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Studies of excised lungs show that significant airway attrition in the "quiet" zone occurs early in chronic obstructive pulmonary disease (COPD).To determine if the total number of airways quantified in vivo using computed tomography (CT) reflects early airway-related disease changes and is associated with lung function decline independent of emphysema in COPD.Participants in the multicenter, population-based, longitudinal CanCOLD (Canadian Chronic Obstructive Lung Disease) study underwent inspiratory/expiratory CT at visit 1; spirometry was performed at four visits over 6 years. Emphysema was quantified as the CT inspiratory low-attenuation areas below -950 Hounsfield units. CT total airway count (TAC) was measured as well as airway inner diameter and wall area using anatomically equivalent airways.Participants included never-smokers (n = 286), smokers with normal spirometry at risk for COPD (n = 298), Global Initiative for Chronic Obstructive Lung Disease (GOLD) I COPD (n = 361), and GOLD II COPD (n = 239). TAC was significantly reduced by 19% in both GOLD I and GOLD II compared with never-smokers (P 0.0001) and by 17% in both GOLD I and GOLD II compared with at-risk participants (P 0.0001) after adjusting for low-attenuation areas below -950 Hounsfield units. Further analysis revealed parent airways with missing daughter branches had reduced inner diameters (P 0.0001) and thinner walls (P 0.0001) compared with those without missing daughter branches. Among all CT measures, TAC had the greatest influence on FEVTAC may reflect the airway-related disease changes that accumulate in the "quiet" zone in early/mild COPD, indicating that TAC acquired with commercially available software across various CT platforms may be a biomarker to predict accelerated COPD progression.

Samples of a wild grass showing white leaf symptoms were collected in 2015 in Veracruz, Mexico around sugarcane plantations. DNA amplification, sequencing and phylogenetic analysis revealed the presence of a ‘Candidatus Phytoplasma asteris’-related strain in the plants that were positive using 16S-based and cpn60 PCR assays. The strain determined to be associated with the grass white leaf disease was identified as a member of the 16SrI-B subgroup and a member of the cpn60 I-IIIB subgroup through in silico RFLP analysis. This is the first report of phytoplasma-infected grass plants associated with white leaf disease in Mexico. The implications of these findings are vital for the management of other plant hosts of the family Poaceae such as sugarcane and corn, and point to weedy grasses as a potential source of phytoplasma inoculum for nearby crop plants.

Phytoplasmas are plant-pathogenic bacteria that are associated with yield losses in many crop plants worldwide. Phytoplasma strain differentiation is accomplished using

Phytoplasmas (species of the genus 'CandidatusPhytoplasma') are insect-vectored phytopathogenic bacteria associated with economically and ecologically important crop diseases. Strawberry production represents an important part of agricultural activity in Mexico and elsewhere, and infection of plants with phytoplasma renders the fruit inedible by altering plant development, resulting in virescence and phyllody. In this study we examined samples taken from four strawberry plants showing symptoms associated with strawberry green petal disease and from two periwinkle plants showing virescence, sampled in different areas of Mexico. Analysis of the 16S rRNA-encoding sequences showed that the plants were infected with a phytoplasma previously identified as Mexican periwinkle virescence (MPV; 16SrXIII). Examination of bacterial sequences from these samples revealed that two distinct 16S rRNA gene sequences were present in each sample along with a single chaperonin-60 (cpn60) sequence and a single rpoB sequence, suggesting that this strain displays 16S rRNA gene sequence heterogeneity. Two distinct rrn operons, identified with subgroup 16SrXIII-A and the newly described subgroup 16SrXIII-I, were identified from the six samples analyzed, delineating the novel subgroup 16SrXIII-(A/I)I, following the nomenclature proposed for heterogeneous subgroups.

Cytomegalovirus (CMV) pneumonitis occurs frequently among solid organ transplant recipients and is classically associated with significant viral replication in both blood and bronchoalveolar lavage (BAL) samples. We present a case of a 64‐year‐old lung transplant recipient who presented with CMV pneumonitis that was diagnosed based on the association of viral inclusion in the BAL sample, rapid response to ganciclovir, and absence of other infectious etiology. Surprisingly, we observed very low or undetectable viral load both in blood and BAL samples. Diagnosis of CMV pneumonitis should rely on the association of clinical, pathological, radiological, and microbiological signs, while quantitative nucleic acid amplification testing should be interpreted with caution.

International audience; Background: Scedosporium species and Lomentospora prolificans (S/L) are the second most common causes of invasive mold infections following Aspergillus in lung transplant recipients.Methods: We assessed the current practices on management of S/L colonization/infection of the lower respiratory tract before and after lung transplantation in a large number of lung transplant centers through an international practice survey from October 2016 to March 2017.Results: A total of 51 respondents from 45 lung transplant centers (17 countries, 4 continents) answered the survey (response rate 58%). S/L colonization was estimated to be detected in candidates by 48% of centers. Only 18% of the centers used a specific medium to detect S/L colonization. Scedosporium spp. colonization was a contraindication to transplantation in 10% of centers whereas L prolificans was a contraindication in 31%; 22% of centers declared having had 1-5 recipients infected with S/L in the past 5 years.Conclusions: This survey gives an overview of the current practices regarding S/L colonization and infection in lung transplant centers worldwide and underscores the need of S/L culture procedure standardization before implementing prospective studies.

