Airway Specimens Research Articles

Estimated Incidence of Hospitalizations Attributable to RSV Infection Among Adults in Ontario, Canada, Between 2013 and 2019.

Adult respiratory syncytial virus (RSV) burden is underestimated due to non-specific symptoms, limited standard-of-care and delayed testing, reduced diagnostic test sensitivity-particularly when using single diagnostic specimen-when compared to children, and variable test sensitivity based on the upper airway specimen source. We estimated RSV-attributable hospitalization incidence among adults aged ≥ 18 years in Ontario, Canada, using a retrospective time-series model-based approach. The Institute for Clinical Evaluative Sciences data repository provided weekly numbers of hospitalizations (from 2013 to 2019) for respiratory, cardiovascular, and cardiorespiratory disorders. The number of hospitalizations attributable to RSV was estimated using a quasi-Poisson regression model that considered probable overdispersion and was based on periodic and aperiodic time trends and viral activity. As proxies for viral activity, weekly counts of RSV and influenza hospitalizations in children under 2 years and adults aged 60 years and over, respectively, were employed. Models were stratified by age and risk group. In patients ≥ 60 years, RSV-attributable incidence rates were high for cardiorespiratory hospitalizations (range [mean] in 2013-2019: 186-246 [215] per 100,000 person-years, 3‒4% of all cardiorespiratory hospitalizations), and subgroups including respiratory hospitalizations (144-192 [167] per 100,000 person-years, 5‒7% of all respiratory hospitalizations) and cardiovascular hospitalizations (95-126 [110] per 100,000 person-years, 2‒3% of all cardiovascular hospitalizations). RSV-attributable cardiorespiratory hospitalization incidence increased with age, from 14-18 [17] hospitalizations per 100,000 person-years (18-49 years) to 317-411 [362] per 100,000 person-years (≥ 75 years). Estimated RSV-attributable respiratory hospitalization incidence among people ≥ 60 years in Ontario, Canada, is comparable to other incidence estimates from high-income countries, including model-based and pooled prospective estimates. Recently introduced RSV vaccines could have a substantial public health impact.

Relapsing bronchopneumonia due to community-associated methicillin-resistant Staphylococcus aureus: a case report

BackgroundThe emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has increased the incidence of community-onset MRSA infection. Respiratory tract infections caused by MRSA has been noted for their severity; however, repeated relapses that require extended antibiotic therapy are rare.Case presentationWe report a case of relapsing bronchopneumonia caused by CA-MRSA in a 56-year-old man. The patient responded to antibiotics, but repeatedly relapsed after stopping treatment. MRSA was consistently isolated from airway specimens during each relapse. Extended oral antibiotic treatment with trimethoprim/sulfamethoxazole (TMP/SMX) for 6 months achieved infection control. Whole-genome sequencing of the isolated strain revealed that the causative agent was sequence type (ST)1/staphylococcal cassette chromosome mec (SCCmec) type IVa, a clone that is rapidly increasing in Japan.Discussion and conclusionsThis patient had an unusual course of MRSA bronchopneumonia with repeated relapses. Although the choice of antibiotics for long-term use in MRSA respiratory tract infections has not been well established, TMP/SMX was effective and well tolerated for long-term therapy in this case. The clinical course of infections related to the rapid emerging clone, ST1/SCCmec type IVa warrants further attention.

Mycobacterium chimaera infections in cardiothoracic surgery patients exposed to heating and cooling devices despite infection control measures

