ABSTRACT
During December 11, 2020-March 29, 2022, the US government delivered ≈700 million doses of COVID-19 vaccine to vaccination sites, resulting in vaccination of ≈75% of US adults during that period. We evaluated accessibility of vaccination sites. Sites were accessible by walking within 15 minutes by 46.6% of persons, 30 minutes by 74.8%, 45 minutes by 82.8%, and 60 minutes by 86.7%. When limited to populations in counties with high social vulnerability, accessibility by walking was 55.3%, 81.1%, 86.7%, and 89.4%, respectively. By driving, lowest accessibility was 96.5% at 15 minutes. For urban/rural categories, the 15-minute walking accessibility between noncore and large central metropolitan areas ranged from 27.2% to 65.1%; driving accessibility was 79.9% to 99.5%. By 30 minutes driving accessibility for all urban/rural categories was >95.9%. Walking time variations across jurisdictions and between urban/rural areas indicate that potential gains could have been made by improving walkability or making transportation more readily available.
Subject(s)
COVID-19 Vaccines , COVID-19 , Health Services Accessibility , SARS-CoV-2 , Vaccination , Humans , United States/epidemiology , COVID-19/prevention & control , COVID-19/epidemiology , COVID-19 Vaccines/administration & dosage , SARS-CoV-2/immunology , Health Services Accessibility/statistics & numerical data , Vaccination/statistics & numerical data , Rural Population , Walking , Urban PopulationABSTRACT
Phosphoglucomutase 1 (PGM1) encodes the metabolic enzyme that interconverts glucose-6-P and glucose-1-P. Mutations in PGM1 cause impairment in glycogen metabolism and glycosylation, the latter manifesting as a congenital disorder of glycosylation (CDG). This unique metabolic defect leads to abnormal N-glycan synthesis in the endoplasmic reticulum (ER) and the Golgi apparatus (GA). On the basis of the decreased galactosylation in glycan chains, galactose was administered to individuals with PGM1-CDG and was shown to markedly reverse most disease-related laboratory abnormalities. The disease and treatment mechanisms, however, have remained largely elusive. Here, we confirm the clinical benefit of galactose supplementation in PGM1-CDG-affected individuals and obtain significant insights into the functional and biochemical regulation of glycosylation. We report here that, by using tracer-based metabolomics, we found that galactose treatment of PGM1-CDG fibroblasts metabolically re-wires their sugar metabolism, and as such replenishes the depleted levels of galactose-1-P, as well as the levels of UDP-glucose and UDP-galactose, the nucleotide sugars that are required for ER- and GA-linked glycosylation, respectively. To this end, we further show that the galactose in UDP-galactose is incorporated into mature, de novo glycans. Our results also allude to the potential of monosaccharide therapy for several other CDG.
Subject(s)
Congenital Disorders of Glycosylation/metabolism , Fibroblasts/metabolism , Galactose/administration & dosage , Phosphoglucomutase/deficiency , Uridine Diphosphate Galactose/metabolism , Uridine Diphosphate Glucose/metabolism , Cells, Cultured , Cohort Studies , Congenital Disorders of Glycosylation/drug therapy , Congenital Disorders of Glycosylation/pathology , Fibroblasts/drug effects , Fibroblasts/pathology , Glycosylation , HumansABSTRACT
BACKGROUND: The aim of the BSP090 project is the establishment of European Pharmacopoeia Chemical Reference Substances (CRSs) in combination with corresponding standard ELISA methods for quantification of major allergens in allergen products. Here, we present data of a Phl p 5-specific sandwich ELISA that proved suitable for the quantification of Phl p 5, one of the major Timothy grass (Phleum pratense) pollen allergens. METHODS: A Phl p 5-specific ELISA system was assessed with respect to accuracy, precision, inter-assay (within laboratory) and inter-laboratory variations, in a ring trial including 14 laboratories in Europe and the USA. Model samples containing recombinant Phl p 5a CRS as well as native grass pollen extracts were analysed. Each participant was instructed to perform at least one preliminary assay to familiarise with the protocol, followed by three independent assays. RESULTS: The candidate standard ELISA proved suitable to quantify recombinant and native Phl p 5 with satisfactory precision (93% of results within ±30% acceptance range). Inter-assay variation (max. GCV 24%) and especially inter-laboratory variation (max. GCV 13%) showed conclusive results. When assessing accuracy by means of recovery of recombinant spikes from a grass pollen extract matrix, similarly satisfactory spike recovery results were observed for the two spikes with higher concentrations (all within ±30% acceptance range), whereas recovery of the lowest concentration spike was slightly poorer with mean results of six laboratories exceeding acceptance range. CONCLUSIONS: Based on the collaborative study results, the assessed Phl p 5-specific immunoassay is appropriate to be proposed as European Pharmacopoeia standard method.
