Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19.

SARS-CoV-2 infection can cause severe respiratory COVID-19. However, many individuals present with isolated upper respiratory symptoms, suggesting potential to constrain viral pathology to the nasopharynx. Which cells SARS-CoV-2 primarily targets and how infection influences the respiratory epithelium remains incompletely understood. We performed scRNA-seq on nasopharyngeal swabs from 58 healthy and COVID-19 participants. During COVID-19, we observe expansion of secretory, loss of ciliated, and epithelial cell repopulation via deuterosomal cell expansion. In mild and moderate COVID-19, epithelial cells express anti-viral/interferon-responsive genes, while cells in severe COVID-19 have muted anti-viral responses despite equivalent viral loads. SARS-CoV-2 RNA+ host-target cells are highly heterogenous, including developing ciliated, interferon-responsive ciliated, AZGP1high goblet, and KRT13+ "hillock"-like cells, and we identify genes associated with susceptibility, resistance, or infection response. Our study defines protective and detrimental responses to SARS-CoV-2, the direct viral targets of infection, and suggests that failed nasal epithelial anti-viral immunity may underlie and precede severe COVID-19.

Microwave Ablation for Malignant Central Airway Obstruction: A Pilot Study.

BACKGROUND: Malignant central airway obstruction (CAO) is a debilitating complication of primary lung cancer and pulmonary metastases. Therapeutic bronchoscopy is used to palliate symptoms and/or bridge to further therapy. Microwave ablation (MWA) heats tissue by creating an electromagnetic field around an ablation device. We present a pilot study utilizing endobronchial MWA via flexible bronchoscopy as a novel modality for the management of malignant CAO. METHODS: Therapeutic bronchoscopy with a flexible MWA probe was performed in 8 cases. We reviewed tumor size, previous ablative techniques, number of applications, ablation time, amount of energy delivered, rate of successful recanalization, complications, and 30-day follow-up. RESULTS: Successful airway recanalization was achieved in all cases. No complications were noted. In 1 case, tumor in-growth within a silicone stent was ablated with no damage to the stent. DISCUSSION: Endobronchial MWA is a novel technique for tumor destruction while maintaining an airway axis. The oven effect and air gap around a tumor allow for safe and effective tissue devitalization and hemostasis without a thermal effect on structures surrounding the airway.

Increased ACE2 Levels and Mortality Risk of Patients With COVID-19 on Proton Pump Inhibitor Therapy.

INTRODUCTION: Proton pump inhibitor (PPI) use was recently reported to be associated with increased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and worse clinical outcomes. The underlying mechanism(s) for this association are unclear. METHODS: We performed a prospective study of hospitalized coronavirus disease 2019 (COVID-19) patients and COVID-negative controls to understand how PPI use may affect angiotensin-converting enzyme 2 (ACE2) expression and stool SARS-CoV-2 RNA. Analysis of a retrospective cohort of hospitalized patients with COVID-19 from March 15, 2020 to August 15, 2020 in 6 hospitals was performed to evaluate the association of PPI use and mortality. Covariates with clinical relevance to COVID-19 outcomes were included to determine predictors of in-hospital mortality. RESULTS: Control PPI users had higher salivary ACE2 mRNA levels than nonusers, 2.39 ± 1.15 vs 1.22 ± 0.92 (P = 0.02), respectively. Salivary ACE2 levels and stool SARS-CoV-2 RNA detection rates were comparable between users and nonusers of PPI. In 694 hospitalized patients with COVID-19 (age = 58 years, 46% men, and 65% black), mortality rate in PPI users and nonusers was 30% (68/227) vs 12.1% (53/439), respectively. Predictors of mortality by logistic regression were PPI use (adjusted odds ratio [aOR] = 2.72, P < 0.001), age (aOR = 1.66 per decade, P < 0.001), race (aOR = 3.03, P = 0.002), cancer (aOR = 2.22, P = 0.008), and diabetes (aOR = 1.95, P = 0.003). The PPI-associated mortality risk was higher in black patients (aOR = 4.16, 95% confidence interval: 2.28-7.59) than others (aOR = 1.62, 95% confidence interval: 0.82-3.19, P = 0.04 for interaction). DISCUSSION: COVID-negative PPI users had higher salivary ACE2 expression. PPI use was associated with increased mortality risk in patients with COVID-19, particularly African Americans.

An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection.