Background: LivaNova 3T heating and cooling devices (HCDs) have been associated with Mycobacterium chimaera, a Mycobacterium avium-intracellulare (MAIC) species, infections after cardiothoracic surgery. We describe our outbreak, which persisted despite escalating infection control measures. Methods: We identified patients with a positive MAIC culture following cardiothoracic surgery from January 2015 to the present at our institution. We classified these as “definite,” “possible,” or “operating room contamination” cases based on positive cultures from sterile sites, airway, or surgical specimens without evidence of infection. To identify patient or surgery characteristics associated with risk for MAIC infection, we conducted a case–control study comparing definite cases to randomly selected unmatched controls of patients over the same period without a positive MAIC culture after cardiothoracic surgery. Results: We identified 26 patients with a positive MAIC culture after cardiothoracic surgery: 13 definite, 9 possible, and 4 contamination cases. Among definite cases, the most common surgeries were valve replacements and left ventricular assist devices (5 cases each). The mean time from cardiothoracic surgery to diagnosis was 525 days. Overall, 10 (77%) cases occurred after exposure to our oldest HCDs (manufactured in 2013 or earlier). To date, 16 (62%) have undergone or are undergoing treatment for MAIC infection, and 4 (15%) have died due to NTM infection or complications. Compared to 47 controls, definite cases were associated with chronic kidney disease, implants, procedure type, use of cardiopulmonary bypass, and HCD age. Cases were not associated with time on bypass, time in the operating room, or other comorbid conditions (Table). All cases occurred despite enhanced disinfection and reorienting the HCD within the operating room, according to manufacturer recommendations. Moreover, 18 cases, including 7 definite cases, occurred after most HCDs were either deep cleaned or upgraded by the manufacturer. Also, 5 cases, including 3 possible cases and 2 contamination cases, occurred after physical separation of the HCD from the operating room. In August 2022, we purchased a fleet of glycol-cooled HCDs, and we have not identified additional MAIC cases since their deployment (Fig.). Conclusions: MAIC infections after cardiothoracic surgery were associated with procedure type, especially implants, use of cardiopulmonary bypass, and HCD age. Contrary to prior reports, neither operative nor CPB time was associated with MAIC infection after cardiothoracic surgery. The outbreak persisted despite disinfection and/or deep cleaning and reorienting HCDs within the operating room; some possible and contamination cases occurred even after moving HCDs outside the operating room. Thus, HCD water contamination events in the operating room (eg, spills from HCD tubing) may be a route of exposure, and different infection prevention measures are needed.Disclosure: None

Evaluation of large airway specimens obtained by transbronchial lung cryobiopsy in diffuse parenchymal lung diseases

BackgroundThe difference in diagnostic yield between surgical lung biopsy and transbronchial lung cryobiopsy (TBLC) in diffuse parenchymal lung diseases (DPLD) has been reported to be due to differences in the rate of interpathologist agreement, specimen size, and specimen adequacy. In TBLC, the specimens containing large airway components are generally believed as inadequate specimens for histological evaluation, but the detailed characteristics of TBLC specimens including the large airway and the impact on histological diagnostic rates of DPLD have not been investigated.MethodsWe retrospectively reviewed the specimen characteristics of patients with DPLD who underwent TBLC.ResultsBetween February 2018 and January 2020, 74 patients and 177 specimens were included. There were 85 (48.0%) large airway specimens (LAS) that contained bronchial gland or bronchial cartilage. The ideal specimen ratio was significantly lower in the LAS-positive group than that in the LAS-negative group (5.8% vs. 45.6%), and the proportion of bronchioles, alveoli, and perilobular area were similarly lower in the LAS-positive group. The presence of traction bronchiectasis and diaphragm overlap sign on high-resolution computed tomography (HRCT) were also significantly higher in the LAS-positive group than those in the LAS-negative group. We observed a statistically significant trend in histological diagnostic yield (40.7% in LAS positive group; 60.8% in LAS positive and negative group; 91.6% in LAS negative group) (Cochran-Armitage trend test).ConclusionLAS is a specimen often collected in TBLC and contains a low percentage of bronchioles, alveoli, and perilobular area. Since the histological diagnostic yield tends to be higher in cases that do not contain LAS, it may be important to determine the biopsy site that reduces the frequency of LAS collection by referring to the HRCT findings in TBLC.

