant plasmid molecules were used as internal standards in coamplification with a total of 4729 mycobacterial collection strains and field isolates between 1996 and 2003. The size differences between amplicons obtained from IS900 (258 bp), IS901 (1108 bp), IS1245 (427 bp), and FR300 (300 bp) and from corresponding internal standard molecules ISIS900 (591 bp), ISIS901 (1 336 bp), ISIS1245 (583 bp), and IS901 flanking region of 300 bp ISFR300 (488 bp), respectively, allowed easy discrimination. The internal amplicons were visible by naked aye on agarose gel when 10(1), 10(3), 10(2), and 10(2) molecules for ISIS900, ISIS901, ISIS1245, and ISFR300 were used in the PCR, respectively, when no bacterial DNA was added to the reaction. The system was tested to define the amount of internal standards that could be used in the PCR without affecting the amplification of the specific segment. Non-specific amplifications were observed in M. fortuitum with IS1245 PCR and mixed infections with M. a. avium and M. a. hominissuis from pigs and cattle were found. PCR results of typing were compared with serotyping and Accu-Probes analyses in selected field isolates.

• MeSH
• DNA bakterií chemie   genetika   MeSH
• Mycobacterium klasifikace   genetika   izolace a purifikace   MeSH
• mykobakteriózy diagnóza   mikrobiologie   veterinární   MeSH
• nemoci prasat diagnóza   mikrobiologie   MeSH
• nemoci skotu diagnóza   mikrobiologie   MeSH
• polymerázová řetězová reakce metody   veterinární   MeSH
• prasata MeSH
• referenční standardy MeSH
• sérotypizace MeSH
• skot MeSH
• transpozibilní elementy DNA genetika   MeSH
• zvířata MeSH
• Check Tag
• skot MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA bakterií MeSH
• transpozibilní elementy DNA MeSH