Recent case reports and epidemiological data suggest that fungal infections represent an underappreciated complication among people with severe COVID-19. However, the frequency of fungal colonization in patients with COVID-19 and associations with specific immune responses in the airways remain incompletely defined. We previously generated a single-cell RNA-sequencing data set characterizing the upper respiratory microenvironment during COVID-19 and mapped the relationship between disease severity and the local behavior of nasal epithelial cells and infiltrating immune cells. Our previous study, in agreement with findings from related human cohorts, demonstrated that a profound deficiency in host immunity, particularly in type I and type III interferon signaling in the upper respiratory tract, is associated with rapid progression to severe disease and worse clinical outcomes. We have now performed further analysis of this cohort and identified a subset of participants with severe COVID-19 and concurrent detection of Candida species-derived transcripts within samples collected from the nasopharynx and trachea. Here, we present the clinical characteristics of these individuals. Using matched single-cell transcriptomic profiles of these individuals' respiratory mucosa, we identify epithelial immune signatures suggestive of IL17 stimulation and anti-fungal immunity. Further, we observe a significant expression of anti-fungal inflammatory cascades in the nasal and tracheal epithelium of all participants who went on to develop severe COVID-19, even among participants without detectable genetic material from fungal pathogens. Together, our data suggest that IL17 stimulation-in part driven by Candida colonization-and blunted interferon signaling represent a common feature of severe COVID-19 infection. IMPORTANCE: In this paper, we present an analysis suggesting that symptomatic and asymptomatic fungal coinfections can impact patient disease progression during COVID-19 hospitalization. By looking into the presence of other pathogens and their effect on the host immune response during COVID-19 hospitalizations, we aim to offer insight into an underestimated scenario, furthering our current knowledge of determinants of severity that could be considered for future diagnostic and intervention strategies.

Severe COVID-19 is associated with fungal colonization of the nasopharynx and potent induction of IL-17 responses in the nasal epithelium.

Recent case reports and epidemiological data suggest fungal infections represent an under-appreciated complication among people with severe COVID-19. However, the frequency of fungal colonization in patients with COVID-19 and associations with specific immune responses in the airways remain incompletely defined. We previously generated a single-cell RNA-sequencing (scRNA-seq) dataset characterizing the upper respiratory microenvironment during COVID-19, and mapped the relationship between disease severity and the local behavior of nasal epithelial cells and infiltrating immune cells. Our study, in agreement with findings from related human cohorts, demonstrated that a profound deficiency in host immunity, particularly in type I and type III interferon signaling in the upper respiratory tract, is associated with rapid progression to severe disease and worse clinical outcomes. We have now performed further analysis of this cohort and identified a subset of participants with severe COVID-19 and concurrent detection of Candida species-derived transcripts within samples collected from the nasopharynx and trachea. Here, we present the clinical characteristics of these individuals, including confirmatory diagnostic testing demonstrating elevated serum (1, 3)-ß-D-glucan and/or confirmed fungal culture of the predicted pathogen. Using matched single-cell transcriptomic profiles of these individuals' respiratory mucosa, we identify epithelial immune signatures suggestive of IL-17 stimulation and anti-fungal immunity. Further, we observe significant expression of anti-fungal inflammatory cascades in the nasal and tracheal epithelium of all participants who went on to develop severe COVID-19, even among participants without detectable genetic material from fungal pathogens. Together, our data suggests that IL-17 stimulation - in part driven by Candida colonization - and blunted type I/III interferon signaling represents a common feature of severe COVID-19 infection.

Feasibility of Using the O-Arm Imaging System During ENB-rEBUS-guided Peripheral Lung Biopsy: A Dual-center Experience.

BACKGROUND: There is a paucity of real-time imaging modalities available for the bronchoscopic biopsy of peripheral lung nodules. We aim to demonstrate the feasibility of the O-arm imaging system to guide real-time biopsies of peripheral lung nodules during electromagnetic navigation bronchoscopy. METHODS: A retrospective review was performed at 2 academic medical centers utilizing O-arm guidance. RESULTS: The average nodule size was 2.1×2.0 cm and were mostly solid (66%) with a positive bronchus sign (83%). O-arm imaging confirmed tool-in-lesion in all cases. The diagnostic yield was 33%. Four cases were nondiagnostic of the 6 cases performed. In these cases, necrotic tissue was the most common (75%) and showed resolution following subsequent imaging. The average 3-dimensional (3D) spin time was 23.5 seconds. The average number of 3D spins performed per case was 4.33. The average effective dose per 3D spin was 3.73 mSv. CONCLUSION: We have demonstrated the O-arm's feasibility with electromagnetic navigation bronchoscopy for peripheral lung nodules. The O-arm was able to confirm tool-in-lesion in all cases which added confidence to the biopsy. Four high-resolution 3D spins per case may limit the total computed tomography effective dose. We also noted that both metal and radiation scatter were minimal when appropriate radiation safety standards were met. Although additional experience and data will be required to verify the O-arm approach for routine use, our initial experience is promising.

