Staphylococcus petrasii is recently described coagulase negative staphylococcal species and an opportunistic human pathogen, still often misidentified in clinical specimens. Four subspecies are distinguished in S. petrasii by polyphasic taxonomical analyses, however a comparative study has still not been done on the majority of isolates and their genome properties have not yet been thoroughly analysed. Here, we describe the phenotypic and genotypic characteristics of 65 isolates and the results of de novo sequencing, whole genome assembly and annotation of draft genomes of five strains. The strains were identified by MALDI-TOF mass spectrometry to the species level and the majority of the strains were identified to the subspecies level by fingerprinting methods, (GTG)5 repetitive PCR and ribotyping. Macrorestriction profiling by pulsed-field gel electrophoresis was confirmed to be a suitable strain typing method. Comparative genomics revealed the presence of new mobile genetic elements carrying antimicrobial resistance factors such as staphylococcal cassette chromosome (SCC) mec, transposones, phage-inducible genomic islands, and plasmids. Their mosaic structure and similarity across coagulase-negative staphylococci and Staphylococcus aureus suggest the possible exchange of these elements. Numerous putative virulence factors such as adhesins, autolysins, exoenzymes, capsule formation genes, immunomodulators, the phage-associated sasX gene, and SCC-associated spermidine N-acetyltransferase gene, pseudouridine and sorbitol utilization operons might explain clinical manifestations of S. petrasii isolates. The increasing recovery of S. petrasii isolates from human clinical material, the multi-drug resistance including methicillin resistance of S. petrasii subsp. jettensis strains, and virulence factors homologous to other pathogenic staphylococci demonstrate the importance of the species in human disease.
- MeSH
- Virulence Factors genetics MeSH
- Phenotype MeSH
- Genome, Bacterial * MeSH
- Genomics MeSH
- Genotype MeSH
- Humans MeSH
- Microbial Sensitivity Tests MeSH
- Electrophoresis, Gel, Pulsed-Field MeSH
- Ribotyping MeSH
- Interspersed Repetitive Sequences * MeSH
- Staphylococcus classification genetics pathogenicity MeSH
- Bacterial Typing Techniques MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Comparative Study MeSH
Melting snowfields in polar and alpine regions often exhibit a red and orange colouration caused by microalgae. The diversity of these organisms is still poorly understood. We applied a polyphasic approach using three molecular markers and light and electron microscopy to investigate spherical cysts sampled from alpine mountains in Europe, North America and South America as well as from both polar regions. Molecular analyses revealed the presence of a single independent lineage within the Chlamydomonadales. The genus Sanguina is described, with Sanguina nivaloides as its type. It is distinguishable from other red cysts forming alga by the number of cell wall layers, cell size, cell surface morphology and habitat preference. Sanguina nivaloides is a diverse species containing a total of 18 haplotypes according to nuclear ribosomal DNA internal transcribed spacer 2, with low nucleotide divergence (≤3.5%). Based on molecular data we demonstrate that it has a cosmopolitan distribution with an absence of geographical structuring, indicating an effective dispersal strategy with the cysts being transported all around the globe, including trans-equatorially. Additionally, Sanguina aurantia is described, with small spherical orange cysts often clustered by means of mucilaginous sheaths, and causing orange blooms in snow in subarctic and Arctic regions.
