Pseudomonas karstica sp. nov. and Pseudomonas spelaei sp. nov., isolated from calcite moonmilk deposits from caves.

A taxonomic study of two fluorescent Pseudomonas strains (HJ/4T and SJ/9/1T) isolated from calcite moonmilk samples obtained from two caves in the Moravian Karst in the Czech Republic was carried out. Results of initial 16S rRNA gene sequence analysis assigned both strains into the genus Pseudomonas and showed Pseudomonas yamanorum 8H1T as their closest neighbour with 99.8 and 99.7 % 16S rRNA gene similarities to strains HJ/4T and SJ/9/1T, respectively. Subsequent sequence analysis of rpoD, rpoB and gyrB housekeeping genes confirmed the highest similarity of both isolates to P. yamanorum 8H1T, but phylogeny and sequences similarities implied that they are representatives of two novel species within the genus Pseudomonas. Further study comprising whole-genome sequencing followed by average nucleotide identity and digital DNA-DNA hybridization calculations, repetitive sequence-based PCR fingerprinting with the REP and ERIC primers, automated ribotyping with the EcoRI restriction endonuclease, cellular fatty acid analysis, quinone and polar lipid characterization, and extensive biotyping confirmed clear separation of both analysed strains from the remaining Pseudomonas species and showed that they represent two novel species within the genus Pseudomonas for which the names Pseudomonas karstica sp. nov. (type strain HJ/4T=CCM 7891T=LMG 27930T) and Pseudomonas spelaei sp. nov. (type strain SJ/9/1T=CCM 7893T=LMG 27931T) are suggested.

Bacterial but Not Fungal Gut Microbiota Alterations Are Associated With Common Variable Immunodeficiency (CVID) Phenotype.

Common Variable Immunodeficiency (CVID) is the most frequent symptomatic immune disorder characterized by reduced serum immunoglobulins. Patients often suffer from infectious and serious non-infectious complications which impact their life tremendously. The monogenic cause has been revealed in a minority of patients so far, indicating the role of multiple genes and environmental factors in CVID etiology. Using 16S and ITS rRNA amplicon sequencing, we analyzed the bacterial and fungal gut microbiota, respectively, in a group of 55 participants constituting of CVID patients and matched healthy controls including 16 case-control pairs living in the same household, to explore possible associations between gut microbiota composition and disease phenotype. We revealed less diverse and significantly altered bacterial but not fungal gut microbiota in CVID patients, which additionally appeared to be associated with a more severe disease phenotype. The factor of sharing the same household impacted both bacterial and fungal microbiome data significantly, although not as strongly as CVID diagnosis in bacterial assessment. Overall, our results suggest that gut bacterial microbiota is altered in CVID patients and may be one of the missing environmental drivers contributing to some of the symptoms and disease severity. Paired samples serving as controls will provide a better resolution between disease-related dysbiosis and other environmental confounders in future studies.

The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery.

Our understanding of human gut microbiota in health and disease depends on accurate and reproducible microbial data acquisition. The critical step in this process is to apply an appropriate methodology to extract microbial DNA, since biases introduced during the DNA extraction process may result in inaccurate microbial representation. In this study, we attempted to find a DNA extraction protocol which could be effectively used to analyze both the bacterial and fungal community. We evaluated the effect of five DNA extraction methods (QIAamp DNA Stool Mini Kit, PureLinkTM Microbiome DNA Purification Kit, ZR Fecal DNA MiniPrepTM Kit, NucleoSpin® DNA Stool Kit, and IHMS protocol Q) on bacterial and fungal gut microbiome recovery using (i) a defined system of germ-free mice feces spiked with bacterial or fungal strains, and (ii) non-spiked human feces. In our experimental setup, we confirmed that the examined methods significantly differed in efficiency and quality, which affected the identified stool microbiome composition. In addition, our results indicated that fungal DNA extraction might be prone to be affected by reagent/kit contamination, and thus an appropriate blank control should be included in mycobiome research. Overall, standardized IHMS protocol Q, recommended by the International Human Microbiome Consortium, performed the best when considering all the parameters analyzed, and thus could be applied not only in bacterial, but also in fungal microbiome research.

