{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:55:08Z","timestamp":1792788908558,"version":"4.5.0"},"reference-count":21,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2025,8,5]],"date-time":"2025-08-05T00:00:00Z","timestamp":1754352000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ricerca Corrente, IRCCS MultiMedica"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: The COVID-19 pandemic has profoundly altered the clinical and microbiological landscape of respiratory tract infections (RTIs), potentially reshaping pathogen distribution and antimicrobial resistance (AMR) profiles across care settings. Objectives: The objective of this study was to assess temporal trends in respiratory bacterial pathogens, antimicrobial resistance, and polymicrobial infections across three pandemic phases\u2014pre-COVID (2018\u20132019), COVID (2020\u20132022), and post-COVID (2022\u20132024)\u2014in hospitalized and ambulatory patients. Methods: We retrospectively analyzed 1827 respiratory bacterial isolates (hospitalized patients, n = 1032; ambulatory patients, n = 795) collected at a tertiary care center in Northern Italy. Data were stratified by care setting, anatomical site, and pandemic phase. Species identification and susceptibility testing followed EUCAST guidelines. Statistical analysis included chi-square and Fisher\u2019s exact tests. Results: In hospitalized patients, a significant increase in Pseudomonas aeruginosa (from 45.5% pre-COVID to 58.6% post-COVID, p &lt; 0.0001) and Acinetobacter baumannii (from 1.2% to 11.1% during COVID, p &lt; 0.0001) was observed, with 100% extensively drug-resistant (XDR) rates for A. baumannii during the pandemic. Conversely, Staphylococcus aureus significantly declined from 23.6% pre-COVID to 13.7% post-COVID (p = 0.0012). In ambulatory patients, polymicrobial infections peaked at 41.2% during COVID, frequently involving co-isolation of Candida spp. Notably, resistance to benzylpenicillin in Streptococcus pneumoniae reached 80% (4\/5 isolates) in hospitalized patients during COVID, and carbapenem-resistant P. aeruginosa (CRPA) significantly increased post-pandemic in ambulatory patients (0% pre-COVID vs. 23.5% post-COVID, p = 0.0014). Conclusions: The pandemic markedly shifted respiratory pathogen dynamics and resistance profiles, with distinct trends observed in hospital and community settings. Persistent resistance phenotypes and frequent polymicrobial infections, particularly involving Candida spp. in outpatients, underscore the need for targeted surveillance and antimicrobial stewardship strategies.<\/jats:p>","DOI":"10.3390\/antibiotics14080796","type":"journal-article","created":{"date-parts":[[2025,8,6]],"date-time":"2025-08-06T10:13:51Z","timestamp":1754475231000},"page":"796","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Evolution of Respiratory Pathogens and Antimicrobial Resistance over the COVID-19 Timeline: A Study of Hospitalized and Ambulatory Patient Populations"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8760-1292","authenticated-orcid":false,"given":"Luigi Regenburgh","family":"De La Motte","sequence":"first","affiliation":[{"name":"UOC Laboratory of Clinical Medicine with Specialized Areas, IRCCS MultiMedica, 20138 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Loredana","family":"Deflorio","sequence":"additional","affiliation":[{"name":"UOC Laboratory of Clinical Medicine with Specialized Areas, IRCCS MultiMedica, 20138 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erika","family":"Stefano","sequence":"additional","affiliation":[{"name":"UOC Laboratory of Clinical Medicine with Specialized Areas, IRCCS MultiMedica, 20138 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matteo","family":"Covi","sequence":"additional","affiliation":[{"name":"UOC Laboratory of Clinical Medicine with Specialized Areas, IRCCS MultiMedica, 20138 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela","family":"Uslenghi","sequence":"additional","affiliation":[{"name":"UOC Laboratory of Clinical Medicine with Specialized Areas, IRCCS MultiMedica, 20138 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmen","family":"Sommese","sequence":"additional","affiliation":[{"name":"Lab of Cardiovascular Diabetology and Dysmetabolic Disease, MultiMedica Scientific Institute for Hospitalization and Care (IRCCS), 20138 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5206-540X","authenticated-orcid":false,"given":"Lorenzo","family":"Drago","sequence":"additional","affiliation":[{"name":"UOC Laboratory of Clinical Medicine with Specialized Areas, IRCCS MultiMedica, 20138 Milan, Italy"},{"name":"Clinical Microbiology and Microbiome Laboratory, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e36809","DOI":"10.1016\/j.heliyon.2024.e36809","article-title":"Epidemiological trends in respiratory pathogens infections among children post-COVID-19: A cross-sectional study","volume":"10","author":"Li","year":"2024","journal-title":"Heliyon"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Bondi, A., Koumantakis, E., Curtoni, A., Barbui, A.M., Peradotto, M., Lombardi, D., Casale, R., Alizzi, S., Zanotto, E., and Charrier, L. (2024). Epidemiology and Impact of Anti-Pneumococcal Vaccination and COVID-19 on Resistance of Streptococcus pneumoniae Causing Invasive Disease in Piedmont, Italy. Antibiotics, 13.","DOI":"10.3390\/antibiotics13080740"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1016\/j.arbres.2025.01.001","article-title":"Risk Factors and Outcomes Associated with Polymicrobial Infection in Community-Acquired Pneumonia","volume":"61","author":"Cilloniz","year":"2025","journal-title":"Arch. Bronconeumol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1800560","DOI":"10.2807\/1560-7917.ES.2018.23.42.1800560","article-title":"Antimicrobial resistance surveillance in Europe and beyond","volume":"23","author":"Simonsen","year":"2018","journal-title":"Eurosurveillance"},{"key":"ref_5","unstructured":"Iacchini, S., Boros, S., Pezzotti, P., Errico, G., Del Grosso, M., Camilli, R., Giufr\u00e8, M., Pantosti, A., Maraglino, F., and Palamara, A.T. (2024). AR-ISS: Sorveglianza Nazionale Dell\u2019antibiotico-Resistenza, Istituto Superiore di Sanit\u00e0. (Rapporti ISS Sorveglianza RIS 5\/2024)."