Pseudomonas leptonychotis sp. nov., isolated from Weddell seals in Antarctica.

A taxonomic study was carried out on four Gram-stain-negative strains P5773T, P6169, P4708 and P6245, isolated from anus or mouth samples of Weddell seals at James Ross Island, Antarctica. The results of initial 16S rRNA gene sequence analysis showed that all four strains formed a group placed in the genus Pseudomonas and found Pseudomonas guineae and Pseudomonas peli to be their closest neighbours with 99.9 and 99.2 % sequence similarity, respectively. Sequence analysis of rpoD, rpoB and gyrB housekeeping genes confirmed the highest similarity of isolates to P. peli (rpoD) and to P. guineae (rpoB and gyrB). The average nucleotide identity value below 86 %, as calculated from the whole-genome sequence data, showed the low genomic relatedness of P5773T to its phylogenetic neighbours. The complete genome of strain P5773T was 4.4 Mb long and contained genes encoding proteins with biotechnological potential. The major fatty acids of the seal isolates were summed feature 8 (C18 : 1 ω7c), summed feature 3 (C16 : 1 ω 7 c/C16  : 1 ω6c) and C16:0. The major respiratory quinone was Q9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Putrescine and spermidine are predominant in the polyamine pattern. Further characterization performed using repetitive sequence-based PCR fingerprinting and MALDI-TOF MS analysis showed that the studied isolates formed a coherent cluster separated from the remaining Pseudomonas species and confirmed that they represent a novel species within the genus Pseudomonas, for which the name Pseudomonas leptonychotis sp. nov. is suggested. The type strain is P5773T (=CCM 8849T=LMG 30618T).

[Thyroid carcinomas: the present view on diagnostics and therapy]. / Karcinomy stítné zlázy: soucasný pohled na diagnostiku a lécbu.

Thyroid carcinoma (TC) represents 1-2 % of all human tumors, and is the seventh most common tumor. Women are in large majority among new patients. For women, this is the fifth most common tumor. In the Czech Republic, 1 143 new cases of TC were diagnosed in 2015. It is the tumor with the highest increase in incidence. Among newly diagnosed tumors, most of those are differentiated thyroid gland carcinomas (DTCs) originating from follicular thyroid cells. These tumors are follicular and papillary carcinomas and Hurthle carcinoma, accounting for 95 % of new cases. Due to the great progress in treatment, the prognosis is most commonly good for these tumors. Treatment is more difficult for other types of tumors. Anaplastic thyroid cancer (representing less than 1 % of thyroid tumors) is a rare form of thyroid cancer that is very malignant. Also found in the thyroid gland is Euro-C-cell tumor, which originates in C cells. This is the so-called medullary thyroid carcinoma, which is less common (5 % of all thyroid carcinomas). It emerges from the parapolyclic neuroendocrine cells of the thyroid gland. This tumor often metastasizes to the cervical lymph nodes, and frequently occurs in distant bone, liver and lung metastases. In 2015, in this publication we published an article: Thyroid gland carcinomas, current therapeutic procedures. This article was devoted to the diagnosis of thyroid carcinoma and individual treatment procedures. In this article, we look at differentiated thyroid carcinomas (DTCs), especially current opinions on the treatment of low-risk carcinomas.Key words: differentiated thyroid cancer - radioidine - targeted therapy.

[Thyroid carcinomas - current therapeutic procedures]. / Karcinomy stítné zlázy - soucasné lécebné postupy.

Incidence of differentiated thyroid carcinomas, especially papillary carcinomas, in recent decades worldwide increase. This is especially the detection of small tumor sizes up to two centimeters. Causes of the increase of these cancers are either increased number of thyroid investigations, but also the actual increase of this disease. The subject of expert discussion on this topic is mainly assessment of the severity of newly diagnosed tumors, the choice of treatment strategy and choice of follow-up of patients. Given that a large part of tumor detected in an early stage and due to the success of the current treatment options for the prognosis of thyroid cancer is usually good. Despite the large increase of the incidence, mortality for this type of cancer, in countries with good individualized treatment, decreases. We present a review of literature on the topic.Key words: thyroid carcinoma - post-operation monitoring - radioiodine - stratification of the risk of relapse.

[Risk factors of thyroid carcinoma]. / Rizikové faktory vzniku karcinomu stítné zlázy.

Thyroid cancer is one of the worlds fastest growing tumor incidences. The number of new cases has particularly increased in differentiated papillary thyroid carcinoma. In the Czech Republic it is documented that the incidence of thyroid cancer continues to grow, since 1980 has increased four times. The Czech Republic has a higher incidence than most other European countries and at the same time is a country with average and declining mortality from this disease. This review summarizes the known risk factors that may contribute to the formation and rise of thyroid carcinomas.

