Faculty Bibliography

BACKGROUND:In January 2020, the WHO declared the SARS-CoV-2 outbreak a public health emergency; by March 11, a pandemic was declared. To date in Ireland, over 3300 patients have been admitted to acute hospitals as a result of infection with COVID-19. AIMS/OBJECTIVE:This article aims to describe the establishment of a COVID Recovery Service, a multidisciplinary service for comprehensive follow-up of patients with a hospital diagnosis of COVID-19 pneumonia. METHODS:A hybrid model of virtual and in-person clinics was established, supported by a multidisciplinary team consisting of respiratory, critical care, infectious diseases, psychiatry, and psychology services. This model identifies patients who need enhanced follow-up following COVID-19 pneumonia and aims to support patients with complications of COVID-19 and those who require integrated community care. RESULTS:We describe a post-COVID-19 service structure together with detailed protocols for multidisciplinary follow-up. One hundred seventy-four patients were discharged from Beaumont Hospital after COVID-19 pneumonia. Sixty-seven percent were male with a median age (IQR) of 66.5 (51-97). Twenty-two percent were admitted to the ICU for mechanical ventilation, 11% had non-invasive ventilation or high flow oxygen, and 67% did not have specialist respiratory support. Early data suggests that 48% of these patients will require medium to long-term specialist follow-up. CONCLUSIONS:We demonstrate the implementation of an integrated multidisciplinary approach to patients with COVID-19, identifying those with increased physical and mental healthcare needs. Our initial experience suggests that significant physical, psychological, and cognitive impairments may persist despite clinical resolution of the infection.

Rationale: Chronic airway colonization and recurrent infections are common in advanced stage chronic obstructive pulmonary disease (COPD). However, changes in the lung microbiota in early stages of this disease remain unclear. Here, we characterized the upper and lower airway microbiota of patients with early stage COPD and smoker controls.
Method(s): Upper and lower airway samples (plus appropriate environmental and technical controls) were obtained from patients with GOLD 1-2 COPD (n = 26) and smoker controls (n = 31). Bacterial load was measured with droplet digital PCR while microbiota profiling was performed using 16S rRNA gene sequencing. Data was analyzed using QIIME, Phyloseq, Vegan and DESeq. Parallel RNA metatranscriptome sequencing and host Transcriptome approach were just completed and data is becoming available.
Result(s): Characterization of the lower airway microbial communities with 16S rRNA gene sequencing showed that compared to smoker controls, COPD patients exhibited lower alpha Shannon diversity (Fig.1a, p = 0.0037). Beta diversity analysis based on Bray Curtis Dissimilarity index showed that the composition of the microbial communities in the lower airway samples were clearly distinct from background and upper airway as a whole. Some samples overlapped with both of those areas suggesting that for some subjects their lower airway microbiota was enriched with taxa commonly found in the oral cavity. We then evaluated for differentially enriched taxa in BAL samples using DESeq. The lower airway microbiota of subjects with COPD was enriched with oral commensals such as Veillonella, Prevotella (Fig 1c). Comparison of bacterial load based on bacterial composition was performed based on cluster determination of lower airway samples enriched with oral commensals (SPT for supraglottic predominant taxa) or enriched with background taxa (BPT for background predominant taxa). The bacterial load of lower airway samples categorized as SPT was one log higher than those categorized as BPT among the COPD group but not among the smoker controls (Fig.1d, p < 0.001).
Conclusion(s): Our results suggest that lower airway exposure to oral commensals occurs more frequently among subjects with COPD. Further investigation with functional microbiome approaches such as metatranscriptomics are warranted. This may be of importance given significant data showing that these taxa may contribute to an increase in lower airway inflammatory tone (especially in the Th17 pathway) that may lead to airway/parenchymal inflammatory damage and/or affect treatment response and clinical outcome in this disease

Rational Recent investigations support that the gut microbiota influences anti-PD-1 cancer immunotherapy. Lower airway dysbiosis with enrichment with oral commensals are associated with lung cancer. Recently we had shown, in both a prospective human cohort and preclinical mice model, that lung dysbiotic signatures were associated with clinical lung cancer prognosis and progression. To further understand the role of lung dysbiosis in lung cancer, we examined the role of PD-1 expression and anti- PD treatment in a lung cancer and lung dysbiotic model. Method KrasLSL-G12D/+;p53fl/fl Non-small cell Lung Cancer mice (KP) were challenged with an oral commensal, Veillonella parvula, through intra-tracheal inoculation and exposed to immune inhibition (anti- PD-1). Measurements included tumor burden and lower airway inflammatory markers (PD-1 expression and neutrophils) by FACS. Results In a preclinical lung cancer model, inoculation with Veillonella parvula, a marker taxon for the dysbiotic signature found in humans, led to: 1) decrease survival with increase tumor burden; 2) dysbiosis with oral commensal is associated with elevated level of PD-1 expression and neutrophils level compared to control. With exposure to PD-1 inhibition we observe a reverse of tumor growth (at day 7); there was significant decrease in tumor growth compared with Isotype-control (p=0.030, day7-14) and observed that PD-1+ level (p=0.0007) and Neutrophil level (p=0.0027) were lower as well. Discussion Our study suggests that lower airway dysbiosis induced by microaspiration of oral commensals may affect lung carcinogenesis due to increase in inflammatory markers and increase in the checkpoint inhibitor tone in the lower airways that may lead to suboptimal immune surveillance. These effects of lower airway dysbiosis can be partially blunted by PD-1 blockade. These data supports that treatment in lung cancer may be influenced by lower airway dysbiosis and dynamic changes in the microbial-host interaction in the lower airways

Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal ( Mycoplasma salivarium ), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.

Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal ( Mycoplasma salivarium ), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.

In lung cancer, enrichment of the lower airway microbiota with oral commensals commonly occurs and ex vivo models support that some of these bacteria can trigger host transcriptomic signatures associated with carcinogenesis. Here, we show that this lower airway dysbiotic signature was more prevalent in group IIIB-IV TNM stage lung cancer and is associated with poor prognosis, as shown by decreased survival among subjects with early stage disease (I-IIIA) and worse tumor progression as measured by RECIST scores among subjects with IIIB-IV stage disease. In addition, this lower airway microbiota signature was associated with upregulation of IL-17, PI3K, MAPK and ERK pathways in airway transcriptome, and we identified Veillonella parvula as the most abundant taxon driving this association. In a KP lung cancer model, lower airway dysbiosis with V. parvula led to decreased survival, increased tumor burden, IL-17 inflammatory phenotype and activation of checkpoint inhibitor markers.

False negatives from nasopharyngeal swabs (NPS) using reverse transcriptase PCR (RT-PCR) in SARS-CoV-2 are high. Exhaled breath condensate (EBC) contains lower respiratory droplets that may improve detection. We performed EBC RT-PCR for SARS-CoV-2 genes (E, S, N, ORF1ab) on NPS-positive (n=16) and NPS-negative/clinically positive COVID-19 patients (n=15) using two commercial assays. EBC detected SARS-CoV-2 in 93.5% (29/31) using the four genes. Pre-SARS-CoV-2 era controls (n=14) were negative. EBC was positive in NPS negative/clinically positive patients in 66.6% (10/15) using the identical E and S (E/S) gene assay used for NPS, 73.3% (11/15) using the N/ORF1ab assay and 14/15 (93.3%) combined.