Subject(s)
Allergens , Pollen , Allergens/chemistry , Enzyme-Linked Immunosorbent Assay , Humans , Phleum/chemistry , Plant Proteins/chemistry , Poaceae , Reference StandardsABSTRACT
On October 29, 2021, the Pfizer-BioNTech pediatric COVID-19 vaccine received Emergency Use Authorization for children aged 5-11 years in the United States. For a successful immunization program, both access to and uptake of the vaccine are needed. Fifteen million doses were initially made available to pediatric providers to ensure the broadest possible access for the estimated 28 million eligible children aged 5-11 years, especially those in high social vulnerability index (SVI)§ communities. Initial supply was strategically distributed to maximize vaccination opportunities for U.S. children aged 5-11 years. COVID-19 vaccination coverage among persons aged 12-17 years has lagged (1), and vaccine confidence has been identified as a concern among parents and caregivers (2). Therefore, COVID-19 provider access and early vaccination coverage among children aged 5-11 years in high and low SVI communities were examined during November 1, 2021-January 18, 2022. As of November 29, 2021 (4 weeks after program launch), 38,732 providers were enrolled, and 92% of U.S. children aged 5-11 years lived within 5 miles of an active provider. As of January 18, 2022 (11 weeks after program launch), 39,786 providers had administered 13.3 million doses. First dose coverage at 4 weeks after launch was 15.0% (10.5% and 17.5% in high and low SVI areas, respectively; rate ratio [RR] = 0.68; 95% CI = 0.60-0.78), and at 11 weeks was 27.7% (21.2% and 29.0% in high and low SVI areas, respectively; RR = 0.76; 95% CI = 0.68-0.84). Overall series completion at 11 weeks after launch was 19.1% (13.7% and 21.7% in high and low SVI areas, respectively; RR = 0.67; 95% CI = 0.58-0.77). Pharmacies administered 46.4% of doses to this age group, including 48.7% of doses in high SVI areas and 44.4% in low SVI areas. Although COVID-19 vaccination coverage rates were low, particularly in high SVI areas, first dose coverage improved over time. Additional outreach is critical, especially in high SVI areas, to improve vaccine confidence and increase coverage rates among children aged 5-11 years.
Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , Immunization Programs , Vaccination Coverage , Child , Child, Preschool , Humans , Neighborhood Characteristics , Pharmacies/statistics & numerical data , SARS-CoV-2/immunology , Social VulnerabilityABSTRACT
Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms. However, current methods have limitations due to short read lengths and reverse transcription or amplification biases. Here we demonstrate nanopore direct RNA-seq, a highly parallel, real-time, single-molecule method that circumvents reverse transcription or amplification steps. This method yields full-length, strand-specific RNA sequences and enables the direct detection of nucleotide analogs in RNA.