Pseudomonas petrae sp. nov. isolated from regolith samples in Antarctica.

A polyphasic taxonomic approach was used to characterize the four strains P2653T, P2652, P2498, and P2647, isolated from Antarctic regolith samples. Initial genotype screening performed by PCR fingerprinting based on repetitive sequences showed that the isolates studied formed a coherent cluster separated from the other Pseudomonas species. Identification results based on 16S rRNA gene sequences showed the highest sequence similarity with Pseudomonas graminis (99.7%), which was confirmed by multilocus sequence analysis using the rpoB, rpoD, and gyrB genes. Genome sequence comparison of P2653T with the most related P. graminis type strain DSM 11363T revealed an average nucleotide identity of 92.1% and a digital DNA-DNA hybridization value of 46.6%. The major fatty acids for all Antarctic strains were C16:0, Summed Feature 3 (C16:1ω7c/C16:1ω6c) and Summed Feature 8 (C18:1ω7c/C18:1ω6c). The predominant respiratory quinone was Q-9, and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol. The regolith strains could be differentiated from related species by the absence of arginine dihydrolase, ornithine and lysine decarboxylase and by negative tyrosine hydrolysis. The results of this polyphasic study allowed the genotypic and phenotypic differentiation of four analysed strains from the closest related species, which confirmed that the strains represent a novel species within the genus Pseudomonas, for which the name Pseudomonas petrae sp. nov. is proposed with P2653T (CCM 8850T = DSM 112068T = LMG 30619T) as the type strain.

Evaluation of (GTG)5-PCR for rapid identification of Streptococcus mutans.

Repetitive sequence-based polymerase chain reaction (PCR) fingerprinting using the (GTG)(5) primer was applied for fast screening of bacterial strains isolated from dental plaque of early childhood caries (ECC)-affected children. A group of 29 Gram-positive bacteria was separated into a homogeneous cluster together with Streptococcus mutans reference strains and constituted an aberrant branch after the numerical analysis of (GTG)(5)-PCR fingerprints. Automated ribotyping with EcoRI restriction enzyme (RiboPrinter microbial characterization system) revealed high genetic heterogeneity among the tested group and proved to be a good tool for strain-typing purposes. Further characterization of the studied strains was achieved by extensive phenotyping and whole-cell protein fingerprinting and confirmed all the strains as S. mutans representatives. Obtained results showed rep-PCR fingerprinting with the (GTG)(5) primer to be a fast and reliable method for identification of S. mutans.

Occurance of Staphylococcus nepalensis strains in different sources including human clinical material.

Five isolates of coagulase-negative staphylococci were obtained from human urine, the gastrointestinal tract of squirrel monkeys, pig skin and from the environment. All key biochemical characteristics of the tested strains corresponded with the description of Staphylococcus xylosus species. However, partial 16S rRNA gene sequences obtained from analysed strains corresponded with those of Staphylococcus nepalensis reference strains, except for two strains which differed in one residue. Ribotyping with EcoRI and HindIII restriction enzymes, whole cell protein profile analysis performed by SDS-PAGE and SmaI macrorestriction analysis were used for more precise characterization and identification of the analysed strains. Obtained results showed that EcoRI and HindIII ribotyping and whole cell protein fingerprinting are suitable and reliable methods for the differentiation of S. nepalensis strains from the other novobiocin resistant staphylococci, whereas macrorestriction analysis was found to be a good tool for strain typing. The isolation of S. nepalensis is sporadic, and according to our best knowledge this study is the first report of the occurrence of this species in human clinical material as well as in other sources.

Staphylococcus equorum and Staphylococcus succinus isolated from human clinical specimens.

A polyphasic identification approach was applied to a group of 11 novobiocin-resistant staphylococci isolated from human clinical materials. Phenotypic characteristics obtained by both commercial and conventional tests assigned eight strains as Staphylococcus xylosus and three strains as ambiguous S. xylosus/Staphylococcus equorum. In contrast to biotyping, ribotyping with EcoRI and HindIII restriction endonucleases and whole-cell protein fingerprinting assigned six analysed strains as S. equorum, and five strains as Staphylococcus succinus. Confirmation of the identification was done by partial 16S rRNA gene sequencing and S. equorum isolates were verified by a PCR assay targeting the sodA gene. From the data it has been implied that ribotyping and whole-cell protein analysis can be used to differentiate between the biochemically almost indistinguishable species S. xylosus, S. equorum and S. succinus. The present study confirms what is believed to be the first occurrence of S. equorum in a relevant human clinical material in the Czech Republic and describes what is believed to be the first-ever isolation of S. succinus from human clinical material.

Diabetes mellitus in adults: association of HLA DRB1 and DQB1 diabetes risk alleles with GADab presence and C-peptide secretion.

