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The lower respiratory tract microbiome of critically ill patients with COVID-19.

Abstract
COVID-19 infection may predispose to secondary bacterial infection which is associated with poor clinical outcome especially among critically ill patients. We aimed to characterize the lower respiratory tract bacterial microbiome of COVID-19 critically ill patients in comparison to COVID-19-negative patients. We performed a 16S rRNA profiling on bronchoalveolar lavage (BAL) samples collected between April and May 2020 from 24 COVID-19 critically ill subjects and 24 patients with non-COVID-19 pneumonia. Lung microbiome of critically ill patients with COVID-19 was characterized by a different bacterial diversity (PERMANOVA on weighted and unweighted UniFrac Pr(> F) = 0.001) compared to COVID-19-negative patients with pneumonia. Pseudomonas alcaligenes, Clostridium hiranonis, Acinetobacter schindleri, Sphingobacterium spp., Acinetobacter spp. and Enterobacteriaceae, characterized lung microbiome of COVID-19 critically ill patients (LDA score > 2), while COVID-19-negative patients showed a higher abundance of lung commensal bacteria (Haemophilus influenzae, Veillonella dispar, Granulicatella spp., Porphyromonas spp., and Streptococcus spp.). The incidence rate (IR) of infections during COVID-19 pandemic showed a significant increase of carbapenem-resistant Acinetobacter baumannii (CR-Ab) infection. In conclusion, SARS-CoV-2 infection and antibiotic pressure may predispose critically ill patients to bacterial superinfection due to opportunistic multidrug resistant pathogens.
AuthorsPaolo Gaibani, Elisa Viciani, Michele Bartoletti, Russell E Lewis, Tommaso Tonetti, Donatella Lombardo, Andrea Castagnetti, Federica Bovo, Clara Solera Horna, Marco Ranieri, Pierluigi Viale, Maria Carla Re, Simone Ambretti
JournalScientific reports (Sci Rep) Vol. 11 Issue 1 Pg. 10103 (05 12 2021) ISSN: 2045-2322 [Electronic] England
PMID33980943 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
Topics
  • Aged
  • Bacteria (isolation & purification)
  • Bronchoalveolar Lavage Fluid (microbiology)
  • COVID-19 (diagnosis, microbiology)
  • Critical Illness
  • Dysbiosis (complications, microbiology)
  • Female
  • Humans
  • Lung (microbiology)
  • Male
  • Microbiota
  • Middle Aged
  • SARS-CoV-2 (isolation & purification)

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