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.jinf.2020.05.046","article-title":"Co-infections in people with COVID-19: A systematic review and meta-analysis","volume":"81","author":"Lansbury","year":"2020","journal-title":"J. Infect."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2459","DOI":"10.1093\/cid\/ciaa530","article-title":"Bacterial and Fungal Coinfection in Individuals with Coronavirus: A Rapid Review to Support COVID-19 Antimicrobial Prescribing","volume":"71","author":"Rawson","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.cmi.2020.07.041","article-title":"Incidence of co-infections and superinfections in hospitalized patients with COVID-19: A retrospective cohort study","volume":"27","author":"Sanjuan","year":"2021","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_9","unstructured":"European Centre for Disease Prevention and Control (2023). Antimicrobial Resistance in the EU\/EEA (EARS-Net)\u2014Annual Epidemiological Report 2022, ECDC."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1482","DOI":"10.1093\/cid\/ciy723","article-title":"Prevalence and Etiology of Community-acquired Pneumonia in Immunocompromised Patients","volume":"68","author":"Sotgiu","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1618","DOI":"10.1378\/chest.121.5.1618","article-title":"Incidence and outcome of polymicrobial ventilator-associated pneumonia","volume":"121","author":"Combes","year":"2002","journal-title":"Chest"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/j.ajic.2019.11.002","article-title":"The impact of Candida spp airway colonization on clinical outcomes in patients with ventilator-associated pneumonia: A systematic review and meta-analysis","volume":"48","author":"Huang","year":"2020","journal-title":"Am. J. Infect. Control"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Pendleton, K.M., Huffnagle, G.B., and Dickson, R.P. (2017). The significance of Candida in the human respiratory tract: Our evolving understanding. Pathog. Dis., 75.","DOI":"10.1093\/femspd\/ftx029"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Zuo, Y.H., Wang, W.Q., Chen, Q.J., Liu, B., Zhang, F.Y., Jin, X.Y., Hang, J.Q., Li, H.Y., Bao, Z.Y., and Jie, Z.J. (2020). Candida in Lower Respiratory Tract Increases the Frequency of Acute Exacerbation of Chronic Obstructive Pulmonary Disease: A Retrospective Case-Control Study. Front. Cell. Infect. Microbiol., 10.","DOI":"10.3389\/fcimb.2020.538005"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Liu, J., Yu, Y.T., Xu, C.H., and Chen, D.C. (2020). Candida Colonization in the Respiratory Tract: What Is the Significance?. Front. Med., 7.","DOI":"10.3389\/fmed.2020.598037"},{"key":"ref_16","first-page":"60","article-title":"Silent pandemic in intensive care units: Post-pandemic rise of extensively drugresistant Acinetobacter baumannii and Klebsiella pneumoniae in ventilator-associated pneumonia","volume":"73","author":"Kerget","year":"2025","journal-title":"Tuberc. Thorax"},{"key":"ref_17","unstructured":"(2025, June 10). Centers for Disease Control and Prevention. COVID-19: U.S. Impact on Antimicrobial Resistance, Special Report 2022, Available online: https:\/\/stacks.cdc.gov\/view\/cdc\/119025."},{"key":"ref_18","unstructured":"(2023). Antimicrobial Resistance Surveillance in Europe 2023\u20132021 Data, European Centre for Disease Prevention and Control and World Health Organization."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"iqae009","DOI":"10.1093\/oxfimm\/iqae009","article-title":"The airway mycobiome and interactions with immunity in health and chronic lung disease","volume":"5","author":"Katsoulis","year":"2024","journal-title":"Oxf. Open Immunol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Correa-Moreira, D., da Costa, G.L., de Lima Neto, R.G., Pinto, T., Salomao, B., Fumian, T.M., Mannarino, C.F., Prado, T., Miagostovich, M.P., and de Souza Ramos, L. (2024). Screening of Candida spp. in wastewater in Brazil during COVID-19 pandemic: Workflow for monitoring fungal pathogens. BMC Biotechnol., 24.","DOI":"10.1186\/s12896-024-00868-z"},{"key":"ref_21","first-page":"792","article-title":"Distribution of fungal agents in the respiratory system of patients with underlying lung diseases; molecular identification and antifungal susceptibility profiles","volume":"16","author":"Hassanpour","year":"2024","journal-title":"Iran. J. Microbiol."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/8\/796\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:23:21Z","timestamp":1760034201000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/14\/8\/796"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,5]]},"references-count":21,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2025,8]]}},"alternative-id":["antibiotics14080796"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics14080796","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,5]]}}}