The upper and lower respiratory tract microbiome in severe aspiration pneumonia

Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure

“…In the UPMC-ARF cohort, we enrolled patients with non-COVID etiologies of ARF between March 2015 and June 2022. We collected baseline research biospecimens within 72hrs from intubation, including blood for separation of plasma, oropharyngeal swabs (oral samples), endotracheal aspirates (ETA) collected for research or excess bronchoalveolar lavage fluid (BALF) from clinical bronchoscopy (lung samples), and rectal swabs or stool (gut samples) 3 , 11 , 12 . We repeated research biospecimen sampling between days 3–6 (middle interval) and days 7−12 (late interval) post-enrollment for subjects who remained in the ICU.…”

“…We repeated research biospecimen sampling between days 3–6 (middle interval) and days 7−12 (late interval) post-enrollment for subjects who remained in the ICU. We extracted DNA and performed next-generation sequencing (bacterial 16S rRNA gene sequencing [16S-Seq] for all available samples; fungal Internal Transcribed Spacer sequencing [ITS-Seq] targeting the regions 1 and 2 of the ITS rRNA gene, and Nanopore DNA metagenomics for a subset of samples) to profile microbiota in the oral, lung and gut communities, respectively 3 , 12 , 13 . We measured biomarker proteins in plasma samples and a subset of ETA/BALF supernatants with Luminex panels to profile systemic and regional (lung) host responses 7 , 10 .…”

Noninvasive diagnosis of secondary infections in COVID-19 by sequencing of plasma microbial cell-free DNA

“…SPD has shown predictive value in COVID-19, and we have recently shown that lung microbiota clusters are significantly associated with plasma SPD levels in patients with non-COVID pneumonia. 33 , 34 Our data now connect a circulating microbial biomarker (mcfDNA) with plasma levels of a lung-origin molecule (SPD), suggesting that non-invasive study of host-microbiota interactions in the plasma can offer insights into LRT processes. The case of Herpesvirus DNA identification highlighted the prevalence of viral re-activation in critical illness.…”

“…From available endotracheal aspirate samples collected concurrently with blood samples, we separately extracted genomic DNA and RNA and performed bacterial 16S rRNA gene and SARS-CoV-2 RNA qPCR for assessment of bacterial and viral load in the LRT, respectively. 26 , 34 We measured plasma SARS-CoV-2 viral levels (vRNA) following RNA extraction and qPCR amplification with a sensitive in-house method. 26 …”

Routine Metagenomics Service for ICU Patients with Respiratory Infection

“…Anaerobes with or without S. milleri were found in 10% of samples, findings similar to those of a previous study using the same service framework ( 10 ), and they have been identified in other RMg studies ( 7 ). Anaerobes have been considered respiratory pathogens ( 7 , 18 – 20 ), although their significance has more recently been questioned ( 21 ), given the recognition that they are part of a healthy respiratory microbiome ( 22 , 23 ). Their absence from microbiology reports because of fastidious culture requirements has prevented detailed clinic-pathological correlation, so this metagenomic approach can prompt reassessment of their significance when identified above reporting thresholds.…”