- MeSH
- Chlorophyta classification genetics physiology MeSH
- Ecosystem MeSH
- Phylogeny MeSH
- Phylogeography MeSH
- DNA, Ribosomal Spacer MeSH
- Rhodophyta MeSH
- Snow microbiology MeSH
- Freezing MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Europe MeSH
- South America MeSH
- North America MeSH
Coccoid green algae traditionally classified in Dictyochloropsis have a complex, reticulate chloroplast, when mature, without a pyrenoid. They occupy remarkably diverse ecological niches as free-living organisms or in association with lichen-forming fungi and were recently shown to form two distinct lineages within Trebouxiophyceae. We used a polyphasic approach to revise the taxonomy of the genus. Based on phylogenetic analysis of the 18S rRNA gene, and detailed morphological investigation using comparative conventional light and confocal microscopy, we have assigned these lineages to two genera, Dictyochloropsis and Symbiochloris gen. nov. We have reconsidered the diagnostic generic features as follows: Dictyochloropsis comprises only free-living algae with a reticulate chloroplast, forming lobes in a parallel arrangement at some ontogenetic stages, and which reproduce only by means of autospores. This agrees with Geitler's original diagnosis of Dictyochloropsis, but not with the later emendation by Tschermak-Woess. Consequently, the species of Dictyochloropsis sensu Tschermak-Woess are assigned to Symbiochloris, with new combinations proposed. Symbiochloris encompasses free-living and/or lichenized algae with lobed chloroplasts and that reproduce by forming zoospores characterized by two subapical isokont flagella that emerge symmetrically near the flattened apex. In addition, using coalescent-based approaches, morphological characters and secondary structure of ITS transcripts, we inferred species boundaries and taxonomic relationships within the newly proposed genera. Two species of Dictyochloropsis and nine species of Symbiochloris are delimited, including the newly described species D. asterochloroides, S. handae, S. tropica, and S. tschermakiae. Our results further support the non-monophyly of autosporine taxa within Trebouxiophyceae.
Taxonomie dermatofytů prošla v minulosti řadou výrazných změn a nikdy nebyla příliš stabilní. Poslední rozsáhlejší změny proběhly v souvislosti s revizí skupiny molekulárně genetickými metodami. Hlavním cílem této práce je seznámit čtenáře s pokroky v taxonomii dermatofytů a prostřednictvím seznamu doporučených jmen sjednotit pojmenovávání druhů napříč českými pracovišti. To by mělo nejen usnadnit komunikaci, ale také porovnávání výsledků se zahraniční literaturou. Jedním z doporučení je například ukončení používání jména Trichophyton mentagrophytes v klinické praxi. V úvodu textu se diskutuje o problematickém konceptu druhu u dermatofytů, jehož rozdílná aplikace může mít velký vliv na počet uznávaných druhů. Závěrečná část je věnována budoucím změnám souvisejícím s novým vydáním Mezinárodního kódu nomenklatury řas, hub a rostlin. Jedná se především o ukončení duální nomenklatury hub a vybrání jediného správného jména pro každý druh. Obecně se dá říci, že je vhodné preferovat jméno nepohlavního stadia (Trichophyton, Microsporum, Epidermophyton), s výjimkou případů, kde toto jméno není k dispozici (např. Arthroderma benhamiae). Klíčová slova: Arthroderma – druhový koncept – fylogeneze – Mezinárodní nomenklatorický kód – jedna houba, jedno jméno – polyfázický přístup – Trichophyton interdigitale – Trichophyton mentagrophytes
Taxonomy of dermatophytes has changed significantly in the past and it has never been stable. Last extensive changes appeared after revision of the group by molecular genetic methods. This paper introduces the advances in taxonomy of dermatophytes and helps to unify the species names in use among the Czech laboratories to simplify their communication and comparison of the results with foreign literature. The complicated species concept of dermatophytes that might be applied differently and might influence the number of accepted species is discussed in the beginning. The last part is dedicated to future changes related to a new edition of the International Code of Nomenclature for algae, fungi, and plants namely to termination of a dual nomenclature of fungi and choosing the one correct name for each species. Key words: Atrhroderma – species concept – phylogeny – the International Code of Nomenclature – one fungus one name – polyphasic approach – Trichophyton interdigitale – Trichophyton mentagrophytes