Subject(s)
High-Throughput Nucleotide Sequencing/methods , Nanopores , RNA, Fungal/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Sequence Analysis, RNA/methodsABSTRACT
BACKGROUND: Outbreaks of hypersensitivity pneumonitis (HP) are not uncommon in workplaces where metal working fluid (MWF) is used to facilitate metal turning. Inhalation of microbe-contaminated MWF has been assumed to be the cause, but previous investigations have failed to establish a spatial relationship between a contaminated source and an outbreak. OBJECTIVES: After an outbreak of five cases of HP in a UK factory, we carried out blinded, molecular-based microbiological investigation of MWF samples in order to identify potential links between specific microbial taxa and machines in the outbreak zone. METHODS: Custom-quantitative PCR assays, microscopy and phylogenetic analyses were performed on blinded MWF samples to quantify microbial burden and identify potential aetiological agents of HP in metal workers. MEASUREMENTS AND MAIN RESULTS: MWF from machines fed by a central sump, but not those with an isolated supply, was contaminated by mycobacteria. The factory sump and a single linked machine at the centre of the outbreak zone, known to be the workstation of the index cases, had very high levels of detectable organisms. Phylogenetic placement of mycobacterial taxonomic marker genes generated from these samples indicated that the contaminating organisms were closely related to Mycobacterium avium. CONCLUSIONS: We describe, for the first time, a close spatial relationship between the abundance of a mycobacterium-like organism, most probably M. avium, and a localised outbreak of MWF-associated HP. The further development of sequence-based analytic techniques should assist in the prevention of this important occupational disease.
Subject(s)
Alveolitis, Extrinsic Allergic/epidemiology , Alveolitis, Extrinsic Allergic/microbiology , Disease Outbreaks , Metallurgy , Mycobacterium avium/isolation & purification , Occupational Diseases/microbiology , Alveolitis, Extrinsic Allergic/diagnosis , Humans , Male , Occupational Diseases/diagnosis , Occupational Diseases/epidemiology , Occupational Exposure/adverse effects , United KingdomABSTRACT
RATIONALE: Changes in the respiratory microbiome are associated with disease progression in idiopathic pulmonary fibrosis (IPF). The role of the host response to the respiratory microbiome remains unknown. OBJECTIVES: To explore the host-microbial interactions in IPF. METHODS: Sixty patients diagnosed with IPF were prospectively enrolled together with 20 matched control subjects. Subjects underwent bronchoalveolar lavage (BAL), and peripheral whole blood was collected into PAXgene tubes for all subjects at baseline. For subjects with IPF, additional samples were taken at 1, 3, and 6 months and (if alive) 1 year. Gene expression profiles were generated using Affymetrix Human Gene 1.1 ST arrays. MEASUREMENTS AND MAIN RESULTS: By network analysis of gene expression data, we identified two gene modules that strongly associated with a diagnosis of IPF, BAL bacterial burden (determined by 16S quantitative polymerase chain reaction), and specific microbial operational taxonomic units, as well as with lavage and peripheral blood neutrophilia. Genes within these modules that are involved in the host defense response include NLRC4, PGLYRP1, MMP9, and DEFA4. The modules also contain two genes encoding specific antimicrobial peptides (SLPI and CAMP). Many of these particular transcripts were associated with survival and showed longitudinal overexpression in subjects experiencing disease progression, further strengthening the relationship of the transcripts with disease. CONCLUSIONS: Integrated analysis of the host transcriptome and microbial signatures demonstrated an apparent host response to the presence of an altered or more abundant microbiome. These responses remained elevated in longitudinal follow-up, suggesting that the bacterial communities of the lower airways may act as persistent stimuli for repetitive alveolar injury in IPF.
