Flanders hapavirus in western North America.

Flanders virus (FLAV; family Rhabdoviridae) is a mosquito-borne hapavirus with no known pathology that is frequently isolated during arbovirus surveillance programs. Here, we document the presence of FLAV in Culex tarsalis mosquitoes and a Canada goose (Branta canadensis) collected in western North America, outside of the currently recognized range of FLAV. Until now, FLAV-like viruses detected in the western United States were assumed to be Hart Park virus (HPV, family Rhabdoviridae), a closely related congener.

IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma.

Rationale: Quantification of type 2 inflammation provided a molecular basis for heterogeneity in asthma. Non-type 2 pathways that contribute to asthma pathogenesis are not well understood.

Objectives: To identify dysregulated pathways beyond type 2 inflammation.

Characterization of a novel insect-specific flavivirus from Brazil: potential for inhibition of infection of arthropod cells with medically important flaviviruses.

In the past decade, there has been an upsurge in the number of newly described insect-specific flaviviruses isolated pan-globally. We recently described the isolation of a novel flavivirus (tentatively designated 'Nhumirim virus'; NHUV) that represents an example of a unique subset of apparently insect-specific viruses that phylogenetically affiliate with dual-host mosquito-borne flaviviruses despite appearing to be limited to replication in mosquito cells. We characterized the in vitro growth potential and 3' untranslated region (UTR) sequence homology with alternative flaviviruses, and evaluated the virus's capacity to suppress replication of representative Culex spp.

Longitudinal analysis of sarcoidosis blood transcriptomic signatures and disease outcomes.

Previously, we demonstrated concordance in differentially expressed genes in sarcoidosis blood and lung, implicating shared dysfunction of specific immune pathways. In the present study, we hypothesised that expression levels of candidate genes in sarcoidosis blood could predict and track with disease outcomes longitudinally. We applied Ingenuity Pathway Analysis to a cross-sectional derivation microarray dataset (n=38) to identify canonical pathways and candidate genes associated with sarcoidosis.

A decade of HIV-1 drug resistance in the United States: trends and characteristics in a large protease/reverse transcriptase and co-receptor tropism database from 2003 to 2012.

Background: Drug resistance testing and co-receptor tropism determination are key components of the management of antiretroviral therapy for HIV-1-infected individuals. The purpose of this study was to examine trends of HIV-1 resistance and viral evolution in the past decade by surveying a large commercial patient testing database.

Methods: Temporal trends of drug resistance, viral fitness and co-receptor usage among samples submitted for routine phenotypic and genotypic resistance testing to protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs), as well as for tropism determination were investigated.

A microfluidic DNA library preparation platform for next-generation sequencing.

Next-generation sequencing (NGS) is emerging as a powerful tool for elucidating genetic information for a wide range of applications. Unfortunately, the surging popularity of NGS has not yet been accompanied by an improvement in automated techniques for preparing formatted sequencing libraries. To address this challenge, we have developed a prototype microfluidic system for preparing sequencer-ready DNA libraries for analysis by Illumina sequencing.

A qPCR-based metric of Th2 airway inflammation in asthma.

Background: Using microarray profiling of airway epithelial cells, we previously identified a Th2-high molecular phenotype of asthma based on expression of periostin, CLCA1 and serpinB2 and characterized by specific inflammatory, remodeling, and treatment response features. The goal of the current study was to develop a qPCR-based assay of Th2 inflammation to overcome the limitations of microarray-based methods.

Methods: Airway epithelial brushings were obtained by bronchoscopy from two clinical studies comprising 44 healthy controls and 62 subjects with asthma, 39 of whom were studied before and after a standardized 8 week course of inhaled corticosteroids (ICS).

Peregrine: A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material.

Use of second generation sequencing (SGS) technologies for transcriptional profiling (RNA-Seq) has revolutionized transcriptomics, enabling measurement of RNA abundances with unprecedented specificity and sensitivity and the discovery of novel RNA species. Preparation of RNA-Seq libraries requires conversion of the RNA starting material into cDNA flanked by platform-specific adaptor sequences. Each of the published methods and commercial kits currently available for RNA-Seq library preparation suffers from at least one major drawback, including long processing times, large starting material requirements, uneven coverage, loss of strand information and high cost.

Airway epithelial miRNA expression is altered in asthma.

Rationale: Changes in airway epithelial cell differentiation, driven in part by IL-13, are important in asthma. Micro-RNAs (miRNAs) regulate cell differentiation in many systems and could contribute to epithelial abnormalities in asthma.

Objectives: To determine whether airway epithelial miRNA expression is altered in asthma and identify IL-13-regulated miRNAs.

Periostin is a systemic biomarker of eosinophilic airway inflammation in asthmatic patients.

