Complete Genome Sequence of a Divergent Human Rhinovirus C Isolate from an Infant with Severe Community-Acquired Pneumonia in Colorado, USA.
Ontology highlight
ABSTRACT:
SUBMITTER: Langelier C
PROVIDER: S-EPMC5722057 | biostudies-literature | 2017 Nov
REPOSITORIES: biostudies-literature
Publications
Complete Genome Sequence of a Divergent Human Rhinovirus C Isolate from an Infant with Severe Community-Acquired Pneumonia in Colorado, USA.
Langelier Charles C White Corin V CV Sontag Marci K MK Mourani Peter M PM DeRisi Joseph L JL
Genome announcements 20171130 48
Here, we report the genome sequence of a divergent human rhinovirus C isolate identified from an infant with a severe community-acquired respiratory infection. RNA sequencing performed on an Illumina platform identified reads aligning to human rhinovirus species, which were <i>de novo</i> assembled to produce a coding-complete genome sequence. ...[more]
Similar Datasets
Project description:BackgroundRhinoviruses (RVs) are ubiquitous respiratory pathogens that often cause mild or subclinical infections. Molecular detection of RVs from the upper respiratory tract can be prolonged, complicating etiologic association in persons with severe lower respiratory tract infections. Little is known about RV viremia and its value as a diagnostic indicator in persons hospitalized with community-acquired pneumonia (CAP).MethodsSera from RV-positive children and adults hospitalized with CAP were tested for RV by real-time reverse-transcription polymerase chain reaction. Rhinovirus species and type were determined by partial genome sequencing.ResultsOverall, 57 of 570 (10%) RV-positive patients were viremic, and all were children aged <10 years (n = 57/375; 15.2%). Although RV-A was the most common RV species detected from respiratory specimens (48.8%), almost all viremias were RV-C (98.2%). Viremic patients had fewer codetected pathogens and were more likely to have chest retractions, wheezing, and a history of underlying asthma/reactive airway disease than patients without viremia.ConclusionsMore than 1 out of 7 RV-infected children aged <10 years hospitalized with CAP were viremic. In contrast with other RV species, RV-C infections were highly associated with viremia and were usually the only respiratory pathogen identified, suggesting that RV-C viremia may be an important diagnostic indicator in pediatric pneumonia.
| S-EPMC5724377 | biostudies-literature
Project description:BACKGROUND:Human rhinoviruses (HRVs) are among the most common causes of community-acquired pneumonia (CAP) in children. However, the differential roles of the three HRV species HRV-A, HRV-B, and HRV-C in pediatric CAP are not fully understood. OBJECTIVE:To determine the distribution of HRV species and their roles in children hospitalized with CAP in Beijing, China. STUDY DESIGN:Nasopharyngeal aspirates were collected between April 2007 and March 2008 from 554 children with a primary diagnosis of CAP. HRVs in the clinical samples were detected by RT-PCR and by sequencing. Infections with other respiratory viruses were identified by PCR. RESULTS:HRVs were detected in 99 patients (17.87%). Among these patients, 51.52% tested positive for HRV-A, 38.38% for HRV-C, and 10.10% for HRV-B. HRVs were detected throughout the study period. The monthly distribution of HRV infections varied with HRV species. Median age, gender, symptoms, severity, and duration of hospitalization for single HRV-C infections were similar to those observed for single HRV-A infections. Co-infections with other respiratory viruses were detected in 57.58% of the HRV-positive children. HRV/RSV dual infections were correlated with a higher frequency of shortness of breath (HRV-A group, P(2 tail)= 0.01; HRV-C group, P(2 tail) = 0.015) and lower median ages (HRV-A group, P(2 tail) = 0.049; HRV-C group, P(2 tail) = 0.009). CONCLUSION:Our study shows that HRV-C strains circulate at a prevalence intermediate between HRV-A and HRV-B. The severity of clinical manifestations for HRV-C is comparable to that for HRV-A in children with CAP. These findings point to an important role of both HRV-A and HRV-C in pediatric CAP.