The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort.

To investigate the relationship between intestinal microbiota and SARS-CoV-2-mediated pathogenicity in a United States, majority African American cohort. We prospectively collected fecal samples from 50 SARS-CoV-2 infected patients, 9 SARS-CoV-2 recovered patients, and 34 uninfected subjects seen by the hospital with unrelated respiratory medical conditions (controls). 16S rRNA sequencing and qPCR analysis was performed on fecal DNA/RNA. The fecal microbial composition was found to be significantly different between SARS-CoV-2 patients and controls (PERMANOVA FDR-P = .004), independent of antibiotic exposure. Peptoniphilus, Corynebacterium and Campylobacter were identified as the three most significantly enriched genera in COVID-19 patients compared to controls. Actively infected patients were also found to have a different gut microbiota than recovered patients (PERMANOVA FDR-P = .003), and the most enriched genus in infected patients was Campylobacter, with Agathobacter and Faecalibacterium being enriched in the recovered patients. No difference in microbial community structure between recovered patients and uninfected controls was observed, nor a difference in alpha diversity between the three groups. 24 of the 50 COVID-19 patients (48%) tested positive via RT-qPCR for fecal SARS-CoV-2 RNA. A significant difference in gut microbial composition between SARS-CoV-2 positive and negative samples was observed, with Klebsiella and Agathobacter being enriched in the positive cohort. No significant associations between microbiome composition and disease severity was found. The intestinal microbiota is sensitive to the presence of SARS-CoV-2, with increased relative abundance of genera (Campylobacter, Klebsiella) associated with gastrointestinal (GI) disease. Further studies are needed to investigate the functional impact of SARS-CoV-2 on GI health.

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19.

Infection with SARS-CoV-2, the virus that causes COVID-19, can lead to severe lower respiratory illness including pneumonia and acute respiratory distress syndrome, which can result in profound morbidity and mortality. However, many infected individuals are either asymptomatic or have isolated upper respiratory symptoms, which suggests that the upper airways represent the initial site of viral infection, and that some individuals are able to largely constrain viral pathology to the nasal and oropharyngeal tissues. Which cell types in the human nasopharynx are the primary targets of SARS-CoV-2 infection, and how infection influences the cellular organization of the respiratory epithelium remains incompletely understood. Here, we present nasopharyngeal samples from a cohort of 35 individuals with COVID-19, representing a wide spectrum of disease states from ambulatory to critically ill, as well as 23 healthy and intubated patients without COVID-19. Using standard nasopharyngeal swabs, we collected viable cells and performed single-cell RNA-sequencing (scRNA-seq), simultaneously profiling both host and viral RNA. We find that following infection with SARS-CoV-2, the upper respiratory epithelium undergoes massive reorganization: secretory cells diversify and expand, and mature epithelial cells are preferentially lost. Further, we observe evidence for deuterosomal cell and immature ciliated cell expansion, potentially representing active repopulation of lost ciliated cells through coupled secretory cell differentiation. Epithelial cells from participants with mild/moderate COVID-19 show extensive induction of genes associated with anti-viral and type I interferon responses. In contrast, cells from participants with severe lower respiratory symptoms appear globally muted in their anti-viral capacity, despite substantially higher local inflammatory myeloid populations and equivalent nasal viral loads. This suggests an essential role for intrinsic, local epithelial immunity in curbing and constraining viral-induced pathology. Using a custom computational pipeline, we characterized cell-associated SARS-CoV-2 RNA and identified rare cells with RNA intermediates strongly suggestive of active replication. Both within and across individuals, we find remarkable diversity and heterogeneity among SARS-CoV-2 RNA+ host cells, including developing/immature and interferon-responsive ciliated cells, KRT13+ "hillock"-like cells, and unique subsets of secretory, goblet, and squamous cells. Finally, SARS-CoV-2 RNA+ cells, as compared to uninfected bystanders, are enriched for genes involved in susceptibility (e.g., CTSL, TMPRSS2) or response (e.g., MX1, IFITM3, EIF2AK2) to infection. Together, this work defines both protective and detrimental host responses to SARS-CoV-2, determines the direct viral targets of infection, and suggests that failed anti-viral epithelial immunity in the nasal mucosa may underlie the progression to severe COVID-19.

