Objective: in this study, we evaluate the prevalence, antimicrobial profiles, and vancomycin resistance (van) genotype of fecal Enterococcus isolates from hospitalized and non-hospitalized patients in Khartoum locality hospitals, Sudan.

Methodology: This is a cross-sectional study, conducted between Oct 2018 and March 2020 at four tertiary hospitals in the Khartoum locality. A total number of 588 fecal samples were collected and processed using microbiological culture media (Bile Esculin agar), gram stain, and gram-positive biochemical set tests to identify Enterococci species. Antibiogram of Enterococci strains was performed, and the disk diffusion method of Kirby-Bauer has been used with the broth microdilution method for vancomycin minimum inhibitory concentration. A multiplex polymerase chain reaction assay was used to provide simultaneous identification at the species level and detection of vancomycin resistance (van) genotypes characterization.

Results: All tested enterococci were confirmed to the species level, van genes were detected, and the MIC values determined vancomycin. Overall, Enterococcal species were isolated from 170/588 (28.9%) of the study subjects. Among the Enterococcus isolates, 70 (41.2%) were isolated from hospitalized patients, and 100 (58.8%) were isolated from non-hospitalized patients. The isolates were E. faecium 108 (63.5%), followed by E. faecalis 43 (25.3%) and 19 (11.2%) other Enterococcus spp. Enterococcus isolates show overall high resistance to ceftazidime (80.0%), followed by amoxicillin-clavulanic acid (70%), gentamycin (69.4%), and erythromycin (52.4%). A higher prevalence of resistance to ampicillin, rifampin, and teicoplanin was detected in E. faecium than that in E. faecalis and other Enterococcus spp., while a greater prevalence of resistance to ceftazidime, and ciprofloxacin was found in E. faecalis. Twenty-five (14.7%) strains of fecal Enterococci were found to be vancomycin resistant with vanA 19 (11.2%), vanB 5 (2.9%), and 1 (0.6%) vanC1 genotypes. The most predominant van producer strains were E. faecium [18, 16.7%; vanA (n= 17) & vanB (n= 1)] followed by E. faecalis [6, 14.0%; vanA (n= 2), and vanB (n= 4)] and Other Enterococcus spp. [1, 5.3%; vanC1 (n= 1)].

Conclusion: The present study provides the first comprehensive report of the antimicrobial resistance pattern and shows Khartoum localities are repositories for the vancomycin resistance Enterococcus with vanA, vanB, and vanC1 genotypes in human feces of both hospitalized and non-hospitalized patients. It is imperative to track and implement infection control measures in both settings to prevent the spread of these strains.

Keywords: Fecal enterococci, Vancomycin-resistant enterococci, Van genotypes, Khartoum, Sudan