Complete genome sequence of three Staphylococcus epidermidis strains isolated from patients with skin diseases in Japan.

Staphylococcus epidermidis is a member of the human skin microbiota as a commensal organism but could be an important opportunistic pathogen for immunocompromised individuals. Here, we report the complete genome sequence of three S. epidermidis strains isolated from patients with skin diseases.

Aberrant sparganosis in cat caused by Spirometra mansoni (Cestoda: Diphyllobothriidae): a case report.

BACKGROUND: Sparganosis is a rare zoonotic disease caused by plerocercoid larvae of the genera Spirometra or Sparganum (Cestoda: Diphyllobothriidae). The larvae of Spirometra generally do not undergo asexual reproduction, whereas those of Sparganum can induce proliferative lesions in infected tissues. This paper presents an unusual case of proliferative sparganosis due to infection with Spirometra mansoni in a cat, normally considered a definitive host of the species. CASE PRESENTATION: A 9-year-old male domestic cat was presented with a mass on the right side of the face that underwent progressive enlargement for 1 month. The morphological and histopathological examinations revealed multiple asexual proliferative cestode larvae in the lesions, suggestive of proliferative sparganosis. Next-generation sequencing analysis of formalin-fixed and paraffin-embedded specimens of surgically excised tissue indicated that the worm was Spirometra mansoni. CONCLUSION: Although S. mansoni a common tapeworm species found in the small intestine of domestic cats and dogs in Japan, proliferative sparganosis is extremely rare. This is the first confirmed case of proliferative sparganosis due to infection with S. mansoni in cat.

Microbiome of Zoophytophagous Biological Control Agent Nesidiocoris tenuis.

Many insects are associated with endosymbionts that influence the feeding, reproduction, and distribution of their hosts. Although the small green mirid, Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae), a zoophytophagous predator that feeds on plants as well as arthropods, is a globally important biological control agent, its microbiome has not been sufficiently studied. In the present study, we assessed the microbiome variation in 96 N. tenuis individuals from 14 locations throughout Japan, based on amplicon sequencing of the 16S ribosomal RNA gene. Nine major bacteria associated with N. tenuis were identified: Rickettsia, two strains of Wolbachia, Spiroplasma, Providencia, Serratia, Pseudochrobactrum, Lactococcus, and Stenotrophomonas. Additionally, a diagnostic PCR analysis for three typical insect reproductive manipulators, Rickettsia, Wolbachia, and Spiroplasma, was performed on a larger sample size (n = 360) of N. tenuis individuals; the most prevalent symbiont was Rickettsia (69.7%), followed by Wolbachia (39.2%) and Spiroplasma (6.1%). Although some symbionts were co-infected, their prevalence did not exhibit any specific tendency, such as a high frequency in specific infection combinations. The infection frequency of Rickettsia was significantly correlated with latitude and temperature, while that of Wolbachia and Spiroplasma was significantly correlated with host plants. The predominance of these bacteria and the absence of obligate symbionts suggested that the N. tenuis microbiome is typical for predatory arthropods rather than sap-feeding insects. Rickettsia and Wolbachia were vertically transmitted rather than horizontally transmitted from the prey. The functional validation of each symbiont would be warranted to develop N. tenuis as a biological control agent.

The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus.

BACKGROUND: The first metazoan genome sequenced, that of Caenorhabditis elegans, has motivated animal genome evolution studies. To date > 50 species from the genus Caenorhabditis have been sequenced, allowing research on genome variation. RESULTS: In the present study, we describe a new gonochoristic species, Caenorhabditis niphades n. sp., previously referred as C. sp. 36, isolated from adult weevils (Niphades variegatus), with whom they appear to be tightly associated during its life cycle. Along with a species description, we sequenced the genome of C. niphades n. sp. and produced a chromosome-level assembly. A genome comparison highlighted that C. niphades n. sp. has the smallest genome (59 Mbp) so far sequenced in the Elegans supergroup, despite being closely related to a species with an exceptionally large genome, C. japonica. CONCLUSIONS: The compact genome of C. niphades n. sp. can serve as a key resource for comparative evolutionary studies of genome and gene number expansions in Caenorhabditis species.

piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode.

The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21-22 nt long sRNAs with a 5' uridine (21-22Us) and a 5' monophosphate, and (ii) 27 nt long sRNAs with a 5' guanine/adenine (27GAs) and a 5' modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome. Overall, we have shown that an alternative class of sRNAs compensate for the loss of piRNAs and regulate TE activity in nematodes outside of Clade V.

