Antimicrobial resistance and virulence of Enterococcus faecium isolates from a traditionally fermented dairy beverage from Uganda

Abstract

This study focused on the antimicrobial resistance (AMR) and virulence genes as well as plasmid replicons in three enterococci isolated from Bongo, a fermented dairy beverage from Uganda. They included Enterococcus (E.) faecium BM01, BM55 and BM70. They were tested against seventeen antibiotics using the disk diffusion and epsilon tests. Additionally, the DNA of the three isolates was extracted and subjected to Whole Genome Sequencing (WGS). AMR and virulence genes as well as plasmid replicons were determined by comparing the WGS data with the ResFinder database. Results indicated that the three isolates were resistant to all the antibiotics investigated. They all showed minimum inhibitory concentrations (MICs) at and above the highest concentrations tested (≥ 256 mg/mL for most antibiotics; ≥ 32 mg/mL for ciprofloxacin and levofloxacin). All isolates had the aac(6')-li and msrC AMR genes, the acm and efaAfm virulence genes as well as the repUS15 plasmid replicon. Additionally, a stress gene, CIpL was observed in the three isolates. The results call for the need to strictly control food microbial contamination as well regulate the use of antibiotics both in human and veterinary use so as to improve food safety. This study provides preliminary evidence that a Ugandan fermented dairy beverage can harbor multidrug-resistant E. faecium carrying intrinsic AMR determinants, virulence-associated genes, and a plasmid replicon linked to plasmid replication, underscoring a potential food-safety concern that warrants broader surveillance.