Reducing human DNA bias in cystic fibrosis airway specimens for microbiome analysis

Next generation sequencing (NGS) has transformed our understanding of airway microbiology, however there are methodology limitations that require consideration. The presence of high concentrations of human DNA in clinical specimens can significantly impact sequencing of the microbiome, especially in low biomass samples. Here we compared three different methods (0.025% saponin, NEBNext Microbiome DNA enrichment kit, QIAamp DNA microbiome kit) for the reduction of human DNA from six CF sputum samples and determined the impact on the microbiome detected using 16S rRNA gene sequencing.Human DNA in undepleted CF sputum accounted for 94.3% of the total DNA. Saponin, the NEBNext kit and the QIAamp kit reduced human DNA levels by an average of 38.7%, 61.8% and 94.8%, respectively. None of the depletion methods reduced total bacterial DNA concentrations. QIAamp depletion did not influence taxa richness or alpha diversity however alterations to the core genera were noted following depletion.While all methods reduced human DNA in the CF sputum samples, the QIAamp DNA microbiome kit reduced Human DNA levels significantly while leaving bacterial DNA levels unchanged. Human DNA depletion in low biomass, human DNA-dense CF sputum samples is vital for improving bacterial resolution in the CF airway microbiome.

Duration of Replication-Competent Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Shedding Among Patients With Severe or Critical Coronavirus Disease 2019 (COVID-19).

BackgroundPatterns of shedding replication-competent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in severe or critical COVID-19 are not well characterized. We investigated the duration of replication-competent SARS-CoV-2 shedding in upper and lower airway specimens from patients with severe or critical coronavirus disease 2019 (COVID-19).MethodsWe enrolled patients with active or recent severe or critical COVID-19 who were admitted to a tertiary care hospital intensive care unit (ICU) or long-term acute care hospital (LTACH) because of COVID-19. Respiratory specimens were collected at predefined intervals and tested for SARS-CoV-2 using viral culture and reverse transcription–quantitative polymerase chain reaction (RT-qPCR). Clinical and epidemiologic metadata were reviewed.ResultsWe collected 529 respiratory specimens from 78 patients. Replication-competent virus was detected in 4 of 11 (36.3%) immunocompromised patients up to 45 days after symptom onset and in 1 of 67 (1.5%) immunocompetent patients 10 days after symptom onset (P = .001). All culture-positive patients were in the ICU cohort and had persistent or recurrent symptoms of COVID-19. Median time from symptom onset to first specimen collection was 15 days (range, 6–45) for ICU patients and 58.5 days (range, 34–139) for LTACH patients. SARS-CoV-2 RNA was detected in 40 of 50 (80%) ICU patients and 7 of 28 (25%) LTACH patients.ConclusionsImmunocompromise and persistent or recurrent symptoms were associated with shedding of replication-competent SARS-CoV-2, supporting the need for improving respiratory symptoms in addition to time as criteria for discontinuation of transmission-based precautions. Our results suggest that the period of potential infectiousness among immunocompetent patients with severe or critical COVID-19 may be similar to that reported for patients with milder disease.

Effectiveness of Endobronchial Ultrasound-Guided Transbronchial Biopsy Combined With Tissue Culture for the Diagnosis of Sputum Smear-Negative Pulmonary Tuberculosis.

BackgroundMicroorganisms of tuberculosis (TB) are frequently difficult to identify from the airway specimen; therefore, lung biopsy for further histologic and microbiologic study is required. Endobronchial ultrasound-guided transbronchial biopsy (EBUS-TBB) is used for the diagnosis of pulmonary malignancy, but is rarely in the TB population. The purpose of this study was to verify the effectiveness and safety of EBUS-TBB with histologic study and tissue culture in the diagnosis of sputum smear-negative pulmonary TB.MethodsPatients who underwent EBUS-TBB with histologic study and TB tissue culture for clinically suspected, but sputum smear-negative pulmonary TB from January 2016 to December 2018, were included. The accuracy of each diagnostic modality was calculated, respectively. Factors that might influence the positive rate of TB culture (washing fluid and tissue specimen) were also evaluated.ResultsOne hundred sixty-one patients who underwent EBUS-TBB for clinically suspected, but sputum smear-negative pulmonary TB, were enrolled, and 43 of them were finally diagnosed as having pulmonary TB. The sensitivity of washing fluid (a combination of smear, culture, and polymerase chain reaction for TB) and tissue specimen (a combination of pathology and tissue culture) via EBUS-TBB for TB diagnosis were 48.8 and 55.8%, respectively. The sensitivity for TB diagnosis would be elevated to 67.4% when both washing fluid and tissue specimens are used. The positive TB culture rate would not statistically increase with a combination of tissue specimens and washing fluid. Univariate analysis revealed that TB microorganisms would be more easily cultivated when lesions had an abscess or cavity on the computed tomography (CT) image (presence vs. absence; 62.5 vs. 26.3%, p = 0.022), heterogeneous echogenicity on the EBUS finding (heterogeneous vs. homogeneous; 93.3 vs. 21.4%, p = 0.001), or a necrotic pattern via histologic study (presence vs. absence; 70.6 vs. 30.8%, p = 0.013). Heterogeneous echogenicity in the EBUS finding was the independent predictor according to the results of multivariate analysis. None of our patients encountered major adverse events or received further intensive care after EBUS-TBB.ConclusionEndobronchial ultrasound-guided transbronchial biopsy is safe and effective for use in diagnosing sputum smear-negative pulmonary TB. EBUS echoic feature is also a predictor of the positive TB culture rate in pulmonary TB. However, tissue culture via EBUS-TBB has little effect in improving the positive TB culture rate.