Subject(s)
Host-Pathogen Interactions , Idiopathic Pulmonary Fibrosis/metabolism , Idiopathic Pulmonary Fibrosis/microbiology , Aged , Bronchoalveolar Lavage Fluid/microbiology , Female , Follow-Up Studies , Humans , Male , Microbiota , Prospective Studies , TranscriptomeSubject(s)
Microbiota , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Adult , Animals , Humans , Lung , Mice , Mice, Inbred BALB C , Respiratory SystemABSTRACT
PURPOSE: Population-based prescription opioid abuse studies in which one drug is compared to another, or drugs are compared across time, often account for the availability of those drugs in the community. The objective of this investigation is to assess consistency in the relative abuse ratios (RARs) across different approaches for adjusting for drug availability. METHODS: For the years 2004 through 2010, RARs for each of four prescription opioids (hydrocodone, oxycodone, hydromorphone, and morphine) were calculated using negative binomial regression. Measures of abuse (outcome) were misuse/abuse-related emergency department visits obtained from the Drug Abuse Warning Network. Measures of drug availability (offsets) were drug utilization estimates obtained from IMS Health. Separate regression models were run using each of five measures of drug utilization: unique patients (URDD), prescriptions dispensed (RX), tablets dispensed (TD), kilograms (KGs) sold, and morphine-equivalents (MEs) of kilograms sold. These results were compared for consistency. RESULTS: Aside from oxycodone-combination products, across molecules, RARs adjusted by RXs, TDs, and URDDs were generally similar to each other while RARs adjusted by KGs and MEs were different. For example, compared to hydrocodone, oxycodone had statistically significantly increased RARs of 3.6 (95%CI: 2.0-6.5), 3.5 (95%CI: 1.9-6.4), and 2.7 (95%CI: 1.5-5.0) when adjusted by URDDs, RXs, and TDs, respectively, but not when adjusted by KGs or MEs. CONCLUSIONS: Different drug utilization adjustment approaches may yield inconsistent RAR estimates in population-based prescription opioid abuse analyses. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
Subject(s)
Analgesics, Opioid/administration & dosage , Emergency Service, Hospital/statistics & numerical data , Opioid-Related Disorders/epidemiology , Prescription Drug Misuse/statistics & numerical data , Analgesics, Opioid/adverse effects , Drug Utilization/statistics & numerical data , Humans , Population Surveillance , Regression AnalysisABSTRACT
BACKGROUND: Long-term antibiotic therapy is used to prevent exacerbations of COPD but there is uncertainty over whether this reduces airway bacteria. The optimum antibiotic choice remains unknown. We conducted an exploratory trial in stable patients with COPD comparing three antibiotic regimens against placebo. METHODS: This was a single-centre, single-blind, randomised placebo-controlled trial. Patients aged ≥45â years with COPD, FEV1<80% predicted and chronic productive cough were randomised to receive either moxifloxacin 400â mg daily for 5â days every 4â weeks, doxycycline 100â mg/day, azithromycin 250â mg 3 times a week or one placebo tablet daily for 13â weeks. The primary outcome was the change in total cultured bacterial load in sputum from baseline; secondary outcomes included bacterial load by 16S quantitative PCR (qPCR), sputum inflammation and antibiotic resistance. RESULTS: 99 patients were randomised; 86 completed follow-up, were able to expectorate sputum and were analysed. After adjustment, there was a non-significant reduction in bacterial load of 0.42 log10â cfu/mL (95% CI -0.08 to 0.91, p=0.10) with moxifloxacin, 0.11 (-0.33 to 0.55, p=0.62) with doxycycline and 0.08 (-0.38 to 0.54, p=0.73) with azithromycin from placebo, respectively. There were also no significant changes in bacterial load measured by 16S qPCR or in airway inflammation. More treatment-related adverse events occurred with moxifloxacin. Of note, mean inhibitory concentrations of cultured isolates increased by at least three times over placebo in all treatment arms. CONCLUSIONS: Total airway bacterial load did not decrease significantly after 3â months of antibiotic therapy. Large increases in antibiotic resistance were seen in all treatment groups and this has important implications for future studies. TRIAL REGISTRATION NUMBER: clinicaltrials.gov (NCT01398072).
Subject(s)
Anti-Bacterial Agents/therapeutic use , Azithromycin/therapeutic use , Doxycycline/therapeutic use , Fluoroquinolones/therapeutic use , Pulmonary Disease, Chronic Obstructive/microbiology , Respiratory System/microbiology , Aged , Bacterial Load , Female , Humans , Male , Middle Aged , Moxifloxacin , Outcome Assessment, Health Care , Pulmonary Disease, Chronic Obstructive/complications , Single-Blind Method , Sputum/microbiologyABSTRACT
The incidence of Mycobacterium bovis, the causative agent of bovine tuberculosis, in cattle herds in the United Kingdom is increasing, resulting in substantial economic losses. The European badger (Meles meles) is implicated as a wildlife reservoir and is the subject of control measures aimed at reducing the incidence of infection in cattle populations. Understanding the epidemiology of M. bovis in badger populations is essential for directing control interventions and understanding disease spread; however, accurate diagnosis in live animals is challenging and currently uses invasive methods. Here we present a noninvasive diagnostic procedure and sampling regimen using field sampling of latrines and detection of M. bovis with quantitative PCR tests, the results of which strongly correlate with the results of immunoassays in the field at the social group level. This method allows M. bovis infections in badger populations to be monitored without trapping and provides additional information on the quantities of bacterial DNA shed. Therefore, our approach may provide valuable insights into the epidemiology of bovine tuberculosis in badger populations and inform disease control interventions.
