Clinical and Biological Impact of Gut Microbiota in Adult Patients With Bacteremia During the COVID-19 Pandemic

Overview

The widespread use of antibiotics in healthcare, veterinary, and agricultural sectors has significantly contributed to the rise of antimicrobial resistance (AMR), affecting both commensal and pathogenic microorganisms. AMR infections are linked to poorer patient outcomes, prolonged hospital stays, and increased mortality. The COVID-19 pandemic exacerbated this issue through the overuse of antibiotics in hospitalized patients, worsening global resistance trends. Six bacterial species-Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.-are considered urgent targets for new drug development. Advanced diagnostic methods, particularly Next Generation Sequencing (NGS), show promise in improving the detection and management of sepsis and resistant infections. However, effective application of NGS requires interdisciplinary collaboration and specialized expertise, highlighting the need for integrated efforts between research institutions and clinical centers to improve AMR surveillance, diagnostics, and treatment strategies.

Excessive consumption of antibiotics in clinical, veterinary, and agricultural settings has led to a huge influx of antibiotics into the environment. This has driven the evolution of antimicrobial resistance (AMR) in commensal and pathogenic microorganisms. Infections related to AMR microorganisms are associated with an increased incidence of negative outcomes for patients, longer hospital stays, and higher morbidity and mortality rates. A list of six bacterial species has been drawn up for which it is mandatory to discover and develop new drugs: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. The pandemic has led to an exponential increase in the use of antibiotics in hospitalized COVID-19 patients, resulting in increased antibiotic resistance and a worsening of the global epidemiological picture. Laboratories are focusing on certain multi-resistant microorganisms (MDR) such as A. baumannii, P. aeruginosa, K. pneumoniae, and E. coli, considered critical priorities by the World Health Organization (WHO), but Staphylococcus aureus and Enterococcus fecium also continue to pose a problem in the management of patients admitted to intensive care. Faced with this critical issue, there is an increasingly urgent need for new and more effective diagnostic and therapeutic tools capable of controlling its spread. Data collection, as well as analysis of the impact that the pandemic has had on AMR, is essential for implementing surveillance, monitoring, and control systems. The most studied diagnostic pathway in infectious diseases is that of the septic patient, as sepsis is the most serious complication of any infection, even minor ones. Sepsis is difficult to diagnose and must be treated promptly. The implementation of Next Generation Sequencing (NGS) technologies in infectious diseases is also very promising in the field of sepsis diagnostics, as well as in the study of SARS COV-2 variants, microbiota, and bacterial resistance. However, it requires clinical microbiological and bioinformatic know-how to interpret and evaluate NGS data and place this data in the appropriate clinical context. For this reason, scientific collaboration between universities and hospitals is crucial.