Gut dysbiosis, exacerbated by excessive antimicrobial use, is a significant concern in patients with post-COVID-19 syndrome, often persisting beyond the resolution of SARS-CoV-2 infection. Dysbiosis contributes to microbiota imbalance and antimicrobial resistance, necessitating alternative approaches for rehabilitating post-COVID-19 patients.

A pilot study included 24 post-COVID-19 patients with gut dysbiosis (men: 45%). The ages of patients ranged from 46 to 80 years, with a median of 58 (51; 71) years. Intestinal content samples were obtained on the first day of admission from the 24 patients, who had recovered from the disease and received outpatient or inpatient treatment for periods of two to six months by the time of the study. Antibacterial therapy was administered in most patients during the stage of acute illness (third-generation cephalosporins or amoxicillin in combination with beta-lactamase inhibitors). The composition of the gut microbiota was analyzed using Colonoflor-16 (biocenosis) kits (AlphaLab, St. Petersburg, Russia), and real-time PCR detection (CFX 96, BioRad, Hercules, CA, USA) was performed on patients on the day of admission.

The levels of the Bacteroides fragilis group, Klebsiella oxytoca, K. pneumoniae, Candida spp., Staphylococcus aureus, Proteus vulgaris / Proteus mirabilis, Enterococcus spp., Enterobacter spp., and Citrobacter spp. exceeded the reference values by 1.5–2 times in the stool samples of patients. Additionally, the presence of Clostridium difficile, Clostridium perfringens, Fusobacterium nucleatum, and Parvimonas micra, microorganisms that are absent in the gut microbiota of healthy subjects, was detected. A high ratio of the Bacteroides fragilis/Faecalibacterium prausnitzii group was also found, which is a sign of anaerobic imbalance and inflammation.

These results support the need for further studies aimed at identifying and correcting intestinal microbiota dysbiosis in patients who have recovered from COVID-19.