Etiological structure and antibiotic resistance of sepsis pathogens in patients with COVID-19

The purpose — to study the etiological structure and antibiotic resistance of sepsis pathogens in patients with COVID-19. Material and methods. A retrospective observational, uncontrolled study was conducted. We analyzed the results of an examination survey of 584 patients with severe and extremely severe forms of COVID-19 hospitalized at the Republic Clinical Infectious Diseases Hospital in Kazan from April 1, 2020 to October 1, 2022. Identification of the pathogen in blood and other biological materials was carried out using a Microflex LT Bruker mass spectrometer. The antibiotic sensitivity of the isolated bacterial strains was determined by the disk diffusion method using an ADAGIO analyzer (France). Results. Various types of bacteria were isolated from the blood of 76 (13%) patients with severe and critical forms of COVID-19, including: A. baumannii (23.7%), K. pneumoniae (19.7%), S. haemolyticus (19.7%), S. aureus (7.9%), E. faecium (11.8%), E. faecalis (7.9%), E. coli (3.9%), R. planticola (2.6%), P. aeruginosa (2.6%), S. pneumoniae (2.6%), S. maltophilia (1.3%), and B. cereus (1.3%). In 15 patients (19.7%) associations of 2–3 types of bacteria were isolated from the blood. A. baumannii isolates were resistant to carbapenems (94.5%), fluoroquinolones and aminoglycosides (100%), and trimethoprim-sulfamethoxazole (83.3%) strains. K. рneumoniae strains were resistant to carbapenems (60%), cephalosporins (cefixime, ceftazidime) (73.3%), fluoroquinolones (ciprofloxacin) (80%), aminoglycosides (60%), and semisynthetic penicillins (100%). 33.3% of S. aureus strains were resistant to trimethoprim-sulfamethoxazole, 16.7% — to oxacillin, erythromycin and gentamicin. Resistance of S. haemolyticus to trimethoprim-sulfamethoxazole was detected in 86.7%, to erythromycin — in 80%, to norfloxacin — in 50% of strains. 93.3% of S. haemolyticus strains were methicillin-resistant. 88.9% of E. faecium strains were resistant to ampicillin, 22.2% to tigecycline, 11.1% to linezolid. 50% of E. faecalis strains were resistant to norfloxacin, 16.7% of strains were resistant to amoxicillin, ampicillin and piperacillin. P. aeruginosa 50% of strains were resistant to levofloxacin. R. planticola was resistant to all antibiotics tested. S. maltophilia demonstrated sensitivity to co-trimoxazole only with increased exposure. Conclusion. Bacterial sepsis was diagnosed in 13% of severe and extremely severe patients with COVID-19. The etiological structure of sepsis includes a wide range of pathogens with a predominance of multi-resistant bacteria from the group of ESKAPE pathogens. Data on the etiological structure and antibiotic resistance of isolated pathogens should be taken into account for the rational use of antimicrobial drugs in the treatment of sepsis in patients with COVID-19.