Subject(s)
Bacterial Shedding , Disease Reservoirs , Mustelidae/microbiology , Mycobacterium bovis/isolation & purification , Tuberculosis/veterinary , Animals , Cattle , Feces/microbiology , Tuberculosis/epidemiology , Tuberculosis/microbiology , United Kingdom/epidemiologyABSTRACT
Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5 ≤ pH <7), or alkalinophilic (pH ≥ 7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5-8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5-7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.
Subject(s)
Adaptation, Biological/genetics , Ammonia/metabolism , Archaea/genetics , Oxidoreductases/genetics , Oxidoreductases/metabolism , Soil Microbiology , Soil/chemistry , Amino Acid Sequence , Archaea/metabolism , Bayes Theorem , Computational Biology , DNA Primers/genetics , Genetic Variation , Hydrogen-Ion Concentration , Likelihood Functions , Models, Genetic , Molecular Sequence Data , Oxidation-Reduction , Phylogeny , Polymerase Chain Reaction , Sequence Analysis, DNA , United KingdomABSTRACT
Feminization Laryngoplasty evolved from the aim to change a voice from a male quality to a female quality. Larynx and pharynx in a male have undergone enlargement during puberty and as there is no endocrine method for shrinking structures, a surgery that reduces the size of male structures toward the size of female structures might appropriately alter the voice. A smaller larynx and pharynx might raise both the fundamental frequency of the voice and the resonant frequency of the vocal tract. The surgery is used for transgender individuals who desire a female voice, for individuals who fail speech therapy and for complications of tracheal shave procedures whereby the vocal cords have been loosened.
Subject(s)
Laryngoplasty , Larynx , Female , Feminization/surgery , Humans , Laryngoplasty/methods , Larynx/surgery , Male , Pharynx/surgery , Vocal Cords/surgery , Voice QualityABSTRACT
Case: We present a case of dysplasia epiphysealis hemimelica (DEH) involving the posteromedial distal femur in a 4-year-old girl. The patient underwent lesion resection with internal fixation of the articular cartilage followed by autologous chondrocyte implantation (ACI) to restore the articular surface and epiphysis. At the 7-year follow-up, the patient had no pain or difficulty with participation in sports. Advanced imaging showed a stable articular surface with evidence of durable cartilage integration. Conclusion: DEH is a rare disease often treated by resection. In cases where the articular surface of the knee is involved, we have demonstrated that augmentation with ACI can be an effective treatment option.
Subject(s)
Bone Diseases, Developmental , Cartilage, Articular , Bone Diseases, Developmental/diagnostic imaging , Bone Diseases, Developmental/pathology , Bone Diseases, Developmental/surgery , Cartilage, Articular/surgery , Child, Preschool , Chondrocytes , Female , Femur/abnormalities , Femur/pathology , Femur/surgery , Humans , Tibia/abnormalitiesABSTRACT
Despite recognition of the importance of soil bacteria to terrestrial ecosystem functioning there is little consensus on the factors regulating belowground biodiversity. Here we present a multi-scale spatial assessment of soil bacterial community profiles across Great Britain (> 1000 soil cores), and show the first landscape scale map of bacterial distributions across a nation. Bacterial diversity and community dissimilarities, assessed using terminal restriction fragment length polymorphism, were most strongly related to soil pH providing a large-scale confirmation of the role of pH in structuring bacterial taxa. However, while α diversity was positively related to pH, the converse was true for ß diversity (between sample variance in α diversity). ß diversity was found to be greatest in acidic soils, corresponding with greater environmental heterogeneity. Analyses of clone libraries revealed the pH effects were predominantly manifest at the level of broad bacterial taxonomic groups, with acidic soils being dominated by few taxa (notably the group 1 Acidobacteria and Alphaproteobacteria). We also noted significant correlations between bacterial communities and most other measured environmental variables (soil chemistry, aboveground features and climatic variables), together with significant spatial correlations at close distances. In particular, bacterial and plant communities were closely related signifying no strong evidence that soil bacteria are driven by different ecological processes to those governing higher organisms. We conclude that broad scale surveys are useful in identifying distinct soil biomes comprising reproducible communities of dominant taxa. Together these results provide a baseline ecological framework with which to pursue future research on both soil microbial function, and more explicit biome based assessments of the local ecological drivers of bacterial biodiversity.
