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Volume 71, Issue 12

Massive sequencing of the V3–V4 hypervariable region of bronchoalveolar lavage from patients with COVID-19 and VAP reveals the collapse of the pulmonary microbiota Open Access

Abstract

. 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.

. VAP is caused by ESKAPE bacteria and other pathogens not detected by microbiological culture.

. 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.

. Analysis of ribosomal libraries of the V3–V4 hypervariable region obtained by Illumina sequencing of bronchoalveolar lavages from COVID-19 and VAP (first wave) patients from Hospital Juárez de México.

. and were the main bacterial genera in the bronchoalveolar lavages (BALs) analysed. Other members of the ESKAPE group, such as and , were also identified. Taxonomic composition per patient showed that non-ESKAPE genera were present with significant relative abundances, such as , , , , and . Kruskal–Wallis analysis proved that VAP acquisition is an adverse event that is not influenced by the sex and age of COVID-19 patients.

. 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).

. Timely identification of bacteria ‘not sought’ 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bioinformatics , DNA sequencing , dysbiosis lug , ESKAPE bacteria , SARS-CoV-2 and ventilator-associated pneumonia
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. The Microbiology Society waived the open access fees for this article.
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2022-12-20
2024-04-20
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Massive sequencing of the V3–V4 hypervariable region of bronchoalveolar lavage from patients with COVID-19 and VAP reveals the collapse of the pulmonary microbiota
J. Med. Microbiol. 71, 001634 (2022); https://doi.org/10.1099/jmm.0.001634
/content/journal/jmm/10.1099/jmm.0.001634
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