Comparison of microbiota in the upper versus lower respiratory tract in children during health and respiratory disease: protocol for a systematic review

BackgroundThe upper respiratory tract of children is colonized by various microbial species during the healthy state, whereas the lungs are believed to be sterile. In children with respiratory infections, micro-organisms can be recovered from the upper respiratory sites, as well as the lungs. However, the correlation of microbial yield between the two sites is unclear. This systematic review is designed to explore the microbial composition of the respiratory system in healthy children, comparing the organisms identified in the upper airways versus the lungs. We will also compare the prevalence and pattern of upper respiratory micro-organisms in healthy children versus those with various respiratory diseases. We will additionally compare the organisms identified in the upper airway versus the lungs in children with respiratory disease.MethodsWe will search the following electronic databases: Epistemonikos and Cochrane Library for systematic reviews and MEDLINE (through PubMed), EMBASE, Cochrane CENTRAL, LIVIVO, Web of Science, Scopus, and CINAHL databases for primary studies. Reference lists of relevant studies will be examined for links to potential related articles. Two reviewers will independently determine eligibility for inclusion. The methodological quality and risk of bias of the included observational studies will be scored using the Newcastle–Ottawa Scale tool, and JBI Critical Appraisal Checklist for case series. We will present the data with descriptive statistics and provide pooled estimates of outcomes, wherever it is feasible to perform a meta-analysis. Heterogeneity in studies will be explored by using the Higgins and Thompson I2 method. Sensitivity analysis will be done to explore the impact of study quality, and subgroup analysis will be done based on age, health condition, type of respiratory specimen, and method of identifying organisms. We will prepare a summary of findings’ table and assess the confidence in the evidence using the GRADE methodology.ResultsThis is a protocol; hence, there are no results at this stage.DiscussionThe proposed systematic review will provide comparisons of the microbiota in the upper respiratory tract versus the lungs, in children, during health as well as respiratory disease. Similarly, the site-specific yield will be compared between healthy children and those with respiratory disease. This will provide clinicians, microbiologists, and respiratory therapists a better understanding of the respiratory system microbiota, suitability (or otherwise) of upper airway specimens in various respiratory diseases, and the potential role of upper airway colonization on specific respiratory diseases. We will disseminate the review through a peer-reviewed journal publication. Data that cannot be included in the published version will be made available on request.Systematic review registrationPROSPERO CRD42020202115.