Viral genome changes and the impact of viral genome persistence in myocardium of patients with inflammatory cardiomyopathy.

INTRODUCTION: Viral infections are considered the most frequent cause of myocarditis and dilated cardiomyopathy (DCM). MATERIAL AND METHODS: We investigated the changes in viral presence and the impact of viral genome persistence in the myocardium on echocardiographic parameters, functional status and some laboratory parameters in a 6-month follow-up. Fifty-four patients with recent onset DCM, left ventricular ejection fraction < 40% and biopsy-proven myocarditis (> 14 mononuclear leukocytes/mm2 and/or > 7 T-lymphocytes/mm2) were enrolled. Polymerase chain reaction (PCR) was performed to detect pathogens in the myocardium. Patients were divided according to the administered therapy: standard heart failure medication (46 patients) and immunosuppressive therapy (8 patients). RESULTS: In the standard heart failure medication group viral clearance was observed in 13 patients and viral persistence in 24 patients in the follow-up period. Comparing both groups, there was no statistically significant difference - LVEF improvement of 12.0 ±11.4% vs. 18.3 ±12.6%, decrease in NYHA class of 0.7 ±0.7 vs. 1.0 ±0.7, decline in NT-proBNP of 1335 ±1933 ng/l vs. 1942 ±3242 ng/l and decrease in infiltrating leukocytes of 11.1 ±15.8 vs. 6.7 ±23.0 cells/mm2 and T-lymphocytes of 5.8 ±15.1 vs. 1.8 ±10.9 cells/mm2 (all p = NS). A decrease in PCR positive patients from 37 to 29 was observed. The number of PVB19 positive PCR findings decreased from 5 to 4 in patients with immunosuppressive therapy. CONCLUSIONS: A decrease in the number of positive PCR findings in control endomyocardial biopsy was observed. Viral genome persistence was not associated with worse outcome in short-term follow-up.

Analysis of diffusion tensor measurements of the human cervical spinal cord based on semiautomatic segmentation of the white and gray matter.

BACKGROUND: Segmentation of the gray and white matter (GM, WM) of the human spinal cord in MRI images as well as the analysis of spinal cord diffusivity are challenging. When appropriately segmented, diffusion tensor imaging (DTI) of the spinal cord might be beneficial in the diagnosis and prognosis of several diseases. PURPOSE: To evaluate the applicability of a semiautomatic algorithm provided by ITK-SNAP in classification mode (CLASS) for segmenting cervical spinal cord GM, WM in MRI images and analyzing DTI parameters. STUDY TYPE: Prospective. SUBJECTS: Twenty healthy volunteers. SEQUENCES: 1.5T, turbo spin echo, fast field echo, single-shot echo planar imaging. ASSESSMENT: Three raters segmented the tissues by manual, CLASS, and atlas-based methods (Spinal Cord Toolbox, SCT) on T2 -weighted and DTI images. Masks were quantified by similarity and distance metrics, then analyzed for repeatability and mutual comparability. Masks created over T2 images were registered into diffusion space and fractional anisotropy (FA) values were statistically evaluated for dependency on method, rater, or tissue. STATISTICAL TESTS: t-test, analysis of variance (ANOVA), coefficient of variation, Dice coefficient, Hausdorff distance. RESULTS: CLASS segmentation reached better agreement with manual segmentation than did SCT (P < 0.001). Intra- and interobserver repeatability of SCT was better for GM and WM (both P < 0.001) but comparable with CLASS in entire spinal cord segmentation (P = 0.17 and P = 0.07, respectively). While FA values of whole spinal cord were not influenced by choice of segmentation method, both semiautomatic methods yielded lower FA values (P < 0.005) for GM than did the manual technique (mean differences 0.02 and 0.04 for SCT and CLASS, respectively). Repeatability of FA values for all methods was sufficient, with mostly less than 2% variance. DATA CONCLUSION: The presented semiautomatic method in combination with the proposed approach to data registration and analyses of spinal cord diffusivity can potentially be used as an alternative to atlas-based segmentation. LEVEL OF EVIDENCE: 1 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018;47:1217-1227.