Tracking tidal volume noninvasively in volunteers using a tightly controlled temperature-based device: A proof of concept paper.

INTRODUCTION: There is a paucity of noninvasive respiratory monitors for patients outside of critical care settings. The Linshom respiratory monitoring device is a novel temperature-based respiratory monitor that measures the respiratory rate as accurately as capnography. OBJECTIVES: Determine whether the amplitude of the Linshom temperature profile was an accurate, surrogate and qualitative metric of the tidal volume (VT ) that tracks VT in healthy volunteers. METHODS: Forty volunteers breathed room air spontaneously through a tight-fitting continuous positive airway pressure mask with a Linshom device mounted in the mask. VT was measured contemporaneously using a standalone Maquet Servo-i ICU ventilator. The amplitudes of the Linshom temperature profiles were paired with the contemporaneous VT measurements using least squares linear regression analysis and the coefficient of variation (R2 ) was determined. RESULTS: Forty volunteers completed the study. The data from 30 of the volunteers were analysed and are presented; data from 10 volunteers were not included due to protocol violations and/or technical issues unrelated to Linshom. The fluctuations in the amplitude of the Linshom temperature profiles mapped closely with the measured VT using least squares linear regression analyses yielding a mean R2 (95% CI) value of 0.87 (0.84-0.90). CONCLUSION: These results support the notion that the Linshom temperature profile is an accurate and reliable surrogate that tracks changes in VT in healthy volunteers. Further studies are warranted in patients in clinical settings to establish the effectiveness of this monitor.

Tamponade precedes diagnosis of systemic lupus erythematosus.

The most common cardiovascular manifestation of Systemic Lupus Erythematosus is pericardial disease. Tamponade in SLE is rarely described. The patient discussed in this case report presented with symptoms of heart failure. Physical exam, laboratory testing, echocardiography, and right heart catheterization revealed multiple morbid conditions including tamponade. The diagnoses satisfied four criteria for the classification of SLE. This case emphasizes the importance of a thorough physical exam in guiding diagnostic and therapeutic measures.

Endobronchial recurrence of gastric mucosa-associated lymphoid tissue lymphoma.

Mucosa-associated lymphoid tissue (MALT) lymphoma is a diagnostic challenge when arising from bronchiolar submucosal tissue. The case herein describes a man with a lung mass and a remote history of gastric MALT lymphoma. After undergoing a bronchoscopic examination and tissue sampling, he was diagnosed with pulmonary recurrence of gastric MALT lymphoma. The diagnosis of MALT lymphoma in the lung can be challenging. Radiographic findings are typically nonspecific, and tissue biopsy by surgical means is often required. The diagnosis of bronchus-associated lymphoid tissue lymphoma has been previously demonstrated bronchoscopically when a needle aspiration is performed. This case supports the position that bronchoscopy with needle aspiration, and flow cytometry should be performed in all patients in whom pulmonary MALT lymphoma is suspected.

The air apparent: a rare complication during flexible bronchoscopy.

Flexible bronchoscopy is a common and safe outpatient procedure, with complications arising in less than 1% of cases. The case presented herein details the occurrence of pneumomediastinum, pneumopericardium, pneumoperitoneum, interstitial lung emphysema and subcutaneous emphysema during flexible bronchoscopy. Although these complications have been reported individually in various circumstances, they have not been reported concomitantly in this setting. Recovery was rapid and complete, requiring only supplemental oxygen and monitoring. After a literature and chart review, the authors postulate that the complications were not a direct result of bronchoscopy but rather the simple act of placing an oxygen delivery cannula in a patient with possible prior trauma to the site.

Effects of static electromagnetic fields on characteristics of MG-63 osteoblasts grown in culture.

The effects of static electromagnetic fields (SEFs) on MG-63, a human osteoblast cell-line, were investigated. We examined proliferation, proline uptake and gene expression in an SEF approximately 1/728th the intensity of those previously reported. Cells were placed within an SEF apparatus (average field intensity of 0.618mT) with appropriate controls. Proliferation was measured by 3H-thymidine incorporation and showed a 34% decrease in cells exposed to SEF (P = .0001; N = 3). Proline, a major component of collagen necessary for bone formation by osteoblasts, incorporation was reduced 37% (P = 0.006; N = 3). Reverse-transcription-polymerase chain reaction revealed that collagen I, alkaline phosphatase, parathyroid hormone-receptor, and osteocalcin mRNA's were down regulated with the low intensity SEF. Exposure to very low SEFs affects the MG-63 osteoblasts in a manner that may be detrimental to bone formation.