Pilot Gene Expression and Histopathologic Analysis of Tracheal Resections in Tracheobronchomalacia

BackgroundThe airway structures and messenger RNA expression of genes that regulate airway inflammation and remodeling may be altered in the trachea of patients with tracheobronchomalacia (TBM). MethodsFourteen tracheal specimens obtained from 2005 to 2018 were used in this study. Surgical resection specimens from patients with TBM and tracheal stenosis (TS) were compared with control tracheal specimens obtained from autopsy cases. We investigated the messenger RNA expression of genes encoding fibroblast growth factor (FGF) binding protein 2 (FGFBP2), FGF receptor R3 (FGFR3), interleukin-1β (IL1β), tumor growth factor-β1 (TGFβ1), tissue inhibitor of metalloproteinases 1 (TIMP1), and intercellular adhesion molecule 1 (ICAM1) as well as established markers of airway inflammation including interferon-γ (IFNγ) and tumor necrosis factor (TNF). The relative expression of target transcripts was assessed by quantitative real-time polymerase chain reaction. A histologic examination of the same resected airway specimens was performed on formalin-fixed paraffin-embedded tissue sections. ResultsFGFBP2 and FGFR3 showed higher expression in TBM compared with TS and control groups (P < .05 and P < .01, respectively). Furthermore, both TGFβ1 and TIMP1 were elevated in TBM patients compared with control subjects (P < .05). Conversely ICAM1 was downregulated in TBM versus TS and control subjects (P < .05). IL1β, IFNγ, and TNF were increased in TBM, although it did not achieve statistical significance. Histologically compared with control airways both TBM and TS demonstrated submucosal fibrotic changes, with TBM additionally demonstrating alterations in elastin fiber quality and density in the posterior membrane. ConclusionsSignificant changes in gene expression are observed in the tracheal walls of patients with TBM and TS compared with control subjects.

A review of significance of Aspergillus detection in airways of ICU COVID-19 patients.

It is now well known that patients with SARS‐CoV‐2 infection admitted in ICU and mechanically ventilated are at risk of developing invasive pulmonary aspergillosis (IPA). Nevertheless, symptomatology of IPA is often atypical in mechanically ventilated patients, and radiological aspects in SARS‐CoV‐2 pneumonia and IPA are difficult to differentiate. In this context, the significance of the presence of Aspergillus in airway specimens (detected by culture, galactomannan antigen or specific PCR) remains to be fully understood. To decipher the relevance of the detection of Aspergillus, we performed a comprehensive review of all published cases of respiratory Aspergillus colonisation and IPA in COVID‐19 patients. The comparison of patients receiving or not antifungal treatment allowed us to highlight the most important criteria for the decision to treat. The comparison of surviving and non‐surviving patients made it possible to unveil criteria associated with mortality that should be taken into account in the treatment decision.

Respiratory microbes detected in hospitalized adults with acute respiratory infections: associations between influenza A(H1N1)pdm09 virus and intensive care unit admission or fatal outcome in Vietnam (2015\u20132017)

BackgroundAcute respiratory tract infection (ARI) is a leading cause of hospitalization, morbidity, and mortality worldwide. Respiratory microbes that were simultaneously detected in the respiratory tracts of hospitalized adult ARI patients were investigated. Associations between influenza A(H1N1)pdm09 virus (H1N1pdm) detection and intensive care unit (ICU) admission or fatal outcome were determined.MethodsThis prospective observational study was conducted between September 2015 and June 2017 at Bach Mai Hospital, Hanoi, Vietnam. Inclusion criteria were hospitalized patients aged ≥15 years; one or more of symptoms including shortness of breath, sore throat, runny nose, headache, and muscle pain/arthralgia in addition to cough and fever > 37.5 °C; and ≤ 10 days from the onset of symptoms. Twenty-two viruses, 11 bacteria, and one fungus in airway specimens were examined using a commercial multiplex real-time PCR assay. Associations between H1N1pdm detection and ICU admission or fatal outcome were investigated by univariate and multivariate logistic regression analyses.ResultsThe total of 269 patients (57.6% male; median age, 51 years) included 69 ICU patients. One or more microbes were detected in the airways of 214 patients (79.6%). Single and multiple microbes were detected in 41.3 and 38.3% of patients, respectively. Influenza A(H3N2) virus was the most frequently detected (35 cases; 13.0%), followed by H1N1pdm (29 cases; 10.8%). Hematological disease was associated with ICU admission (p < 0.001) and fatal outcomes (p < 0.001) using the corrected significance level (p = 0.0033). Sex, age, duration from onset to sampling, or number of detected microbes were not significantly associated with ICU admission or fatal outcomes. H1N1pdm detection was associated with ICU admission (odds ratio [OR] 3.911; 95% confidence interval [CI] 1.671–9.154) and fatal outcome (OR 5.496; 95% CI 1.814–16.653) after adjusting for the confounding factors of comorbidities, bacteria/Pneumocystis jirovecii co-detection, and age.ConclusionsH1N1pdm was associated with severe morbidity and death in adult patients hospitalized with respiratory symptoms. The diagnosis of subtype of influenza virus may be epidemiologically important.