Contrast-enhanced ultrasonography in the evaluation of incidental focal liver lesions: A cost-effectiveness analysis.

AIM: To determine whether contrast-enhanced ultrasonography (CEUS) as the first-line method is more cost-effective in evaluating incidentally discovered focal liver lesions (FLLs) than is computed tomography (CT) and magnetic resonance imaging (MRI). METHODS: Between 2010 and 2015, our prospective study enrolled 459 patients with incidentally found FLLs. The biological nature of FLLs was assessed by CEUS in all patients. CT or MRI examinations were added in unclear cases. The sensitivity and specificity of CEUS were calculated. The total costs of CEUS examinations and of the added examinations performed in inconclusive cases were calculated. Afterwards, the theoretical expenses for evaluating incidentally discovered FLLs using CT or MRI as the first-line method were calculated. The results were compared. RESULTS: The total cost of the diagnostic process using CEUS for all enrolled patients with FLLs was 75884 USD. When the expenses for additional CT and MRI examinations performed in inconclusive cases were added, the total cost was 90540 US dollar (USD). If all patients had been examined by CT or MR as the first-line method, the costs would have been 78897 USD or 384235 USD, respectively. The difference between the cost of CT and CEUS was 3013 USD (4%) and that between MRI and CEUS was 308352 USD (406.3%). We correctly described 97.06% of benign or malignant lesions, with 96.99% sensitivity and 97.09% specificity. Positive predictive value was 94.16% and negative predictive value was 98.52%. In cases with 4 and more lesions, malignancy is significantly more frequent and inconclusive findings significantly less frequent (P < 0.001). CONCLUSION: While the costs of CEUS and CT in evaluating FLLs are comparable, CEUS examination is far more cost-effective in comparison to MRI.

Evaluation of Fluorescent Capillary Electrophoresis for Rapid Identification of Candida Fungal Infections.

Early diagnosis of fungal infection is critical for initiating antifungal therapy and reducing the high mortality rate in immunocompromised patients. In this study, we focused on rapid and sensitive identification of clinically important Candida species, utilizing the variability in the length of the ITS2 rRNA gene and fluorescent capillary electrophoresis (f-ITS2-PCR-CE). The method was developed and optimized on 29 various Candida reference strains from which 26 Candida species were clearly identified, while Candida guilliermondii, C. fermentati, and C. carpophila, which are closely related, could not be distinguished. The method was subsequently validated on 143 blinded monofungal clinical isolates (comprising 26 species) and was able to identify 88% of species unambiguously. This indicated a higher resolution power than the classical phenotypic approach which correctly identified 73%. Finally, the culture-independent potential of this technique was addressed by the analysis of 55 retrospective DNA samples extracted directly from clinical material. The method showed 100% sensitivity and specificity compared to those of the combined results of cultivation and panfungal PCR followed by sequencing used as a gold standard. In conclusion, this newly developed f-ITS2-PCR-CE analytical approach was shown to be a fast, sensitive, and highly reproducible tool for both culture-dependent and culture-independent identification of clinically important Candida strains, including species of the "psilosis" complex.

Correlations of the changes in bioptic findings with echocardiographic, clinical and laboratory parameters in patients with inflammatory cardiomyopathy.

