{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T05:50:07Z","timestamp":1790833807472,"version":"4.1.0"},"reference-count":52,"publisher":"Microbiology Society","issue":"12","license":[{"start":{"date-parts":[[2022,12,19]],"date-time":"2022-12-19T00:00:00Z","timestamp":1671408000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,19]]},"abstract":"\n Background<\/jats:bold>. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is a predisposing factor for the development of healthcare-associated infections, of which ventilator-associated pneumonia (VAP) is one.<\/jats:p>\n \n Hypothesis<\/jats:bold>. VAP is caused by ESKAPE bacteria and other pathogens not detected by microbiological culture.<\/jats:p>\n \n Aim<\/jats:bold>. To elucidate the bacterial pathogens of severe coronavirus disease 2019 (COVID-19) and VAP patients by massive sequencing and to predict their degree of relationship with the age and sex of the patients.<\/jats:p>\n \n Methods<\/jats:bold>. Analysis of ribosomal libraries of the V3\u2013V4 hypervariable region obtained by Illumina sequencing of bronchoalveolar lavages from COVID-19 and VAP (first wave) patients from Hospital Ju\u00e1rez de M\u00e9xico.<\/jats:p>\n \n Results<\/jats:bold>. \n \n Acinetobacter<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> and \n \n Pseudomonas<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> were the main bacterial genera in the bronchoalveolar lavages (BALs) analysed. Other members of the ESKAPE group, such as \n \n Enterococcus<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> and \n \n Klebsiella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>, were also identified. Taxonomic composition per patient showed that non-ESKAPE genera were present with significant relative abundances, such as \n \n Prevotella<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>, Stenotrophomas<\/jats:italic>, \n \n Enterococcus<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>, \n \n Mycoplasma<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>, \n \n Serratia<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> and \n \n Corynebacterium<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>. Kruskal\u2013Wallis analysis proved that VAP acquisition is an adverse event that is not influenced by the sex and age of COVID-19 patients.<\/jats:p>\n \n Discussion<\/jats:bold>. Metagenomic findings in COVID-19\/VAP patients highlight the importance of implementing comprehensive microbiological diagnostics by including alternative tools for the detection of the causal agents of healthcare-associated infections (HAIs).<\/jats:p>\n \n Conclusions<\/jats:bold>. Timely identification of bacteria \u2018not sought\u2019 in diagnostic bacteriology laboratories will allow specific and targeted treatments. Implications for the restricted diagnosis of VAP causative agents in COVID-19 patients and the presence of pathogens not detected by classical microbiology are analysed and discussed.<\/jats:p>","DOI":"10.1099\/jmm.0.001634","type":"journal-article","created":{"date-parts":[[2022,12,20]],"date-time":"2022-12-20T16:16:40Z","timestamp":1671553000000},"source":"Crossref","is-referenced-by-count":13,"title":["Massive sequencing of the V3\u2013V4 hypervariable region of bronchoalveolar lavage from patients with COVID-19 and VAP reveals the collapse of the pulmonary microbiota"],"prefix":"10.1099","volume":"71","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8985-486X","authenticated-orcid":false,"given":"Emilio Mariano","family":"Dur\u00e1n-Manuel","sequence":"first","affiliation":[{"name":"Divisi\u00f3n de Investigaci\u00f3n, Hospital Ju\u00e1rez de M\u00e9xico, Mexico City, Mexico"},{"name":"Secci\u00f3n de Estudios de Posgrado e Investigaci\u00f3n, Escuela Superior de Medicina, 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