Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain

Abstract

The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn916-carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn916-carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.

Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas

“…The genome distances tree ( Fig. 1 ) of the entire set of genomes of E. faecium strains available to date (June 2021) in the GenBank database ( n = 2,167 E. faecium strains) and the set of UAMS isolates ( n = 106 E. faecium strains), constructed using Fast alignment-free computation of whole-genome average nucleotide identity (FastANI) ( 29 ), shows a clear division of the strains of this species into the two previously described groups, A and B, as well as a subsequent division of the A strains into clades A1 and A2 (see Table S1 in the supplemental material) ( 30 , 31 ). Clade A1 (1,384 total strains), formerly known as clonal complex 17 [CC17]) ( 32 , 33 ), harbors strains obtained almost entirely from clinical and human sources ( Fig.…”

Facile Modification of Medical-Grade Silicone for Antimicrobial Effectiveness and Biocompatibility: A Potential Therapeutic Strategy against Bacterial Biofilms

“…Gm+ E. faecalis has a dual nature with some strains recognized as probiotics, but others are ESKAPE pathogens with multidrug resistance and virulence. , For E. faecalis , a 5 log (∼99.999%) reduction was obtained for the shake flask test.…”

Top-Down Genomic Surveillance Approach to Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns ofEnterococcus faeciumDetected in Cancer Patients in Arkansas

“…The genome distances tree (Figure 1) of the entire set of genomes of E. faecium strains available to date (June, 2021) in the GenBank database (n=2167 E. faecium strains) and the set of UAMS isolates (n=106 E. faecium strains), constructed using Fast alignment-free computation of whole-genome Average Nucleotide Identity (FastANI, (29)), shows a clear division of the strains of this species into the two previously described groups, A and B, as well as a subsequent division of the A strains into clades A1 and A2 (Suppl. Table 1) (30, 31). Clade A1 (n=1384 total strains), formerly known as clonal complex 17 [CC17]), (32, 33), harbors strains obtained almost entirely from clinical and human sources (Figure 1, blue inner ring), with only one “avian” source sample, while clade A2 (n=695 strains) comprises E. faecium strains mainly from environmental and animal sources (Figure 1, orange inner ring).…”