Patients with myocarditis and left ventricular (LV) dysfunction may improve after standard heart failure therapy. This improvement seems to be related to retreat of myocardial inflammation. The aim of the present study was to assess changes in clinical, echocardiographic and some laboratory parameters and to correlate them with changes in the number of inflammatory infiltrating cells in endomyocardial biopsy (EMB) samples during the 6-month follow-up, and to define predictors of LV function improvement among baseline parameters. Forty patients with biopsy-proven myocarditis and impaired LV function (LV ejection fraction-LVEF <40 %) with heart failure symptoms ≤ 6 months were evaluated. Myocarditis was defined as the presence of >14 mononuclear leukocytes/mm(2) and/or >7 T-lymphocytes/mm(2) in the baseline EMB. The EMB, echocardiography and clinical evaluation were repeated after 6 months of standard heart failure therapy. LVEF improved on average from 25 ± 9 to 42 ± 12 % (p < 0.001); LV end-systolic volume and LV end-diastolic volume (LVEDV) decreased from 158 ± 61 to 111 ± 58 ml and from 211 ± 69 to 178 ± 63 ml (both p < 0.001). NYHA class decreased from 2.6 ± 0.5 to 1.6 ± 0.6 (p < 0.001) and NTproBNP from 2892 ± 3227 to 851 ± 1835 µg/ml (p < 0.001). A decrease in the number of infiltrating leukocytes (CD45+/LCA+) from 23 ± 15 to 13 ± 8 cells/mm(2) and in the number of infiltrating T lymphocytes (CD3+) from 7 ± 5 to 4 ± 3 cells/mm(2) (both p < 0.001) was observed. The decline in the number of infiltrating CD45+ cells significantly correlated with the change in LVEF (R = -0.43; p = 0.006), LVEDV (R = 0.39; p = 0.012), NYHA classification (R = 0.35; p = 0.025), and NTproBNP (R = 0.33; p = 0.045). The decrease in the number of CD3+ cells correlated with the change of systolic and diastolic diameters of the left ventricle (R = -0.33; p = 0.038 and R = -0.45; p = 0.003) and with the change in LVEDV (R = -0.43; p = 0.006). Tricuspid annular plane systolic excursion (TAPSE) (OR 0.61; p = 0.005) and early transmitral diastolic flow velocity (E wave) (OR 0.89; p = 0.002) were identified as predictors of LVEF improvement. Improvements in clinical status, LV function and NTproBNP levels correlated with decrease in the number of infiltrating inflammatory cells. TAPSE and E wave velocity were significant predictors of improvement in multivariate regression. Our observations suggest that contemporary guidelines-based therapy of heart failure is an effective treatment option in patients with recent onset biopsy-proven inflammatory cardiomyopathy.

Rapid identification of medically important Candida isolates using high resolution melting analysis.

An increasing trend in non albicans infections and various susceptibility patterns to antifungal agents implies a requirement for the quick and reliable identification of a number of medically important Candida species. Real-time PCR followed by high resolution melting analysis (HRMA) was developed, tested on 25 reference Candida collection strains and validated on an additional 143 clinical isolates in this study. All reference strains and clinical isolates inconclusive when using phenotypic methods and/or HRMA were analysed using ITS2 sequencing. Considering reference and clinical strains together, 23 out of 27 Candida species could be clearly distinguished by HRMA, while the remaining 4 species were grouped in 2 pairs, when applying the mean Tm ± 3 SD values, the shape of the derivative melting curve (dMelt curve) and, in some cases, the normalized and temperature-shifted difference plot against C. krusei. HRMA as a simple, rapid and inexpensive tool was shown to be useful in identifying a wide spectrum of clinically important Candida species. It may complement the current clinical diagnostic approach based on commercially available biochemical kits.

The variable clinical course of peripartum cardiomyopathy.

