{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:08:51Z","timestamp":1792789731074,"version":"4.5.0"},"reference-count":27,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2021,1,16]],"date-time":"2021-01-16T00:00:00Z","timestamp":1610755200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Italian Ministry of University and Scientific Research","award":["FIL"],"award-info":[{"award-number":["FIL"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The aim of this study was the detection of infectious agents from lower respiratory tract (LRT) samples in order to describe their distribution in patients with severe acute respiratory failure and hospitalized in intensive care units (ICU) in an Italian tertiary-care hospital. LRT samples from 154 patients admitted to ICU from 27 February to 10 May 2020 were prospectively examined for respiratory viruses, including SARS-CoV-2, bacteria and\/or fungi. SARS-CoV-2 was revealed in 90 patients (58.4%, 72 males, mean age 65 years). No significant difference was observed between SARS-CoV-2 positives and SARS-CoV-2 negatives with regard to sex, age and bacterial and\/or fungal infections. Nonetheless, fungi were more frequently detected among SARS-CoV-2 positives (44\/54, 81.4%, p = 0.0053). Candida albicans was the overall most frequently isolated agent, followed by Enterococcus faecalis among SARS-CoV-2 positives and Staphylococcus aureus among SARS-CoV-2 negatives. Overall mortality rate was 40.4%, accounting for 53 deaths: 37 among SARS-CoV-2 positives (mean age 69 years) and 16 among SARS-CoV-2 negatives (mean age 63 years). This study highlights the different patterns of infectious agents between the two patient categories: fungi were prevalently involved among SARS-CoV-2-positive patients and bacteria among the SARS-CoV-2-negative patients. The different therapies and the length of the ICU stay could have influenced these different patterns of infectious agents.<\/jats:p>","DOI":"10.3390\/microorganisms9010185","type":"journal-article","created":{"date-parts":[[2021,1,19]],"date-time":"2021-01-19T11:39:55Z","timestamp":1611056395000},"page":"185","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Detection of SARS-CoV-2 and Other Infectious Agents in Lower Respiratory Tract Samples Belonging to Patients Admitted to Intensive Care Units of a Tertiary-Care Hospital, Located in an Epidemic Area, during the Italian Lockdown"],"prefix":"10.3390","volume":"9","author":[{"given":"Adriana","family":"Calderaro","sequence":"first","affiliation":[{"name":"Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mirko","family":"Buttrini","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara","family":"Montecchini","sequence":"additional","affiliation":[{"name":"Unit of Clinical Virology, University Hospital of Parma, Viale A. Gramsci 14, 43126 Parma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanna","family":"Piccolo","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monica","family":"Martinelli","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, University Hospital of Parma, Viale A. Gramsci 14, 43126 Parma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Loretana","family":"Dell'Anna","sequence":"additional","affiliation":[{"name":"Unit of Clinical Virology, University Hospital of Parma, Viale A. Gramsci 14, 43126 Parma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan","family":"Di Maio","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, University Hospital of Parma, Viale A. Gramsci 14, 43126 Parma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Cristina","family":"Arcangeletti","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clara","family":"Maccari","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery, University of Parma, Viale A. 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Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1152\/physrev.00020.2020","article-title":"SARS-CoV-2 and COVID-19: From the Bench to the Bedside","volume":"100","author":"Romagnoli","year":"2020","journal-title":"Physiol. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1620","DOI":"10.1038\/s41467-020-15562-9","article-title":"Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV","volume":"11","author":"Ou","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_4","unstructured":"World Health Organization (2020). Coronavirus Disease 2019 (COVID-19) Situation Report\u2014111, WHO."},{"key":"ref_5","unstructured":"World Health Organization (2020). Coronavirus Disease 2019 (COVID-19) Weekly Epidemiological Update\u201415 December 2020, WHO."},{"key":"ref_6","unstructured":"World Health Organization (2020). Coronavirus Disease 2019 (COVID-19) Situation Report\u201424, WHO."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.ijid.2020.01.050","article-title":"Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak","volume":"92","author":"Zhao","year":"2020","journal-title":"Int. J. Infect. Dis. Off. Publ. Int. Soc. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Majumder, M.S., and Mandl, K.D. (2020). Early Transmissibility Assessment of a Novel Coronavirus in Wuhan, China. SSRN, 3524675.","DOI":"10.2139\/ssrn.3524675"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Read, J.M., Bridgen, J.R.E., Cummings, D.A.T., Ho, A., and Jewell, C.P. (2020). Novel coronavirus 2019-nCoV: Early estimation of epidemiological parameters and epidemic predictions. medRxiv.","DOI":"10.1101\/2020.01.23.20018549"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.1021\/acschemneuro.0c00251","article-title":"SARS-CoV-2, More than a Respiratory Virus: Its Potential Role in Neuropathogenesis","volume":"11","author":"Singal","year":"2020","journal-title":"ACS Chem. Neurosci."