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.

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

Convalescent Plasma to Treat COVID-19: A Two-Center, Randomized, Double-Blind Clinical Trial.

BACKGROUND: The use of convalescent plasma (CP) has been considered for its immunological mechanisms that could benefit patients in moderate and severe stages of COVID-19. This study evaluated the safety and efficacy of the use of donor CP for COVID-19. MATERIAL AND METHODS: A double-blind, randomized controlled clinical trial was conducted from May to October 2020. Thirty-nine participants with moderate (II) and severe (III) stages of COVID-19 confirmed by RT-PCR were included. The study randomization rate was set at 3:1. CPs were chosen for application with a neutralizing antibody titer of ≥1:32. RESULTS: We observed a significantly lower 21-day post-transfusion mortality HR: 0.17 (95.0% CI [0.07-0.45, p < 0.001]) in the group receiving CP compared with the control group; protective units (PU) in the group receiving convalescent plasma after seven days were significantly higher (512 (32-16,384) vs. 96 (32-256), p = 0.01); the PAO2/FIO2 index showed a significant improvement in the group receiving CP (251.01 (109.4) vs. 109.2 (62.4), p < 0.001, in the control group). CONCLUSION: CP is safe and effective, as it decreased mortality in the CP group compared with the control group.

ESKAPE bacteria characterization reveals the presence of Acinetobacter baumannii and Pseudomonas aeruginosa outbreaks in COVID-19/VAP patients.

INTRODUCTION: A decrease of detection of outbreaks by multidrug-resistant bacteria in critical areas has been reduced due to COVID-19 pandemic. Therefore, molecular epidemiological surveillance should be a primary tool to reveal associations not evident by classical epidemiology. The aim of this work was to demonstrate the presence of hidden outbreaks in the first wave of the COVID-19 pandemic and to associate their possible origin. METHODS: A population of 96 COVID-19 patients was included in the study (April to June 2020) from Hospital Juárez de México. Genetic identification and antimicrobial susceptibility testing of VAP causative agents isolated from COVID-19 patients was performed. Resistance phenotypes were confirmed by PCR. Clonal association of isolates was performed by analysis of intergenic regions obtained. Finally, the association of clonal cases of VAP patients was performed by timelines. RESULTS: ESKAPE and non-ESKAPE bacteria were identified as causative agents of VAP. ESKAPE bacteria were classified as MDR and XDR. Only A. baumannii and P. aeruginosa were identified as clonally distributed in 13 COVID-19/VAP patients. Time analysis showed that cross-transmission existed between patients and care areas. CONCLUSIONS: Acinetobacter baumannii and Pseudomonas aeruginosa were involved in outbreaks non-detected in COVID-19/VAP patients in the first wave of COVID-19 pandemic.