Association between Mycoplasma and Ureaplasma airway positivity, ammonia levels, and outcomes post-lung transplantation: A prospective surveillance study.

Hyperammonemia syndrome (HS) is a rare complication with high mortality described after lung transplantation. Its pathophysiology is still unclear, but previous studies, including murine models, have linked the identification of Mycoplasmataceae in airway specimens with HS occurrence. This study explores the association between Mycoplasmataceae polymerase chain reaction (PCR) positivity, ammonia levels, HS, and mortality post-lung transplant. Adults who underwent lung transplantation between July 2017 and August 2019 had prospective surveillance testing for Mycoplasma and Ureaplasma using PCR on post-operative bronchoscopy samples. One hundred and fifty-nine patients underwent lung transplantation during the study period. Mean age was 54 (±13)years; baseline diseases were predominantly pulmonary fibrosis (37.7%) and chronic obstructive pulmonary disease (35.8%). Mycoplasma and/or Ureaplasma airway positivity was found in 42 (26.4%) of tested patients, represented mostly by M. salivarium (26/43; 60.4%), U. parvum (7/43; 16.2%), and U. urealyticum (5/43; 11.6%). Median peak ammonia levels were higher in those with Ureaplasma colonization compared to uncolonized patients (p=.04), however, only three patients developed HS. Recipient airway Ureaplasma positivity was independently associated with younger (aOR 0.94, 95% CI 0.88-0.99, p=.04) and female donors (aOR 4.29; 95% CI 1.01-18.2, p=.05).

The Role of Bronchoscopy in Diagnosis of Chronic Cough in Adults: A Retrospective Single-Center Study

Cough is one of the most frequent symptoms reported to pulmonologists. The role of bronchoscopy in the diagnostic work-up of chronic cough is not clearly defined. The aim of this study was to evaluate the utility of fiberoptic bronchoscopy (FOB) and additional testing of samples collected during FOB in the differential diagnosis of chronic cough in adults. This was a single-center retrospective study. Out of 7115 conventional white light FOB examinations, we finally selected 198 with cough as the only indication. In 40.9% of bronchoscopic examinations, no visible cause of cough was found. Visual signs of chronic bronchitis (CB) were detected in 57.6% of reports. Only in 3 cases (1.5%) bronchoscopy revealed a potential cause of chronic cough other than CB. Mycobacterium tuberculosis or other mycobacteria were spotted in none of the samples. In 91.1% of bronchoalveolar lavage (BAL) cytologic examinations, at least one cell count abnormality was detected, but only in case of increased percentage of eosinophils, it might be considered clinically relevant. In 53% of bacteriological culture results, at least one potentially pathogenic bacterium was isolated. The present study results strengthen the evidence that FOB combined with additional testing of airway specimens obtained during FOB is not a powerful tool in the differential diagnosis of chronic cough, and FOB as a diagnostic tool may be overused. The appropriate timing and decision regarding referral for FOB and additional testing of achieved material requires careful clinical consideration.