Subject(s)
Bacteria/genetics , Soil Microbiology , Soil/chemistry , Bacteria/classification , Bacteria/isolation & purification , Base Sequence , Biodiversity , Ecosystem , Genetic Variation , Molecular Sequence Data , Phylogeny , Polymorphism, Restriction Fragment Length , United KingdomABSTRACT
RATIONALE: The airway microbiota is important in chronic suppurative lung diseases, such as primary ciliary dyskinesia (PCD) and cystic fibrosis (CF). This comparison has not previously been described but is important because difference between the two diseases may relate to the differing prognoses and lead to pathological insights and potentially, new treatments. OBJECTIVES: To compare the longitudinal development of the airway microbiota in children with PCD to that of CF and relate this to age and clinical status. METHODS: Sixty-two age-matched children (age range 0.5-17 years) with PCD or CF (n=31 in each group) were recruited prospectively and followed for 1.1 years. Throat swabs or sputum as well as clinical information were collected at routine clinical appointments. 16S rRNA gene sequencing was performed. MEASUREMENTS AND MAIN RESULTS: The microbiota was highly individual and more diverse in PCD and differed in community composition when compared with CF. While Streptococcus was the most abundant genus in both conditions, Pseudomonas was more abundant in CF with Haemophilus more abundant in PCD (Padj=0.0005). In PCD only, an inverse relationship was seen in the relative abundance of Streptococcus and Haemophilus with age. CONCLUSIONS: Bacterial community composition differs between children with PCD and those with CF. Pseudomonas is more prevalent in CF and Haemophilus in PCD, at least until infection with Pseudomonas supervenes. Interactions between organisms, particularly members of Haemophilus, Streptococcus and Pseudomonas genera appear important. Study of the interactions between these organisms may lead to new therapies or risk stratification.
Subject(s)
Cystic Fibrosis , Microbiota , Adolescent , Child , Child, Preschool , Cystic Fibrosis/therapy , Humans , Infant , Microbiota/genetics , RNA, Ribosomal, 16S/genetics , Sputum , ThoraxABSTRACT
We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore Sequencing. OCEANS allows accurate detection of somatic mutations with VAF limits of detection between 0.05 and 1%. We construct 4 distinct multi-gene OCEANS panels targeting recurrent mutations in acute myeloid leukemia, melanoma, non-small- cell lung cancer, and hepatocellular carcinoma and validate them on clinical samples. By demonstrating detection of low VAF single nucleotide variant mutations using Nanopore Sequencing, OCEANS is poised to enable same-day clinical sequencing panels.
Subject(s)
Mutation , Nanopore Sequencing/methods , Neoplasms/genetics , Oncogenes/genetics , Carcinoma, Non-Small-Cell Lung/genetics , High-Throughput Nucleotide Sequencing , Humans , Leukemia, Myeloid, Acute/genetics , Lung Neoplasms/genetics , MelanomaABSTRACT
BACKGROUND: Normal airway microbial communities play a central role in respiratory health but are poorly characterized. Cigarette smoking is the dominant global environmental influence on lung function, and asthma has become the most prevalent chronic respiratory disease worldwide. Both conditions have major microbial components that are incompletely defined. METHODS: We investigated airway bacterial communities in a general population sample of 529 Australian adults. Posterior oropharyngeal swabs were analyzed by sequencing of the 16S rRNA gene. The microbiota were characterized according to their prevalence, abundance and network memberships. FINDINGS: The microbiota were similar across the general population, and were strongly organized into co-abundance networks. Smoking was associated with diversity loss, negative effects on abundant taxa, profound alterations to network structure and expansion of Streptococcus spp. By contrast, the asthmatic microbiota were selectively affected by an increase in Neisseria spp. and by reduced numbers of low abundance but prevalent organisms. INTERPRETATION: Our study shows that the healthy airway microbiota in this population were contained within a highly structured ecosystem, suggesting balanced relationships between the microbiome and human host factors. The marked abnormalities in smokers may contribute to chronic obstructive pulmonary disease (COPD) and lung cancer. The narrow spectrum of abnormalities in asthmatics encourages investigation of damaging and protective effects of specific bacteria. FUNDING: The study was funded by the Asmarley Trust and a Wellcome Joint Senior Investigator Award to WOCC and MFM (WT096964MA and WT097117MA). The Busselton Healthy Ageing Study is supported by the Government of Western Australia (Office of Science, Department of Health) the City of Busselton, and private donations.