In our study, we investigated the relationship of HLA class II alleles to antibody production against glutamic acid decarboxylase (GADab) and to C-peptide secretion (CP) in diabetic patients. A group of 334 patients (190 women) diagnosed after 35 years of age and 99 control subjects were studied. Patients were divided into four groups according to concentrations of CP and GADab, respectively (CP high/low, GADab positive/negative). HLA DQB1 and DRB1 alleles were genotyped by SSP-PCR. The significance of DQB1 and DRB1 risk alleles was evaluated by examination of their odds ratios computed by testing 2x2 tables considering Bonferonis' corrected P<0.05 as significant. We found strong association between the HLA DRB1*03 risk allele and presence of GADab, and close relationship of the HLA DRB1*04 and HLA DQB1*0302 risk alleles with decreased CP level. Taken together we conclude that the DRB1*04 and DQB1*0302 alleles are associated with progressive decrease of CP level, while DRB1*03 is a significant genetic marker of autoantibody (GADab) development.

Evaluation of the strain identity between isolates from caries lesions and root canals in early childhood caries cases.

Early childhood caries (ECC) has become a serious medical problem worldwide in the last decade. Bacterial microflora of the dental plaque and oral cavity is considered an important factor in the formation and progression of dental caries. The aim of this study was strain typing and comparison of bacterial isolates retrieved from caries lesions and root canal contents of the same teeth. In total, 18 pairs of presumptive streptococci and lactobacilli retrieved from dental caries and root canals isolated from ECC-affected children, were selected on the basis of biotyping results and rep-PCR fingerprinting with (GTG)5 primer. Strain typing was further done using the RiboPrinter microbial characterization system (DuPont Qualicon). The automated ribotyping determined 14 pairs of the strains (77.8 %) to be identical. The results obtained confirmed that identical bacterial strains colonized both the decayed dental surface and the necrotic content of the dental pulp cavity during the cariogenesis. Our finding supports the assumption that bacteria could penetrate through the damaged dental surface to the inner parts of the teeth.

Identification of Staphylococcus spp. using (GTG)5-PCR fingerprinting.

A group of 212 type and reference strains deposited in the Czech Collection of Microorganisms (Brno, Czech Republic) and covering 41 Staphylococcus species comprising 21 subspecies was characterised using rep-PCR fingerprinting with the (GTG)5 primer in order to evaluate this method for identification of staphylococci. All strains were typeable using the (GTG)5 primer and generated PCR products ranging from 200 to 4500 bp. Numerical analysis of the obtained fingerprints revealed (sub)species-specific clustering corresponding with the taxonomic position of analysed strains. Taxonomic position of selected strains representing the (sub)species that were distributed over multiple rep-PCR clusters was verified and confirmed by the partial rpoB gene sequencing. Staphylococcus caprae, Staphylococcus equorum, Staphylococcus sciuri, Staphylococcus piscifermentans, Staphylococcus xylosus, and Staphylococcus saprophyticus revealed heterogeneous fingerprints and each (sub)species was distributed over several clusters. However, representatives of the remaining Staphylococcus spp. were clearly separated in single (sub)species-specific clusters. These results showed rep-PCR with the (GTG)5 primer as a fast and reliable method applicable for differentiation and straightforward identification of majority of Staphylococcus spp.

Staphylococcus microti sp. nov., isolated from the common vole (Microtus arvalis).

Two strains of Gram-positive cocci were isolated from viscera of common voles (Microtus arvalis Pallas) with generalized Brucella microti infection in the Czech Republic. Biochemical features and phylogenetic analysis based on 16S rRNA gene sequences showed that the strains are representatives of the genus Staphylococcus and assigned Staphylococcus muscae as the nearest relative. A detailed characterization done by ribotyping, rpoB and hsp60 gene sequencing, whole-cell protein analysis and rep-PCR using the (GTG)(5) primer differentiated the two strains from all described staphylococci. DNA-DNA hybridization with the type strain of S. muscae demonstrated that the two strains should be considered as members of a novel species (26.8 % reassociation). The two analysed strains were found to be coagulase-negative, novobiocin-susceptible, oxidase-negative cultures, phenotypically close to one another, but showing differences in ribotype profiles. The major fatty acids were iso-C(15 : 0), iso-C(17 : 0), anteiso-C(15 : 0), C(18 : 2 )omega6,9c/anteiso-C(18 : 0), C(18 : 0) and C(18 : 1) omega9c. MK-7 was the predominant isoprenoid quinone, with minor amounts of MK-6 and MK-8. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylglycerol and several unknown lipids. These results proved that the two isolates represent a novel staphylococcal species. The name proposed for this novel taxon is Staphylococcus microti sp. nov.; the type strain is 4005-LJ(m)(T) (=CCM 4903(T) =CCUG 55861(T) =DSM 22147(T)).