- Keywords
- druhový koncept, Trichophyton mentagrophytes, Trichophyton interdigitale, polyfázický přístup, Mezinárodní nomenklatorický kód, zoofilní druhy, geofilní druhy,
- MeSH
- Arthrodermataceae classification MeSH
- Dermatomycoses microbiology MeSH
- Epidermophyton classification MeSH
- Phylogeny * MeSH
- Fungi classification MeSH
- Humans MeSH
- Microsporum classification MeSH
- Mitosporic Fungi * isolation & purification classification MeSH
- Mycological Typing Techniques MeSH
- Terminology as Topic * MeSH
- Trichophyton classification MeSH
- Zoonoses MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
Aeromonas P2973 was isolated from the water of a brook in a cavern in the Czech Republic. This isolate could not be biochemically identified at the species level, considering all updated species descriptions. Subsequent extensive phenotypic characterisation, DNA-DNA hybridisation, 16S rRNA gene sequencing and a Multi-Locus Phylogenetic Analysis (MLPA) of the concatenated sequence of 7 housekeeping genes (gyrB, rpoD, recA, dnaJ, gyrA, dnaX and atpD; 4705 bp) was employed in an attempt to ascertain the taxonomy of this isolate. Based on this polyphasic approach, we describe a novel species of the genus Aeromonas, for which the name Aeromonas cavernicola sp. nov. is proposed, with strain CCM7641(T) (DSM24474(T), CECT7862(T)) as the type strain.
- MeSH
- Aeromonas classification genetics isolation & purification physiology MeSH
- Bacterial Proteins genetics MeSH
- DNA, Bacterial chemistry genetics MeSH
- Phylogeny MeSH
- Nucleic Acid Hybridization MeSH
- Caves MeSH
- Molecular Sequence Data MeSH
- Molecular Typing MeSH
- DNA, Ribosomal chemistry genetics MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Sequence Analysis, DNA MeSH
- Cluster Analysis MeSH
- Fresh Water microbiology MeSH
- Bacterial Typing Techniques MeSH
- Microscopy, Electron, Transmission MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
Artificial neural networks (ANN) methodology, molecular analyses and comparative morphology of the male postabdomen were used successfully in parallel for species identification and resolution of some taxonomic problems concerning West Palaearctic species of the genus Tachina Meigen, 1803. Supervised feed-forward ANN with back-propagation of errors was applied on morphometric and qualitative characters to solve known taxonomic discrepancies. Background molecular analyses based on mitochondrial markers CO I, Cyt b, 12S and 16S rDNA and study of male postabdominal structures were published separately. All three approaches resolved taxonomic doubts with identical results in the following five cases: case 1, the four presently recognized subgenera of the genus Tachina were confirmed and the description of a new subgenus was recommended; case 2, the validity of a new boreo-alpine species (sp.n.) was confirmed; case 3, the previously supposed presence of T. casta (Rondani, 1859) in central Europe was not supported; case 4, West Palaearctic T. nupta (Rondani, 1859) was contrasted with East Palaearctic specimens from Japan, which seem to represent a valid species not conspecific with central European specimens; T. nupta needs detailed further study; case 5, T. nigrohirta (Stein, 1924) resurrected recently from synonymy with T. ursina Meigen, 1824 was confirmed as a valid species. This parallel application of three alternative methods has enabled the principle of 'polyphasic taxonomy' to be tested and verified using these separate results. For the first time, the value of using the ANN approach in taxonomy was justified by two non-mathematical methods (molecular and morphological).