Bronchoalveolar lavage-based COVID-19 testing in patients with cancer

Objective/BackgroundA few case reports in the setting of coronavirus disease 2019 (COVID-19) and multiplex polymerase chain reaction (PCR)-based assays for common respiratory pathogens have shown a higher yield of bronchoalveolar lavage (BAL) samples than upper airway specimens in immunocompromised patients. MethodsA retrospective study was conducted reviewing patients diagnosed with COVID-19 at the Medical College of Wisconsin (Milwaukee, WI, USA) between March 13, 2020 and June 11, 2020. All patients tested positive for SARS-CoV-2 via real-time reverse transcriptase PCR (RT-PCR), through a nasopharyngeal or a bronchoscopy specimen. ResultsDuring the study period, 53 bronchoscopy procedures were performed at the institution, of which five patients tested positive for COVID-19. Of the five patients, three underwent BAL testing based on high clinical suspicion for COVID-19 after the nasopharyngeal (NP) swab(s) was negative. All three patients had underlying cancers and had lymphopenia for a considerable duration prior to being diagnosed with COVID-19. Two patients had better outcomes that could be attributed to earlier BAL specimen testing resulting in timely medical intervention. ConclusionThis study underscores the need for early lower respiratory tract sampling, whenever possible, in patients with cancer and prolonged lymphopenia. High clinical suspicion ought to supersede false-negative NP reverse transcriptase–PCR as early bronchoscopic evaluation in cancer patients, who are either receiving active treatment or are immunosuppressed, can allow timely institution of efficacious treatment, enrollment into clinical trials, as well as effective infection control. In the apt clinical setting in patients with cancer, presumptive treatment may also be considered to minimize exposure to healthcare providers and proceduralists.

The Healthy Airway Mycobiome in Individuals of Asian Descent

The Healthy Airway Mycobiome in Individuals of Asian Descent

Prevalence and clinical significance of common respiratory pathogens in the upper respiratory tract of children with community-acquired pneumonia in Zunyi, China.

To estimate the prevalence of common respiratory pathogens among children with community-acquired pneumonia (CAP) in Zunyi City, Guizhou, China, and to assess whether the presence of common respiratory pathogens in patients is associated with disease severity. This retrospective study assessed the prevalence of common respiratory viruses and bacteria in the upper respiratory tract of among infants and children aged 1 month to 5 years hospitalized with radiologically confirmed CAP between April 2017 and March 2018. Direct immunofluorescence assay and bacterial culture were used to identify viruses and bacteria in the upper airway specimens, respectively. The association between severe CAP and the presence of pathogens was determined using multivariate logistic regression models. Of the 685 patients enrolled, 583 cases had viral and/or bacterial pathogens detected, which included the presence of only viral pathogens, only bacterial pathogens, and mixed viral and bacterial pathogens in 34.3%, 29.7%, and 36.0% of cases, respectively. Respiratory syncytial virus (RSV) was the most common viral pathogen, with a prevalence rate of 39.9% (273/685). Haemophilus influenzae was the most commonly detected bacterial pathogen, with a prevalence rate of 15.3% (105/685). The presence of RSV (adjusted odds ratio [aOR], 1.9; 95% confidence interval [CI], 1.3-2.8) and Staphylococcus aureus (aOR, 13.7; 95% CI, 5.5-33.9) in children with CAP was associated with severe pneumonia. In a cohort of Zunyi infants and children hospitalized with CAP, RSV was the most common pathogen.

In vivo and in vitro observation of nasal ciliary motion in a guinea pig model.

Cilia play an important role in the airway defense mechanism. So far, studies on ciliary function have mainly been based on in vitro methods. Images of in vivo ciliary motion are very difficult to capture. In this study, we describe a novel approach to observe and analyze nasal ciliary motion in living animals with comparison to in vitro observation. Such images of ciliary motion from living animals have not been reported to date. The result of the study indicates that in vivo ciliary physiological function differs from ex vivo and in vitro conditions in many ways, such as the stability over time and response to temperature variation. This is a good foundation for further in vivo analysis of airway ciliary physiological function in animals as well as humans.

Inhibition of glutaminase to reverse fibrosis in iatrogenic laryngotracheal stenosis.