Background: Eosinophilic airway inflammation is heterogeneous in asthmatic patients. We recently described a distinct subtype of asthma defined by the expression of genes inducible by T(H)2 cytokines in bronchial epithelium. This gene signature, which includes periostin, is present in approximately half of asthmatic patients and correlates with eosinophilic airway inflammation.

Sarcoidosis blood transcriptome reflects lung inflammation and overlaps with tuberculosis.

Rationale: Sarcoidosis is a granulomatous disease of unknown etiology, although M. tuberculosis may play a role in the pathogenesis. The traditional view holds that inflammation in sarcoidosis is compartmentalized to involved organs.

Accumulation of intraepithelial mast cells with a unique protease phenotype in T(H)2-high asthma.

Background: Previously, we found that mast cell tryptases and carboxypeptidase A3 (CPA3) are differentially expressed in the airway epithelium in asthmatic subjects. We also found that asthmatic subjects can be divided into 2 subgroups ("T(H)2 high" and "T(H)2 low" asthma) based on epithelial cell gene signatures for the activity of T(H)2 cytokines.

Objectives: We sought to characterize intraepithelial mast cells (IEMCs) in asthma.

Rapid changes in rotaviral genotypes in Ecuador.

Previous studies suggest that the emerging G9P[8] genotype was the most prevalent rotavirus genotype in Ecuador during 2005. This present study provides a temporal analysis of the distribution of rotavirus genotypes in two locations within Ecuador by adding additional years (2006 - early 2008) to the originally reported 2005 data. Data were collected in a rural (northern coastal Ecuador) and urban (Quito) area.

Global spread of mobile antimicrobial drug resistance determinants in human and animal Escherichia coli and Salmonella strains causing community-acquired infections.

Background: Antimicrobial drugs used in human infection treatment and animal husbandry may select for drug-resistant bacterial pathogens, which are increasingly observed worldwide. We sought to examine the extent to which identical mobile drug resistance elements are shared across common pathogens isolated from human and animal sources.

Methods: We compared the distribution of one class of mobile elements--integrons and gene cassettes--among uropathogenic Escherichia coli isolates, Salmonella enterica serovar Typhimurium isolates from human diarrhea cases, and E.

Characterization of novel VP7, VP4, and VP6 genotypes of a previously untypeable group A rotavirus.

Rotavirus is the most common cause of acute gastroenteritis among infants and young children throughout the world, but rotavirus cases in developing countries account for nearly all of the approximately 600,000 annual deaths. We studied the epidemiology of rotavirus in 22 rural communities in northern coastal Ecuador over a five-year period. From 250 rotavirus positive stool specimens, the percentage that could not be RT-PCR genotyped for VP4 and VP7 was 77% and 63%, respectively.

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies.

This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database.

Genotypic analyses of uropathogenic Escherichia coli based on fimH single nucleotide polymorphisms (SNPs).

The application of genotyping techniques for subtyping uropathogenic Escherichia coli has contributed to better understanding of the epidemiology of community-acquired urinary tract infection (UTI). However, the current techniques are hampered by limited reproducibility, poor discriminatory power, labour-intensive performance or high cost. A screening test that is sequence-based would provide an inexpensive, reproducible way to subtype E.

Symptomatic and subclinical infection with rotavirus P[8]G9, rural Ecuador.

During the past decade, rotavirus genotype G9 has spread throughout the world, adding to and sometimes supplanting the common genotypes G1-G4. We report evidence of this spread in a population sample within rural Ecuador. A total of 1,656 stool samples were collected from both patients with diarrhea and from asymptomatic residents in 22 remote communities in northwestern Ecuador from August 2003 through February 2006.

High prevalence of enteroinvasive Escherichia coli isolated in a remote region of northern coastal Ecuador.

Enteroinvasive Escherichia coli (EIEC) causes dysentery; however, it is less widely reported than other etiological agents in studies of diarrhea worldwide. Between August 2003 and July 2005, stool samples were collected in case-control studies in 22 rural communities in northwestern Ecuador. Infection was assessed by PCR specific for LT and STa genes of enterotoxigenic E.

Origin of class 1 and 2 integrons and gene cassettes in a population-based sample of uropathogenic Escherichia coli.

The prevalence of urinary tract infections (UTI) caused by trimethoprim-sulfamethoxazole (TMP-SMX)-resistant Escherichia coli is increasing and varies geographically in the United States. Recent community-based UTI studies have demonstrated geographic clustering of an Escherichia coli clonal group, suggesting occurrence of a community outbreak of UTI. A large proportion of this clonal group (designated CgA) isolated from women in a California college community was found to be resistant to TMP-SMX.

Analysis of a uropathogenic Escherichia coli clonal group by multilocus sequence typing.

Although many strain typing methods exist for pathogenic Escherichia coli, most have drawbacks in terms of resolving power, interpretability, or scalability. For this reason, multilocus sequence typing (MLST) is an appealing alternative. However, its applicability to different pathogens in specific epidemiologic contexts is not well understood.