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Background  The increase in drug resistance to affordable antibiotics used to treat Gram positive bacterial infections has complicated the management of enterococcal infections. Resistance to vancomycin, one of the most powerful antibiotics, is of utmost concern as both intrinsic and acquired forms of resistance do occur in enterococci. This cross-sectional study aimed to determine the species, antibiotic susceptibility profiles and  vanA / vanB  gene frequencies among enterococci isolated from patients at Mulago Hospital in Kampala, Uganda.    Methods  Between November 2011 and October 2012, stool, urine, sputum and blood samples, as well as vaginal, endocervical, pus, ear and urethra swabs from 3229 patients were processed for isolation of bacteria, yielding 162 enterococci of which 115 were available for analysis (one isolate per specimen/patient). Species-level confirmation and susceptibility testing were determined with the Phoenix™ AST/ID Automated System, while  vanA / vanB  gene carriage was determined by PCR.    Results  Species-level identification revealed 72 isolates of  E. faecalis , 20  E. gallinarum/casseliflavus,  5  E. faecium,  4  E. raffinosus  and 2 isolates each for  E. hirae  and  E. durans . Ten isolates could not be identified to species level. Antibiotic resistance was generally low especially to ampicillin, quinolones, nitrofurantoin, glycopeptides and linezolid, but high for erythromycin and tetracycline. Equally,  vanA  and  vanB  gene frequencies were low (i.e. 15.8 and 7.9%, respectively) and detected only in  E. casseliflavus/gallinarum  species that are intrinsically resistant to vancomycin .  Vancomycin resistant isolates of  E. faecalis  and  E. faecium  were not detected.    Conclusions  Enterococcus species are frequent in clinical specimens at Mulago Hospital but they are highly susceptible to common antibiotics especially ampicillin. While vancomycin resistant enterococcal (VRE) isolates of  E. faecium  and  E. faecalis  are rare in the hospital and frequency of multidrug resistance is low, non- faecium  and non- faecalis  VRE isolates (i.e.  E. gallinarum / casseliflavus ) are frequent, some with VanA/VanB (high-level) vancomycin resistance. Therefore, species-level identification of enterococci is necessary in resource limited settings to guide infection control and treatment of enterococcal infections.    Electronic supplementary material  The online version of this article (10.1186/s12879-019-4136-7) contains supplementary material, which is available to authorized users.

bmc infectious diseases

Species, antibiotic susceptibility profiles and van gene frequencies among enterococci isolated from patients at Mulago National Referral Hospital in Kampala, Uganda