High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach

Abstract

Multidrug-resistant (MDR) Enterococcus faecium (Efm) infections continue to increase worldwide, although epidemiological studies remain scarce in lower middle-income countries. We aimed to explore which strains circulate in E. faecium causing human infections in Tunisian healthcare institutions in order to compare them with strains from non-human sources of the same country and finally to position them within the global E. faecium epidemiology by genomic analysis. Antibiotic susceptibility testing was performed and transfer of vancomycin-vanA and ampicillin-pbp5 resistance was performed by conjugation. WGS-Illumina was performed on Tunisian strains, and these genomes were compared with Efm genomes from other regions present in the GenBank/NCBI database (n = 10,701 Efm genomes available May 2021). A comparison of phenotypes with those predicted by the recent ResFinder 4.1-CGE webtool unveiled a concordance of 88%, with discordant cases being discussed. cgMLST revealed three clusters [ST18/CT222 (n = 13), ST17/CT948 strains (n = 6), and ST203/CT184 (n = 3)], including isolates from clinical, healthy-human, retail meat, and/or environmental sources in different countries over large time spans (10–12 years). Isolates within each cluster showed similar antibiotic resistance, bacteriocin, and virulence genetic patterns. pbp5-AmpR was transferred by VanA-AmpR-ST80 (clinical) and AmpR-ST17-Efm (bovine meat). Identical chromosomal pbp5-platforms carrying metabolic/virulence genes were identified between ST17/ST18 strains of clinical, farm animal, and retail meat sources. The overall results emphasize the role of high-resolution genotyping as provided by WGS in depicting the dispersal of MDR-Efm strains carrying relevant adaptive traits across different hosts/regions and the need of a One Health task force to curtail their spread.

Distinction between Enterococcus faecium and Enterococcus lactis by a gluP PCR-Based Assay for Accurate Identification and Diagnostics

“…Although 3 of them carried some pbp5 amino acid mutations and the ResFinder 4.1-predicted phenotype was one of resistance in those cases, all presented a sensitive phenotype against ampicillin (MICs of 0.05 to 0.75 mg/L). This may be explained by the absence of key mutations that are frequent among clinical ampicillin-resistant E. faecium strains ( 7 ). Regarding antibiotic resistance genes, only aac(6′)-Ii and msr(C) genes were found, although both are intrinsic for E. faecium and should be for E. lactis as well.…”

“…In general, we used EUCAST v12.0 criteria; in cases in which EUCAST did not specify a clinical breakpoint, we referred to CLSI guidelines ( 23 ). Additionally, ampicillin MICs were determined by Etest (Liofilchem) ( 7 ).…”

Dissemination of Enterococcal Genetic Lineages: A One Health Perspective

“…A recent report [119] observed identical antibiotic resistance to ampicillin, virulence patterns, and bacteriocin production within clusters of clinical, farm animal, and retail meat samples, which indicates the transference of enterococcal genetic traits between animals and animal-based foods. This transmission between humans and animals was also confirmed in a previous report [120], which evaluated the spread of antimicrobial-resistant enterococci between dogs and owners in three different households.…”

Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome

“…There are several cases of our observed co-abundant ARGs that have been reported in the literature, and some of the strongest correlation pairs have been detected due to the ARGs sitting together in the same genome. For example, the gene cassette vanHAX has been found together with msr(C) and aac(6') in genomes of human isolates 52 and mef(A) linked with tet(O) 53 and mdf(A) with blaTEM, aph( 6), sul2, and, tet(A) 54 (Figure S7).…”

“…These cases were often due to the ARGs being present in the same microbial genome. For example, the gene cassette vanHAX has been found together with msr(C) and aac (6') in genomes of human isolates 46 and mef(A) linked with tet(O) 47 and mdf(A) with blaTEM, aph (6), sul2, and, tet(A) 48 (Figure S7).…”