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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(&gt;\u2009F)\u2009=\u20090.001) compared to COVID-19-negative patients with pneumonia. <jats:italic>Pseudomonas alcaligenes<\/jats:italic>,<jats:italic> Clostridium hiranonis<\/jats:italic>,<jats:italic> Acinetobacter schindleri<\/jats:italic>, <jats:italic>Sphingobacterium<\/jats:italic> spp.,<jats:italic> Acinetobacter<\/jats:italic> spp. and <jats:italic>Enterobacteriaceae<\/jats:italic>, characterized lung microbiome of COVID-19 critically ill patients (LDA score\u2009&gt;\u20092), while COVID-19-negative patients showed a higher abundance of lung commensal bacteria (<jats:italic>Haemophilus influenzae<\/jats:italic>, <jats:italic>Veillonella dispar<\/jats:italic>, <jats:italic>Granulicatella<\/jats:italic> spp., <jats:italic>Porphyromonas<\/jats:italic> spp., and <jats:italic>Streptococcus<\/jats:italic> spp.). The incidence rate (IR) of infections during COVID-19 pandemic showed a significant increase of carbapenem-resistant <jats:italic>Acinetobacter baumannii<\/jats:italic> (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.<\/jats:p>","DOI":"10.1038\/s41598-021-89516-6","type":"journal-article","created":{"date-parts":[[2021,5,12]],"date-time":"2021-05-12T10:03:45Z","timestamp":1620813825000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":69,"title":["The lower respiratory tract microbiome of critically ill patients with COVID-19"],"prefix":"10.1038","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3791-8635","authenticated-orcid":false,"given":"Paolo","family":"Gaibani","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisa","family":"Viciani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michele","family":"Bartoletti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Russell E.","family":"Lewis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9676-3595","authenticated-orcid":false,"given":"Tommaso","family":"Tonetti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donatella","family":"Lombardo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Castagnetti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federica","family":"Bovo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clara Solera","family":"Horna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Ranieri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierluigi","family":"Viale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Carla","family":"Re","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone","family":"Ambretti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,12]]},"reference":[{"key":"89516_CR1","unstructured":"World Health Organization. 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