Complete Genome Sequences of Two Streptococcus suis Strains Isolated from Asymptomatic Pigs.

Streptococcus suis is an important zoonotic pathogen that causes major economic problems in the pig industry worldwide and serious infections in humans, including meningitis and septicemia. Here, we report the complete genome sequences of two strains isolated from asymptomatic pigs.

Nearly Complete Genome Assembly of the Pinewood Nematode Bursaphelenchus xylophilus Strain Ka4C1.

Bursaphelenchus xylophilus has been destroying pine forests in East Asia and western Europe. Here, we report its nearly complete genomic sequence containing five ∼12-Mb scaffolds and one ∼15-Mb scaffold representing six chromosomes. Large repeat regions that were previously unidentified are now reasonably integrated, particularly in the ∼15-Mb scaffold.

Complete Genome Sequences of Streptococcus pyogenes Serotype M3, M28, and M89 Strains Isolated from Human Patients in Japan, 1994 to 2009.

Streptococcus pyogenes (group A Streptococcus [GAS]) is a major human pathogen that occasionally causes severe and life-threatening invasive diseases. Here, we report the complete genome sequences of four GAS strains of three M types, which were isolated from patients with severe invasive disease in Japan.

Telomere-to-Telomere Genome Assembly of Bursaphelenchus okinawaensis Strain SH1.

Bursaphelenchus okinawaensis is a self-fertilizing, hermaphroditic, fungus-feeding nematode used as a laboratory model for the genus Bursaphelenchus, which includes the important pathogen Bursaphelenchus xylophilus Here, we report the nearly complete genome sequence of B. okinawaensis The 70-Mbp assembly contained six scaffolds (>11 Mbp each) with telomere repeats on their ends, indicating complete chromosomes.

Improved 18S and 28S rDNA primer sets for NGS-based parasite detection.

The development and application of next-generation sequencing (NGS) have enabled comprehensive analyses of the microbial community through extensive parallel sequencing. Current analyses of the eukaryotic microbial community are primarily based on polymerase chain reaction amplification of 18S rRNA gene (rDNA) fragments. We found that widely-used 18S rDNA primers can amplify numerous stretches of the bacterial 16S rRNA gene, preventing the high-throughput detection of rare eukaryotic species, particularly in bacteria-rich samples such as faecal material. In this study, we employed in silico and NGS-based analyses of faecal samples to evaluated the existing primers targeting eukaryotic 18S and 28S rDNA in terms of avoiding bacterial read contamination and improving taxonomic coverage for eukaryotes, with a particular emphasis on parasite taxa. Our findings revealed that newly selected primer sets could achieve these objectives, representing an alternative strategy for NGS.

Complete Genome Sequences of Eight Methicillin-Resistant Staphylococcus aureus Strains Isolated from Patients in Japan.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen causing nosocomial infections, and the clinical manifestations of MRSA range from asymptomatic colonization of the nasal mucosa to soft tissue infection to fulminant invasive disease. Here, we report the complete genome sequences of eight MRSA strains isolated from patients in Japan.

Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level.

Strongyloides spp., gastrointestinal nematode parasites of humans and other animals, have genetically identical parasitic and free-living adult life cycle stages. This is an almost unique feature amongst nematodes and comparison of these two stages can provide insights into the genetic basis and evolution of Strongyloides nematode parasitism. Here, we present RNAseq data for S. venezuelensis, a parasite of rodents, and identify genes that are differentially expressed in parasitic and free-living life cycle stages. Comparison of these data with analogous RNAseq data for three other Strongyloides spp., has identified key protein-coding gene families with a putative role in parasitism including WAGO-like Argonautes (at the genus level) and speckle-type POZ-like coding genes (S. venezuelensis-S. papillosus phylogenetic subclade level). Diverse gene families are uniquely upregulated in the parasitic stage of all four Strongyloides species, including a distinct upregulation of genes encoding cytochrome P450 in S. venezuelensis, suggesting some diversification of the molecular tools used in the parasitic life cycle stage among individual species. Together, our results identify key gene families with a putative role in Strongyloides parasitism or features of the parasitic life cycle stage, and deepen our understanding of parasitism evolution among Strongyloides species.

The predictability of renin-angiotensin-aldosterone system factors for clinical outcome in patients with acute decompensated heart failure.