Glutamine metabolism is a critical energy source for iatrogenic laryngotracheal stenosis (iLTS) scar fibroblasts, and glutaminase (GLS) is an essential enzyme converting glutamine to glutamate. We hypothesize that the GLS-specific inhibitor BPTES will block glutaminolysis and reduce iLTS scar fibroblast proliferation, collagen deposition, and fibroblast metabolism in vitro. Test-tube Lab Research. Immunohistochemistry of a cricotracheal resection (n = 1) and a normal airway specimen (n = 1) were assessed for GLS expression. GLS expression was assessed in brush biopsies of subglottic/tracheal fibrosis and normal airway from patients with iLTS (n = 6). Fibroblasts were isolated and cultured from biopsies of subglottic/tracheal fibrosis (n = 6). Fibroblast were treated with BPTES and BPTES + dimethyl α-ketoglutarate (DMK), an analogue of the downstream product of GLS. Fibroblast proliferation, gene expression, protein production, and metabolism were assessed in all treatment conditions and compared to control. GLS was overexpressed in brush biopsies of iLTS scar specimens (P = .029) compared to normal controls. In vitro, BPTES inhibited iLTS scar fibroblast proliferation (P = .007), collagen I (Col I) (P < .0001), collagen III (P = .004), and α-smooth muscle actin (P = .0025) gene expression and protein production (P = .031). Metabolic analysis demonstrated that BPTES reduced glycolytic reserve (P = .007) but had no effects on mitochondrial oxidative phosphorylation. DMK rescued BPTES inhibition of Col I gene expression (P = .0018) and protein production (P = .021). GLS is overexpressed in iLTS scar. Blockage of GLS with BPTES significantly inhibits iLTS scar fibroblasts proliferation and function, demonstrating a critical role for GLS in iLTS. Targeting GLS to inhibit glutaminolysis may be a successful strategy to reverse scar formation in the airway. NA Laryngoscope, 2020.

NOTTO transplant specific guidelines with reference to COVID-19

NOTTO transplant specific guidelines with reference to COVID-19

Remdesivir Potently Inhibits SARS-CoV-2 in Human Lung Cells and Chimeric SARS-CoV Expressing the SARS-CoV-2 RNA Polymerase in Mice

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 as the causative agent of the novel pandemic viral disease COVID-19. With no approved therapies, this pandemic illustrates the urgent need for safe, broad-spectrum antiviral countermeasures against SARS-CoV-2 and future emerging CoVs. We report that remdesivir (RDV), a monophosphoramidate prodrug of an adenosine analog, potently inhibits SARS-CoV-2 replication in human lung cells and primary human airway epithelial cultures (EC50 = 0.01 µM). Weaker activity was observed in Vero E6 cells (EC50 = 1.65 µM) due to their low capacity to metabolize RDV. To rapidly evaluate in vivo efficacy, we engineered a chimeric SARS-CoV encoding the viral target of RDV, the RNA-dependent RNA polymerase, of SARS-CoV-2. In mice infected with chimeric virus, therapeutic RDV administration diminished lung viral load and improved pulmonary function as compared to vehicle treated animals. These data provide evidence that RDV is potently active against SARS-CoV-2 in vitro and in vivo, supporting its further clinical testing for treatment of COVID-19.Funding: This project was funded in part by the National Institute of Allergy and Infectious Diseases, National 284 Institutes of Health, Department of Health and Human Service awards: 1U19AI142759 (Antiviral Drug 285 Discovery and Development Center awarded to M.R.D. and R.S.B); 5R01AI132178 awarded to T.P.S. 286 and R.S.B.; and 5R01AI108197 awarded to M.R.D. and R.S.B. D.R.M was funded by T32 AI007151 and 287 a Burroughs Wellcome Fund Postdoctoral Enrichment Program Award. The Marsico Lung Institute 288 Tissue Procurement and Cell Culture Core is supported by NIH grant DK065988 and Cystic Fibrosis 289 Foundation grant BOUCHE15RO. We also are grateful for support from the Dolly Parton COVID-19 290 Research Fund, the VUMC Office of Research, and the Elizabeth B. Lamb Center for Pediatric Research 291 at Vanderbilt University. Conflict of Interest: The authors affiliated with Gilead Sciences, Inc. are employees of the company and own company stock. The other authors have no conflict of interest to report.Ethical Approval: Human tracheobronchial epithelial cells provided by Dr. Scott Randell were obtained from airway specimens resected from patients undergoing surgery under University of North Carolina Institutional Review Board-approved protocols (#03-1396) by the Cystic Fibrosis Center Tissue Culture Core.