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Backer, J.A., Klinkenberg, D., and Wallinga, J. (2020). Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travellers from Wuhan, China, 20\u201328 January 2020. Euro Surveill. Bull. Eur. Mal. Transm. Eur. Commun. Dis. Bull., 25.","DOI":"10.2807\/1560-7917.ES.2020.25.5.2000062"},{"key":"ref_12","unstructured":"World Health Organization (2020, December 18). Preliminary Clinical Description of Severe Acute Respiratory Syndrome. Available online: https:\/\/www.who.int\/csr\/sars\/clinical\/en\/."},{"key":"ref_13","unstructured":"Centers for Disease Control and Prevention (2020, December 18). MERS Clinical Features, Available online: https:\/\/www.cdc.gov\/coronavirus\/mers\/clinical-features.html."},{"key":"ref_14","unstructured":"Jilani, T.N., Jamil, R.T., and Siddiqui, A.H. (2020). H1N1 Influenza. StatPearls, StatPearls Publishing."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Spiteri, G., Fielding, J., Diercke, M., Campese, C., Enouf, V., Gaymard, A., Bella, A., Sognamiglio, P., Sierra Moros, M.J., and Riutort, A.N. (2020). First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020. Eurosurveillance, 25.","DOI":"10.2807\/1560-7917.ES.2020.25.9.2000178"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.ijid.2020.05.035","article-title":"SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby","volume":"96","author":"Calderaro","year":"2020","journal-title":"Int. J. Infect. Dis. Off. Publ. Int. Soc. Infect. Dis."},{"key":"ref_17","unstructured":"Ministero della Salute (2020, May 20). Covid-19\u2014Situazione in Italia, Available online: http:\/\/www.salute.gov.it\/portale\/nuovocoronavirus\/homeNuovoCoronavirus.jsp."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.ijid.2020.09.1473","article-title":"Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019\u20132020 in Parma, Northern Italy","volume":"102","author":"Calderaro","year":"2020","journal-title":"Int. J. Infect. Dis. Off. Publ. Int. Soc. Infect. Dis."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.diagmicrobio.2019.01.008","article-title":"Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy","volume":"94","author":"Conversano","year":"2019","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_20","first-page":"O468","article-title":"Comparison of peptide nucleic acid fluorescence in situ hybridization assays with culture-based matrix-assisted laser desorption\/ionization-time of flight mass spectrometry for the identification of bacteria and yeasts from blood cultures and cerebrospin","volume":"20","author":"Calderaro","year":"2014","journal-title":"Clin. Microbiol. Infect. Off. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis."},{"key":"ref_21","first-page":"427","article-title":"Two rare cases of Acremonium acute endophthalmitis after cataract surgery in a tertiary care hospital","volume":"36","author":"Calderaro","year":"2013","journal-title":"New Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"139278","DOI":"10.1016\/j.scitotenv.2020.139278","article-title":"A chronicle of SARS-CoV-2: Part-I\u2014Epidemiology, diagnosis, prognosis, transmission and treatment","volume":"734","author":"Kumar","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1574","DOI":"10.1001\/jama.2020.5394","article-title":"Baseline Characteristics and Outcomes of 1591 Patients Infected With SARS-CoV-2 Admitted to ICUs of the Lombardy Region, Italy","volume":"323","author":"Grasselli","year":"2020","journal-title":"JAMA"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"de Lusignan, S., Dorward, J., Correa, A., Jones, N., Akinyemi, O., Amirthalingam, G., Andrews, N., Byford, R., Dabrera, G., and Elliot, A. (2020). Risk factors for SARS-CoV-2 among patients in the Oxford Royal College of General Practitioners Research and Surveillance Centre primary care network: A cross-sectional study. Lancet Infect. Dis.","DOI":"10.1016\/S1473-3099(20)30371-6"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2341","DOI":"10.1053\/j.jvca.2020.05.005","article-title":"Regional COVID-19 Network for Coordination of SARS-CoV-2 outbreak in Veneto, Italy","volume":"34","author":"Pasin","year":"2020","journal-title":"J. Cardiothorac. Vasc. Anesth."},{"key":"ref_26","unstructured":"(2020, December 18). Istituto Superiore di Sanit\u00e0 Coronavirus. Available online: https:\/\/www.epicentro.iss.it\/coronavirus\/."},{"key":"ref_27","unstructured":"World Health Organization (2020). Coronavirus Disease 2019 (COVID-19) Weekly Epidemiological Update\u20143 November 2020, WHO."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/1\/185\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:11:55Z","timestamp":1760159515000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/9\/1\/185"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,1,16]]},"references-count":27,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,1]]}},"alternative-id":["microorganisms9010185"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms9010185","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,1,16]]}}}