BACKGROUND: In Europe, peripartum cardiomyopathy (PPCM) is a rare disorder, often difficult to diagnose and it has a variable clinical course. The aim of this report was to describe and discuss the individual variability of this disorder and its management. PATIENTS AND METHODS: Three cases of PPCM manifesting as severe heart failure are compared. Common was the presence of myocardial inflammation detected by endomyocardial biopsy. Different were treatment methods and clinical course. Modern therapeutic concepts such as immunosuppressive therapy and bromocriptin administration are discussed, as well as non-pharmacological approaches. CONCLUSION: In the differential diagnostics of dyspnea associated with pregnancy and childbirth, PPCM should be considered. The potentially severe course of the disease requires hospitalization with the possibility of comprehensive heart failure treatment, including non-pharmacological approaches such as device therapy and heart transplantation.

Separation of phenotypically indistinguishable Candida species, C. orthopsilosis, C. metapsilosis and C. parapsilosis, by capillary electromigration techniques.

At the current state of laboratory diagnostics, methods for fast identification of phenotypically indistinguishable species are difficult or inaccurate. An example is represented by Candida parapsilosis, which is the second most common yeast species isolated from bloodstream infections. C. parapsilosis comprises a complex of three genetically distinct groups. Genotypes II and III have been designated as the separate species Candida orthopsilosis and Candida metapsilosis, phenotypically indistinguishable. The considerable genetic variability of these newly described yeasts species has caused difficulties in the development of molecular techniques for their precise identification. Similarly, the detection of biofilm formation, which is considered as an important yeast virulence factor, is accompanied by difficulties. In this study we optimize the first precise and reproducible method for the separation and possible identification of C. orthopsilosis, C. metapsilosis and C. parapsilosis as well as the detection of their ability to form biofilm. The method is based on capillary isoelectric focusing and capillary electrophoresis with UV detection. In capillary isoelectric focusing, very narrow pH gradients were established. With such gradients, differences in isoelectric points of biofilm-negative and biofilm-positive species calculated from the migration times of the selected pI markers were below 0.03 pI units. In the capillary zone electrophoresis narrow zones of the cells of Candida species were detected with sufficient resolution. The values of the isoelectric point and the migration velocities of the examined species were independent on the origin of the tested strains. Capillary isoelectric focusing was examined also for the separation and detection of the cultivated biofilm-negative C. parapsilosis in the blood serum.

Differentiation of Staphylococcus spp. by high-resolution melting analysis.

High-resolution melting analysis (HRMA) is a fast (post-PCR) high-throughput method to scan for sequence variations in a target gene. The aim of this study was to test the potential of HRMA to distinguish particular bacterial species of the Staphylococcus genus even when using a broad-range PCR within the 16S rRNA gene where sequence differences are minimal. Genomic DNA samples isolated from 12 reference staphylococcal strains (Staphylococcus aureus, Staphylococcus capitis, Staphylococcus caprae, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus intermedius, Staphylococcus saprophyticus, Staphylococcus sciuri, Staphylococcus simulans, Staphylococcus warneri, and Staphylococcus xylosus) were subjected to a real-time PCR amplification of the 16S rRNA gene in the presence of fluorescent dye EvaGreen™, followed by HRMA. Melting profiles were used as molecular fingerprints for bacterial species differentiation. HRMA of S. saprophyticus and S. xylosus resulted in undistinguishable profiles because of their identical sequences in the analyzed 16S rRNA region. The remaining reference strains were fully differentiated either directly or via high-resolution plots obtained by heteroduplex formation between coamplified PCR products of the tested staphylococcal strain and phylogenetically unrelated strain.

Detection of Cardiobacterium valvarum in a patient with aortic valve infective endocarditis by broad-range PCR.

Cardiobacterium valvarum, a fastidious Gram-negative bacterium, was detected in the aortic valve of a previously healthy 63-year-old man by broad-range PCR and 16S rRNA gene sequencing. In contrast to the patients in five previously published cases, our patient had neither a congenital bicuspid nor a prosthetic aortic valve. Here, we present a case of C. valvarum native tricuspid aortic valve infective endocarditis and a review of the literature.