- MeSH
- Anatomy, Comparative MeSH
- Cytochrome b Group genetics MeSH
- Diptera anatomy & histology classification genetics MeSH
- Species Specificity MeSH
- Genes, Insect MeSH
- DNA, Mitochondrial genetics MeSH
- Molecular Sequence Data MeSH
- Neural Networks, Computer MeSH
- RNA, Ribosomal, 16S genetics MeSH
- RNA, Ribosomal genetics MeSH
- Sequence Analysis, DNA MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Evaluation Study MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Europe MeSH
Častými „kontaminantami" zachycenými při mykobakteriologické kultivaci dekontaminovaných vzorků jsou bakterie řádu Actinomycetales. Jsou to obvykle bakterie klasifikované v čeledi Corynehacterineae rodů Corynebacteríum, Dietzia, Gordonia, Nocardia, Rhodococcus a Tsukamurella. Tyto bakterie často kolonizují dýchací cesty a za určitých podmínek mohou vyvolat život ohrožující onemocnění. U pacientů s těžkou imunodeficiencí jsou pravidelným vyvolavatelem život ohrožujících infekcí bakterie rodu Nocardia. Jsou to vláknité bakterie, vytvářející v kultuře vzdušné mycelium, jsou částečně acidorezistentní a jsou rezistentní na lysozym. Vyvolávají nokardiózu, tj. vzácné ale závažné onemocnění pacientů s různými typy imunodeficience. Diferenciálně diagnosticky je třeba odlišit rody Streptomyces, Actinomadura, Nocardiopsis a další půdní saprofyty, které nejsou acidorezistentní, jsou citlivé na lysozym a rychleji rostou. Často kolonizují dýchací cesty u pacientů s postižením plic, onemocnění vyvolávají velmi vzácně. Diagnostika aerobních aktinomycet a vyšetření citlivosti na antibiotika mají svá úskalí vyplývající z delší růstové doby, obtížné barvitelnosti a necharakteristických biochemických reakcí. K přesné identifikaci do rodu a species je nutná polyfázová identifikace izolatu s využitím metod molekulární mikrobiologie. Při včasné diagnóze bývají infekce vyvolané aerobními aktinomycetami dobře léčitelné cílenou terapií antibiotiky.
Frequent "contaminants" detected during mycobacterial culture of decontaminated samples are bacteria of the order Actinomycetales. These are usually bacteria classified as the family Corynebacterineae, genera Corynebacterium, Dietzia, Gordonia, Nocardia, Rhodococcus and Tsukamurella. These bacteria frequently colonize the airways and, under certain circumstances, they may cause life-threatening diseases. In severely immunocompromised patients, they regularly cause life-threatening infections with bacteria of the genus Nocardia. These filamentous bacteria, developing aerial mycelium in the culture, are partly acid-resistant and resistant to lysozyme. They cause nocardiosis, a rare but serious disease in patients with various types of immune deficiency. Differential diagnosis must distinguish between the genera Streptomyces, Actinomadura and Nocardiopsis and other soil saprophytes that are not acid-resistant, sensitive to lysozyme and faster growing. They frequently colonize the airways of patients with lung disease but very rarely cause diseases. The diagnosis of aerobic actinomycetes and determination of their sensitivity to antibiotics are problematic since they grow longer, are difficult to stain and are involved in atypical biochemical reactions. Precise identification of the genera and species requires polyphasic identification of isolates using molecular microbiology methods. If diagnosed early, infections caused by aerobic actinomycetes are easy to treat with targeted antibiotic therapy.
