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

Abstract

<b>Background</b>. 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.<b>Hypothesis</b>. VAP is caused by ESKAPE bacteria and other pathogens not detected by microbiological culture.<b>Aim</b>. 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.<b>Methods</b>. 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.<b>Results</b>. <i>Acinetobacter</i> and <i>Pseudomonas</i> were the main bacterial genera in the bronchoalveolar lavages (BALs) analysed. Other members of the ESKAPE group, such as <i>Enterococcus</i> and <i>Klebsiella</i>, were also identified. Taxonomic composition per patient showed that non-ESKAPE genera were present with significant relative abundances, such as <i>Prevotella</i>, <i>Stenotrophomas</i>, <i>Enterococcus</i>, <i>Mycoplasma</i>, <i>Serratia</i> and <i>Corynebacterium</i>. Kruskal-Wallis analysis proved that VAP acquisition is an adverse event that is not influenced by the sex and age of COVID-19 patients.<b>Discussion</b>. 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).<b>Conclusions</b>. 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.