The DNA methylation epigenetic signature is a key determinant during development. Rules governing its establishment and maintenance remain elusive especially at repetitive sequences, which account for the majority of methylated CGs. DNA methylation is altered in a number of diseases including those linked to mutations in factors that modify chromatin. Among them, SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain Containing 1) has been of major interest following identification of germline mutations in Facio-Scapulo-Humeral Dystrophy (FSHD) and in an unrelated developmental disorder, Bosma Arhinia Microphthalmia Syndrome (BAMS). By investigating why germline SMCHD1 mutations lead to these two different diseases, we uncovered a role for this factor in de novo methylation at the pluripotent stage. SMCHD1 is required for the dynamic methylation of the D4Z4 macrosatellite upon reprogramming but seems dispensable for methylation maintenance. We find that FSHD and BAMS patient's cells carrying SMCHD1 mutations are both permissive for DUX4 expression, a transcription factor whose regulation has been proposed as the main trigger for FSHD. These findings open new questions as to what is the true aetiology for FSHD, the epigenetic events associated with the disease thus calling the current model into question and opening new perspectives for understanding repetitive DNA sequences regulation.

Molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with universal PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. Unfortunately both amplicon-based and shotgun sequencing approaches have significant shortcomings that limit the ability to study microbiome dynamics. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. This new method generates a quantitative, pan-Domain community profile with significantly less expenditure and sequencing effort than a shotgun metagenomic sequencing approach. Molecular microbial profiles were compared for antibiotic-amended soil samples using CaptureSeq, shotgun metagenomics, and amplicon-based techniques. The CaptureSeq method generated a microbial profile that provided a much greater depth and sensitivity than shotgun metagenomic sequencing while simultaneously mitigating the bias effects associated with amplicon-based methods. The resulting community profile provided quantitatively reliable information about all three Domains of life (Bacteria, Archaea, and Eukarya). The applications of CaptureSeq are globally impactful and will facilitate highly accurate studies of host-microbiome interactions for environmental, crop, animal and human health. DNA sequencing data associated with this work has been deposited at NCBI under BioProject PRJNA406970 and SRA deposits SRX3181274-SRX3181276 and SRX3187583-SRX3187601.

A draft genome sequence is presented for a strain of “Candidatus Phytoplasma asteris” affecting canola plants in Saskatoon, Canada. This phytopathogenic bacterium was determined to be a 16SrI strain and features 16S rRNA-encoding gene sequence heterogeneity.

We present here a draft genome sequence of Pseudomonas sp. strain 31-12, a plant growth-promoting rhizobacterium of several crop plants that was isolated from the rhizosphere of corn in southern Ontario, Canada.

This protocol describes the laboratory steps required to capture cpn60 gene fragments from microbial community DNA obtained from an environment of interest. This approach facilitates the determination of the taxonomic composition of a sample, providing information that spans all Domains of life (Bacteria, Eukarya, and Archaea). This method is independent of amplification biases associated with PCR, and provides a microbial community profile that is consistent with that generated using whole community shotgun sequencing, with substantially less sequencing effort required for the same community coverage. The protocol involves shearing the whole community genomic DNA by sonication, adding Illumina index primers, then hybridizing the sheared DNA to biotinylated RNA probes that correspond to the entire cpn60 reference database. Hybrids are selected using magnetic streptavidin beads, washed, and sequenced using an Illumina MiSeq platform. The protocol involves approximately five hours of hands-on time per sample over two days, along with a 24 hour hybridization step. In this protocol we describe the major changes we have implemented using the manufacturer’s recommendations as a starting point. We also provide tips and expected results.

Virus–bacteria coinfections are associated with more severe exacerbations and increased risk of hospital readmission in patients with chronic obstructive pulmonary disease (COPD). The airway epithelium responds to such infections by releasing proinflammatory and antimicrobial cytokines, including IL-17C. However, the regulation and role of IL-17C is not well understood. In this study, we examine the mechanisms regulating IL-17C production and its potential role in COPD exacerbations. Human bronchial epithelial cells (HBE) obtained from normal, nontransplanted lungs or from brushings of nonsmokers, healthy smokers, or COPD patients were exposed to bacteria and/or human rhinovirus (HRV). RNA and protein were collected for analysis, and signaling pathways were assessed with pharmacological agonists, inhibitors, or small interfering RNAs. HBE were also stimulated with IL-17C to assess function. HRV–bacterial coinfections synergistically induced IL-17C expression. This induction was dependent on HRV replication and required NF-κB–mediated signaling. Synergy was lost in the presence of an inhibitor of the p38 MAP kinase pathway. HBE exposed to IL-17C show increased gene expression of CXCL1, CXCL2, NFKBIZ, and TFRC, and release CXCL1 protein, a neutrophil chemoattractant. Knockdown of IL-17C significantly reduced induction of CXCL1 in response to HRV–bacterial coinfection as well as neutrophil chemotaxis. HBE from healthy smokers release less IL-17C than cells from nonsmokers, but cells from COPD patients release significantly more IL-17C compared with either nonsmokers or healthy smokers. These data suggest that IL-17C may contribute to microbial-induced COPD exacerbations by promoting neutrophil recruitment.