- Keywords
- léčba, vyšetření citlivosti, identifikace, diagnostika, Tsukamurella, Gordonia, Dietzia, dekontaminované vzorky,
- MeSH
- Actinomycetales classification growth & development MeSH
- Bacteriological Techniques MeSH
- Corynebacterium MeSH
- Epidemiology MeSH
- Actinomycetales Infections diagnosis MeSH
- Humans MeSH
- Mycobacterium growth & development MeSH
- Nocardia MeSH
- Nocardia Infections MeSH
- Rhodococcus MeSH
- Streptomyces MeSH
- Tuberculosis MeSH
- Check Tag
- Humans MeSH
- Publication type
- Review MeSH
Acinetobacter genospecies (genomic species) 10 and 11 were described by Bouvet and Grimont in 1986 on the basis of DNA-DNA reassociation studies and comprehensive phenotypic analysis. In the present study, the names Acinetobacter bereziniae sp. nov. and Acinetobacter guillouiae sp. nov., respectively, are proposed for these genomic species based on the congruence of results of polyphasic analysis of 33 strains (16 and 17 strains of genomic species 10 and 11, respectively). All strains were investigated by selective restriction fragment amplification (i.e. AFLP) analysis rpoB sequence analysis, amplified rDNA restriction analysis and tDNA intergenic length polymorphism analysis, and their nutritional and physiological properties were determined. Subsets of the strains were studied by 16S rRNA gene sequence analysis and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS or had been classified previously by DNA-DNA reassociation. Results indicate that A. bereziniae and A. guillouiae represent two phenetically and phylogenetically distinct groups within the genus Acinetobacter. Based on the comparative analysis of housekeeping genes (16S rRNA and rpoB genes), these species together represent a monophyletic branch within the genus. Despite their overall phenotypic similarity, the ability to oxidize d-glucose and to grow at 38 degrees C can be used in the presumptive differentiation of these two species from each other: with the exception of three strains that were positive for only one test, A. bereziniae strains were positive for both tests, whereas A. guillouiae strains were negative in these tests. The strains of A. bereziniae originated mainly from human clinical specimens, whereas A. guillouiae strains were isolated from different environmental sources in addition to human specimens. The type strain of A. bereziniae sp. nov. is LMG 1003(T) (=CIP 70.12(T) =ATCC 17924(T)) and that of A. guillouiae sp. nov. is LMG 988(T) (=CIP 63.46( T) =ATCC 11171(T) =CCUG 2491(T)).
- MeSH
- Acinetobacter classification genetics isolation & purification physiology MeSH
- Amplified Fragment Length Polymorphism Analysis MeSH
- Species Specificity MeSH
- Phenotype MeSH
- Phylogeny MeSH
- Genotype MeSH
- Genes, rRNA MeSH
- Nucleic Acid Hybridization MeSH
- Acinetobacter Infections microbiology MeSH
- Wound Infection microbiology MeSH
- Humans MeSH
- Molecular Sequence Data MeSH
- Sewage microbiology MeSH
- DNA, Ribosomal analysis genetics MeSH
- RNA, Ribosomal, 16S genetics MeSH
- Sequence Analysis, DNA MeSH
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MeSH
- Bacterial Typing Techniques MeSH
- Base Composition MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Cílem sdělení jsou možnosti dvoustupňové polyfázové identifikace původce nokardiózy u pacienta s abscesem mozku, vyšetření citlivosti na antibiotika a etiologická léčba pacienta po neurochirurgickém zákroku. Pacient léčený kortikoidy pro fibrózu plic byl přijat na neurochirurgickou kliniku s pestrými neurologickými projevy. Při CT vyšetření a při kontrastním zobrazení pomocí magnetické rezonance (MRI) byl zjištěn multilokulární expanzní proces velikosti 4,5 x 3,5 cm v parietálním laloku vlevo, diferenciálně diagnosticky označen jako maligní gliom. Byla provedena punkce ložiska. Histologicky byl diagnostikován absces mozku obsahující leukocyty a nekrotické hmoty. Z hnisu získaného punkcí byly vykultivovány bakterie rodu Nocardia, které byly fenotypovými metodami (grampozitivita, částečná acidorezistence, průkaz vzdušného mycelia, růst při 45 °C, rezistence na lysozym a fenotyp rezistence na antibiotika) v prvním stupni fenotypové diagnostiky zařazeny do fenotypu rezistence V., v.s. N. farcinica (rezistence na aminoglykosidy kromě amikacinu a rezistence na cefalosporiny III. generace). Ve druhém stupni polyfázové diagnostiky byla izolována rDNA a byla provedena sekvenace genu pro 16S rRNA ve velikosti 1000 bp. Získaná sekvence byla určena v databázi GenBank pomocí softwaru BLAST jako N. farcinica (100%). Citlivost kmene byla vyšetřena diluční metodou podle standardu NCCLS /CLSI. Kmen byl dobře citlivý na kotrimoxazol, amikacin a imipenem. Pacient byl dlouhodobě intravenózně léčen kombinací kotrimoxazolu s amikacinem s pokračující úpravou klinického stavu a hodnot zánětlivých parametrů. N.farcinica patří mezi tři nejčastěji izolované nokardie v Evropě i v ČR. Byla opakovaně izolována v České republice zejména z plic a dýchacích cest u případů systémové nokardiózy obvykle u pacientů s imunodeficiencí.