Although counter-regulation between B-type natriuretic peptide (BNP) levels and renin-angiotensin-aldosterone system (RAAS) activation in heart failure (HF) has been suggested, whether the regulation is preserved in acute decompensated heart failure (ADHF) patients remains unclear. This study aimed to determine: (1) the relationship between RAAS activation and clinical outcomes in ADHF patients, and (2) the relationships between plasma BNP levels and degrees of activation in RAAS factors. This study included ADHF patients (n = 103, NYHA3-4, plasma BNP > 200 pg/ml). We studied the predictability of RAAS factors for cardiovascular events and the relationships between plasma BNP levels and the degrees of activation in RAAS factors, which were evaluated by plasma renin activity (PRA) and aldosterone concentration (PAC). PRA was a strong predictor of cardiovascular (CV) events over 1 year, even after accounting for plasma BNP levels (hazard ratio (HR): 1.04, CI [1.02-1.06], p < 0.01) and medication such as RAAS blockers (HR: 1.03, CI [1.01-1.05], p < 0.01), whereas PAC was borderline-significant (univariate analysis, p = 0.06). Cut-off value of PRA (5.3 ng/ml/h) was determined by AUC curve. Of the enrolled patients, higher PRA was found in 40 % of them. Although no correlation between the plasma BNP levels and PRA was found (p = 0.36), after adjusting for hemodynamic parameters, eGFR and medication, a correlation was found between them (p = 0.01). Elevated RAAS factors were found in a substantial number of ADHF patients with high plasma BNP levels in the association with hemodynamic state, which predicts poor clinical outcomes. The measurements of RAAS factors help to stratify ADHF patients at risk for further CV events.

Direct comparison of the diagnostic capability of cardiac magnetic resonance and endomyocardial biopsy in patients with heart failure.

AIMS: The diagnostic performance of cardiac magnetic resonance (CMR) has not been compared with that of other imaging modalities. Therefore, this study investigated the diagnostic capabilities of CMR and endomyocardial biopsy (EMB) in patients with heart failure (HF). METHODS AND RESULTS: We studied 136 patients with cardiomyopathy who underwent both CMR and EMB. Independent diagnoses were made according to the results of (i) CMR alone; (ii) EMB alone; (iii) clinical data plus echocardiogram; (iv) clinical data, echocardiogram, plus CMR; and (v) clinical data, echocardiogram, plus EMB. These diagnoses were then compared with the final diagnosis (gold standard) that was made using the complete clinical data, including EMB and CMR. The sensitivities of the diagnosis strategies of (i-v) relative to the final diagnosis were 67, 79, 86, 97, and 100%, respectively. CMR alone demonstrated better sensitivity for cardiac sarcoidosis and greater specificity for dilated cardiomyopathy than EMB alone. CMR also tended to show better sensitivity for hypertensive heart disease. There was no difference between the diagnostic capability of CMR and EMB for hypertrophic cardiomyopathy (HCM). However, CMR showed excellent sensitivity (100%) for apical and obstructive HCM, whereas EMB displayed better sensitivity for dilated HCM. Moreover, combined diagnosis with clinical data, echocardiogram, plus CMR achieved superior agreement with the final diagnosis in comparison with EMB alone. CONCLUSION: Non-invasive CMR demonstrated excellent diagnostic capability for patients with HF and was as effective as or superior to EMB. In particular, the use of CMR in combination with clinical data unrelated to EMB may provide excellent diagnostic accuracy for HF.

Derivation of a mathematical expression for predicting the time to cardiac events in patients with heart failure: a retrospective clinical study.

The prognoses for patients with certain diseases are estimated by averaging the results of clinical trials. To investigate the possibility of deriving a mathematical formula for the estimation of prognosis, we formulated the equation τ=f(x1, …, xp), where x1, …, xp are clinical features and τ represents the clinical outcome for heart failure (HF). We attempted to determine the function to mathematically formulate the relationship between clinical features and outcomes for these patients. We followed 151 patients (mean age: 68.6±14.6 years; men: 61.6%) who were consecutively hospitalized and discharged as a result of acute decompensated HF (ADHF) between May 2006 and December 2009. The mathematical analysis was performed through a probabilistic modeling of the relational data by assuming a Poisson process for rehospitalization owing to HF and by linearly approximating the relationship between the clinical factors and the mean elapsed time to rehospitalization. The former assumption was validated by a statistical test of the data, and the contribution of each parameter was assessed based on the coefficients of the linear relation. Using a regularization method to analyze 402 clinical parameters, we identified 252 factors that substantially influenced the elapsed time until rehospitalization. With the probability model based on the Poisson process, the actual (X; 388±377 days) and estimated (Y; 398±381 days) elapsed times to rehospitalization were tightly correlated (Y=1.0076X+6.5531, R(2)=0.9879, P<0.0001). We established a mathematical formula that closely predicts the clinical outcomes of patients who are hospitalized with ADHF and discharged after appropriate treatment.