| S-EPMC7185749 | biostudies-literature
Project description:We present a case of severe pneumonia, associated with a prolonged infection by a species C rhinovirus (HRV) in a 3-week old neonate. HRV RNA was identified in nasal and nasopharyngeal secretions, bronchoalveolar lavage and bronchial specimens, stool and urine, collected from the patient during a one-month period. No other viral or bacterial agents were detected. Sequence analysis of two regions of the viral genome, amplified directly from the clinical specimens revealed a novel HRV-C variant. These observations highlight the occurrence of severe neonatal infections caused by HRVs and the need of rapid viral diagnostics for their detection.
| S-EPMC7172304 | biostudies-literature
Project description:Community-acquired pneumonia is a significant clinical and public health problem. Defining and predicting severe pneumonia is difficult but important.Several new predictive models and more sophisticated approaches to describing pneumonia severity have been recently proposed, with subsequent validation in varied patient populations. Early data suggest that biomarkers may be useful in the future.Definitions of pneumonia severity depend on the relevant clinical or public health question. A health services reference definition seems most useful in most settings. The Infectious Disease Society of America/American Thoracic Society 2007 guidelines and SMART-COP are two recent promising methods for predicting severe pneumonia at the time of presentation. The traditional pneumonia severity index and Confusion Uremia Respiratory rate Blood pressure (CURB)-65 models are less useful. Accurate assessment of severity has important implications for triage, outcome, and defining populations for research applications. Novel biomarkers, while somewhat promising, do not yet have a validated role in pneumonia severity assessment.
| S-EPMC2875269 | biostudies-literature
Project description:The objective of this study was to compare systemic and local cytokine profiles and neutrophil responses in patients with severe versus non-severe community-acquired pneumonia (CAP). Hospitalized patients with CAP were grouped according to the pneumonia severity index (PSI), as non-severe (PSI?<?91 points) or severe (PSI???91 points). Blood and sputum samples were collected upon admission. Compared to non-severe CAP patients, the severe CAP group showed higher plasma levels of pro- and anti-inflammatory cytokines but in contrast, lower sputum concentrations of pro-inflammatory cytokines. Blood neutrophil functional responses were elevated in CAP patients compared to healthy controls. However, neutrophils from severe CAP patients showed reduced respiratory burst activity compared to the non-severe group. Results indicate that patients with severe CAP fail to mount a robust local pro-inflammatory response but exhibit instead a more substantial systemic inflammatory response, suggesting that a key driver of CAP severity may be the ability of the patient to generate an optimal local inflammatory response.
| S-EPMC7087758 | biostudies-literature
Project description:Severe sepsis, may be present on hospital arrival in approximately one-third of patients with community-acquired pneumonia (CAP).To determine the host characteristics and micro-organisms associated with severe sepsis in patients hospitalized with CAP.We performed a prospective multicenter cohort study in 13 Spanish hospital, on 4070 hospitalized CAP patients, 1529 of whom (37.6%) presented with severe sepsis. Severe sepsis CAP was independently associated with older age (>65 years), alcohol abuse (OR, 1.31; 95% CI, 1.07-1.61), chronic obstructive pulmonary disease (COPD) (OR, 1.75; 95% CI, 1.50-2.04) and renal disease (OR, 1.57; 95% CI, 1.21-2.03), whereas prior antibiotic treatment was a protective factor (OR, 0.62; 95% CI, 0.52-0.73). Bacteremia (OR, 1.37; 95% CI, 1.05-1.79), S pneumoniae (OR, 1.59; 95% CI, 1.31-1.95) and mixed microbial etiology (OR, 1.65; 95% CI, 1.10-2.49) were associated with severe sepsis CAP.CAP patients with COPD, renal disease and alcohol abuse, as well as those with CAP due to S pneumonia or mixed micro-organisms are more likely to present to the hospital with severe sepsis.