This case report describes a two-step protocol for the identification of the causative agent of nocardiosis in a patient with brain abscess, antibiotic susceptibility testing and etiological treatment after neurosurgery. The patient treated with corticosteroids for pulmonary fibrosis and presenting with multiple neurological manifestations was admitted to a neurosurgery clinic. CT and contrast MRI revealed an expansive multilocular lesion 45 x 35 mm in size in the left parietal lobe, differentially diagnosed as malignant glioma. The lesion was biopsied and the histology showed a brain abscess containing white blood cells and dead tissue. The aspirated pus culture yielded bacteria of the genus Nocardia that were further identified, in the first step, by phenotypic methods (Gram positivity, partial acidoresistance, airborne mycelium detection, growth at 45 °C, lysozyme resistance and antibiotic resistance phenotype) as belonging to resistance phenotype V., v.s. N. farcinica (resistance to aminoglycosides except amikacin and to third-generation cephalosporins). In the second step of the polyphasic identification, rDNA was isolated and a 1000 bp part of the 16S rRNA gene was sequenced. Sequence comparison with the GenBank database using BLAST software identified the agent as N. farcinica (100%). The isolate was tested for susceptibility by the NCCLS /CLSI dilution method and showed good susceptibility to co-trimoxazole, amikacin and imipenem. The patient was treated with long-term intravenous cotrimoxazole acid in combination with amikacin and his clinical condition and laboratory parameters of inflammation improved. N. farcinica is among the three most frequently isolated Nocardia species in Europe as well as in the Czech Republic where it was repeatedly recovered from the lungs and respiratory tract of immunocompromised patients with systemic nocardiosis.
- MeSH
- Brain Abscess drug therapy surgery microbiology MeSH
- Anti-Bacterial Agents administration & dosage MeSH
- Molecular Diagnostic Techniques utilization MeSH
- Financing, Organized MeSH
- Drug Combinations MeSH
- Humans MeSH
- Microbial Sensitivity Tests utilization MeSH
- Microbiological Techniques utilization MeSH
- Nocardia isolation & purification MeSH
- Nocardia Infections diagnosis genetics MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Publication type
- Case Reports MeSH
Nocardia farcinica byla izolována z abscesu mozku u imunosuprimovaného pacienta s plicní fibrózou při léčbě kortikosteroidy. Kmen byl orientačně identifikován podle fenotypu rezistence na antibiotika a ve druhém stupni polyfázově identifikován pomocí sekvenace genu pro 16S rRNA. Účinnost kotrimoxazolu a amikacinu, léků volby pro nokardiózu, byla potvrzena diluční mikrometodou.
Nocardia farcinica was isolated from a cerebral abscess in an immunocompromised patient with lung fibrosis treated with corticosteroids. The strain was identified by a polyphasic approach based on 16S rRNA gene sequencing and antibiotic resistance pattern. Antimicrobial activity of co-trimoxazole and amikacin, the drugs of choice for the treatment of nocardiosis, was confirmed by the standard microdilution method.
- MeSH
- Brain Abscess diagnosis microbiology MeSH
- Anti-Bacterial Agents administration & dosage MeSH
- Drug Resistance, Bacterial MeSH
- Glucocorticoids administration & dosage adverse effects MeSH
- Humans MeSH
- Nocardia isolation & purification pathogenicity drug effects MeSH
- Pulmonary Fibrosis drug therapy MeSH
- Aged MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Aged MeSH
- Publication type
- Case Reports MeSH