Serum blood urea nitrogen and plasma brain natriuretic Peptide and low diastolic blood pressure predict cardiovascular morbidity and mortality following discharge in acute decompensated heart failure patients.

BACKGROUND: Patients with heart failure (HF) have a high risk of cardiovascular (CV) death and re-hospitalization. The purpose of the present study was therefore to investigate predictors of CV death and re-hospitalization for acute decompensated HF (ADHF). METHODS AND RESULTS: A total of 225 patients aged 67.2±15.2 years, including 134 men (59.6%), who were hospitalized for ADHF between 2008 and 2009, were followed up. After discharge, the relationship between clinical parameters and CV events (ie, CV death or re-hospitalization for HF) was examined. Follow-up was continued until 30 April 2011. The most important predictors of re-hospitalization were serum blood urea nitrogen (BUN; adjusted hazard ratio [HR], 1.02; 95% confidence interval [CI]: 1.00-1.03, P=0.01), plasma brain natriuretic peptide (BNP; adjusted HR, 1.85; 95% CI: 1.12-3.04, P=0.02), and diastolic blood pressure (DBP; adjusted HR, 0.97; 95% CI: 0.94-1.00, P=0.049). The only predictor of CV mortality was a high BUN (adjusted HR, 1.05; 95% CI: 1.01-1.09, P=0.01). CONCLUSIONS: High serum BUN (≥22.5mg/dl), high plasma BNP (≥250pg/ml), and low DBP (<60mmHg) predict CV events in patients hospitalized for ADHF. These factors may identify high-risk patients for CV events and provide therapeutic targets for managing HF. (Circ J 2012; 76: 2372-2379).

H(2) mediates cardioprotection via involvements of K(ATP) channels and permeability transition pores of mitochondria in dogs.

PURPOSE: Inhalation of hydrogen (H(2)) gas has been shown to limit infarct size following ischemia-reperfusion injury in rat hearts. However, H(2) gas-induced cardioprotection has not been tested in large animals and the precise cellular mechanism of protection has not been elucidated. We investigated whether opening of mitochondrial ATP-sensitive K+ channels (mK(ATP)) and subsequent inhibition of mitochondrial permeability transition pores (mPTP) mediates the infarct size-limiting effect of H(2) gas in canine hearts. METHODS: The left anterior descending coronary artery of beagle dogs was occluded for 90 min followed by reperfusion for 6 h. Either 1.3% H(2) or control gas was inhaled from 10 min prior to start of reperfusion until 1 h of reperfusion, in the presence or absence of either 5-hydroxydecanoate (5-HD; a selective mK(ATP) blocker), or atractyloside (Atr; a mPTP opener). RESULTS: Systemic hemodynamic parameters did not differ among the groups. Nevertheless, H(2) gas inhalation reduced infarct size normalized by risk area (20.6±2.8% vs. control gas 44.0±2.0%; p<0.001), and administration of either 5-HD or Atr abolished the infarct size-limiting effect of H(2) gas (42.0±2.2% with 5-HD and 45.1±2.7% with Atr; both p<0.001 vs. H(2) group). Neither Atr nor 5-HD affected infarct size per se. Among all groups, NAD content and the number of apoptotic and 8-OHdG positive cells was not significantly different, indicating that the cardioprotection afforded by H(2) was not due to anti-oxidative actions or effects on the NADH dehydrogenase pathway. CONCLUSIONS: Inhalation of H(2) gas reduces infarct size in canine hearts via opening of mitochondrial K(ATP) channels followed by inhibition of mPTP. H(2) gas may provide an effective adjunct strategy in patients with acute myocardial infarction receiving reperfusion therapy.

Intractable Prinzmetal's angina three months after implantation of sirolimus-eluting stent.

Sirolimus-eluting stents (SES) prevent neointimal proliferation and have been widely used to treat stenotic lesions in coronary arteries because of a significant reduction of restenosis in comparison with bare-metal stents. Sirolimus, however, may cause endothelial dysfunction by damage to vascular endothelium or impairing vascular repair. Recent studies report the occurrence of exercise- or acetylcholine-induced coronary vasoconstriction in the vessel segments adjacent to the SES. We report here a clinical case of intractable Prinzmetal's angina 3 months after SES implantation and recommend extended, thorough follow up of patients who have undergone SES implantation.