Subject(s)
Asthma/epidemiology , Microbiota , Respiratory Mucosa/microbiology , Smoking/epidemiology , Adult , Aged , Asthma/etiology , Australia/epidemiology , Computational Biology/methods , Disease Susceptibility , Female , Humans , Male , Metagenomics/methods , Middle Aged , Population Surveillance , RNA, Ribosomal, 16S , Smoking/adverse effects , Tobacco SmokingABSTRACT
BACKGROUND: The prevalence of fungal disease in cystic fibrosis (CF) and non-CF bronchiectasis is increasing and the clinical spectrum is widening. Poor sensitivity and a lack of standard diagnostic criteria renders interpretation of culture results challenging. In order to develop effective management strategies, a more accurate and comprehensive understanding of the airways fungal microbiome is required. The study aimed to use DNA sequences from sputum to assess the load and diversity of fungi in adults with CF and non-CF bronchiectasis. METHODS: Next generation sequencing of the ITS2 region was used to examine fungal community composition (n = 176) by disease and underlying clinical subgroups including allergic bronchopulmonary aspergillosis, chronic necrotizing pulmonary aspergillosis, non-tuberculous mycobacteria, and fungal bronchitis. Patients with no known active fungal disease were included as disease controls. RESULTS: ITS2 sequencing greatly increased the detection of fungi from sputum. In patients with CF fungal diversity was lower, while burden was higher than those with non-CF bronchiectasis. The most common operational taxonomic unit (OTU) in patients with CF was Candida parapsilosis (20.4%), whereas in non-CF bronchiectasis sputum Candida albicans (21.8%) was most common. CF patients with overt fungal bronchitis were dominated by Aspergillus spp., Exophiala spp., Candida parapsilosis or Scedosporium spp. CONCLUSION: This study provides a framework to more accurately characterize the extended spectrum of fungal airways diseases in adult suppurative lung diseases.
Subject(s)
Bronchiectasis/microbiology , Cystic Fibrosis , Lung Diseases, Fungal/microbiology , Mycobiome , Adolescent , Adult , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Prospective StudiesABSTRACT
OBJECTIVES: To describe the use of ultrasound by a professional Australian rules football team in the immediate pregame period to guide local anaesthetic injections, during game time to assess injuries and to guide local anaesthetic injections, and postmatch to assess injuries and to guide therapeutic injections. METHODS: The use of match day ultrasound was documented during four finals matches. Local anaesthetic injections were considered effective if players played without pain and experienced no complication from the injection. The results of the diagnostic scans were assessed against subsequent clinical progress and correlation with any follow-up imaging. Therapeutic injections were considered effective if there was clinical improvement and the player was able to play in subsequent weeks without restriction. RESULTS: Pregame, a total of 11 ultrasound guided local anaesthetic injections were performed on eight players, with a further local anaesthetic during a game. All injections achieved good pain relief without any complication. A single diagnostic scan on one player during a game showed no acute muscle tear, the player successfully completed the game. Postgame, a total of four ultrasound guided steroid injections were performed on three players and all players played in the next match. The injections achieved good therapeutic results. The therapeutic injections given immediately postgame, maximised the recovery period available to the players. CONCLUSIONS: Ultrasound proved useful in guiding local anaesthetic before and during matches and also therapeutic injections after matches. Ultrasound had a limited role in the assessment of injuries during a game.