{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:45:27Z","timestamp":1760060727892,"version":"build-2065373602"},"reference-count":28,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,12]],"date-time":"2025-09-12T00:00:00Z","timestamp":1757635200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Coinfections in COVID-19 patients can worsen disease severity by enhancing SARS-CoV-2 replication and proinflammatory cytokine levels. This study analyzes the characteristics of coinfected COVID-19 patients across the pandemic and their association with in-hospital mortality. We retrospectively examined data from 351 COVID-19 patients hospitalized in a Spanish secondary hospital between March 2020 and February\u2013March 2021. Nasopharyngeal swabs from 340 patients were analyzed using multiplex RT-PCR to identify 26 respiratory pathogens. A total of 136 patients were coinfected with 191 bacteria (100 Gram-negative and 91 Gram-positive), 20 viruses, 18 fungi, and 1 protist. In 2021, empirical cephalosporin use increased (p = 0.009). The incidence of enterococcal coinfections tripled from 2020 to 2021 (p &lt; 0.001). In 2021, a greater proportion of patients experienced urine (p = 0.001) and bloodstream (p = 0.010) coinfections. In 2020, there was one bloodstream infection, while in 2021, there were seven, with half of them being fatal. Coinfected patients experienced longer hospital stays and higher odds of long COVID (p &lt; 0.001; p = 0.014; p = 0.045). Non-respiratory coinfections in 2021 correlated with increased mortality (p = 0.002). Antimicrobial resistance remained stable (p = 0.149). The rise in cephalosporin use correlated with increased Enterococcus infections, notably bloodstream infections, which were linked to mortality (p = 0.016). In 2021, coinfections were linked to prolonged hospital stays and an increased risk of mortality in our patient cohort.<\/jats:p>","DOI":"10.3390\/microorganisms13092141","type":"journal-article","created":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T07:56:51Z","timestamp":1757923011000},"page":"2141","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Retrospective Study on Coinfections, Antimicrobial Resistance, and Mortality Risk Among COVID-19 Patients (2020\u20132021) with Consideration of Long-COVID Outcomes"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3745-6661","authenticated-orcid":false,"given":"Carlos","family":"Rescalvo-Casas","sequence":"first","affiliation":[{"name":"Departamento de Biomedicina y Biotecnolog\u00eda, Facultad de Medicina, Universidad de Alcal\u00e1, 28805 Madrid, Spain"},{"name":"Departamento de Microbiolog\u00eda Cl\u00ednica, Hospital Universitario Pr\u00edncipe de Asturias, 28805 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roc\u00edo","family":"Fern\u00e1ndez-Villegas","sequence":"additional","affiliation":[{"name":"Departamento de Biomedicina y Biotecnolog\u00eda, Facultad de Medicina, Universidad de Alcal\u00e1, 28805 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcos","family":"Hernando-Gozalo","sequence":"additional","affiliation":[{"name":"Departamento de Microbiolog\u00eda Cl\u00ednica, Hospital Universitario Pr\u00edncipe de Asturias, 28805 Madrid, Spain"},{"name":"Departamento de Qu\u00edmica Org\u00e1nica y Qu\u00edmica Inorg\u00e1nica, Facultad de Qu\u00edmica, Universidad de Alcal\u00e1 de Henares, 28805 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9360-7159","authenticated-orcid":false,"given":"Laura","family":"Seijas-Pereda","sequence":"additional","affiliation":[{"name":"Departamento de Biomedicina y Biotecnolog\u00eda, Facultad de Medicina, Universidad de Alcal\u00e1, 28805 Madrid, Spain"},{"name":"Departamento de Microbiolog\u00eda Cl\u00ednica, Hospital Universitario Pr\u00edncipe de Asturias, 28805 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5387-6792","authenticated-orcid":false,"given":"Lourdes","family":"Lled\u00f3 Garc\u00eda","sequence":"additional","affiliation":[{"name":"Departamento de Biomedicina y Biotecnolog\u00eda, Facultad de Medicina, Universidad de Alcal\u00e1, 28805 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0892-1579","authenticated-orcid":false,"given":"Lars","family":"Arendt-Nielsen","sequence":"additional","affiliation":[{"name":"Center for Neuroplasticity and Pain (CNAP), Department of Health Science and Technology, School of Medicine, Aalborg University, 9000 Aalborg, Denmark"},{"name":"Department of Gastroenterology & Hepatology, Mech-Sense, Clinical Institute, Aalborg University Hospital, 9000 Aalborg, Denmark"},{"name":"Steno Diabetes Center, North Denmark, Clinical Institute, Aalborg University Hospital, 9000 Aalborg, Denmark"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan","family":"Cuadros-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Departamento de Biomedicina y Biotecnolog\u00eda, Facultad de Medicina, Universidad de Alcal\u00e1, 28805 Madrid, Spain"},{"name":"Departamento de Microbiolog\u00eda Cl\u00ednica, Hospital Universitario Pr\u00edncipe de Asturias, 28805 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9816-3208","authenticated-orcid":false,"given":"Ram\u00f3n","family":"P\u00e9rez-Tanoira","sequence":"additional","affiliation":[{"name":"Departamento de Biomedicina y Biotecnolog\u00eda, Facultad de Medicina, Universidad de Alcal\u00e1, 28805 Madrid, Spain"},{"name":"Departamento de Microbiolog\u00eda Cl\u00ednica, Hospital Universitario Pr\u00edncipe de Asturias, 28805 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1097\/MCP.0000000000000666","article-title":"Viral Respiratory Infections: A Cause of Community-Acquired Pneumonia or a Predisposing Factor?","volume":"26","author":"Arnold","year":"2020","journal-title":"Curr. 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