| S-EPMC4699794 | biostudies-other
Project description:Porcine epidemic diarrhea virus (PEDV) is newly emerging in the United States. PEDV strain USA/Colorado/2013 (CO/13) was obtained from a 7-day-old piglet with severe diarrhea, and the complete genome was sequenced to further study the PEDV outbreak in the United States.
| S-EPMC3738886 | biostudies-literature
Project description:We report a case of community-acquired pneumonia in a patient in China. We verified Legionella pneumophila infection through next-generation sequencing of blood, sputum, and pleural effusion samples. Our results show the usefulness of next-generation sequencing and of testing different samples early in the course of illness to identify this bacterium.
| S-EPMC6924908 | biostudies-literature
Project description:IntroductionCommunity-acquired pneumonia (CAP) requiring intensive care unit (ICU) treatment commonly causes acute respiratory failure with high mortality. Kallistatin, an endogenous tissue kallikrein inhibitor, has been reported to be protective in various human diseases. The aim of this study was to assess the correlations of kallistatin with other biomarkers and to determine whether kallistatin levels have a prognostic value in severe CAP.MethodsPlasma samples and clinical data were prospectively collected from 54 patients with severe CAP requiring ICU admission. Seventeen healthy control subjects were included for comparison. Plasma kallistatin, kallikrein, and other biomarkers of inflammation (tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, IL-6, IL-8, C-reactive protein (CRP)), and anti-coagulation (protein C, anti-thrombin III) were measured on days 1 and 4 of ICU admission. Comparison between survivors (n = 41) and nonsurvivors (n = 13) was performed.ResultsPlasma kallistatin was significantly consumed in severe CAP patients compared with healthy individuals. Lower day 1 kallistatin levels showed a strong trend toward increased mortality (P = 0.018) and higher day 1 CURB-65 scores (P = 0.004). Plasma kallistatin levels on day 1 of ICU admission were significantly decreased in patients who developed septic shock (P = 0.017) and who had acute respiratory distress syndrome (P = 0.044). In addition, kallistatin levels were positively correlated with anti-thrombin III and protein C and inversely correlated with IL-1β, IL-6, and CRP levels. In a multivariate logistic regression analysis, higher day 1 CURB-65 scores were independent predictors of mortality (odds ratio = 29.9; P = 0.009). Also, higher day 1 kallistatin levels were independently associated with a decreased risk of death (odds ratio, 0.1) with a nearly significant statistical difference (P = 0.056). Furthermore, we found that a cutoff level of 6.5 μg/ml of day 1 kallistatin determined by receiver operating characteristic curves could be used to distinguish between patients who survived in 60 days and those who did not.ConclusionsThese results suggest that kallistatin may serve as a novel marker for severe CAP prognosis and may be involved in the pathogenesis of CAP through antiinflammatory and anticoagulation effects.
| S-EPMC4056893 | biostudies-literature
Project description:Pneumonia is the fourth leading cause of death globally, and the reason for the high mortality rate of patients with severe community-acquired pneumonia (SCAP) remains elusive. Corticosteroid treatment reduces mortality in adults with SCAP but can cause numerous adverse events. Therefore, novel therapeutic targets need to be explored and new adjunctive immune drugs are urgently required. We analyzed the transcriptome data of peripheral blood leukocytes from patients with SCAP and healthy controls from three perspectives: differentially expressed genes, predicted functions of differentially expressed long non-coding RNAs, and transcriptional read-through. We discovered that the NETosis pathway was top-ranked in patients with SCAP caused by diverse kinds of pathogens. This provides a potential therapeutic strategy for treating patients. Furthermore, we calculated the correlation between the expression of genes involved in NETosis and the ratio of arterial oxygen partial pressure to fractional inspired oxygen. We identified four novel potential therapeutic targets for NETosis in patients with SCAP, including H4C15, H3-5, DNASE1, and PRKCB. In addition, a higher occurrence of transcriptional read-through is associated with a worse outcome in patients with SCAP, which probably can explain the high mortality rate of patients with SCAP.
| S-EPMC9709478 | biostudies-literature