The Role of Whole Genome Sequencing in the Surveillance of Antimicrobial Resistant Enterococcus spp.: A Scoping Review

Abstract

Enterococcus spp. have arisen as important nosocomial pathogens and are ubiquitous in the gastrointestinal tracts of animals and the environment. They carry many intrinsic and acquired antimicrobial resistance genes. Because of this, surveillance of Enterococcus spp. has become important with whole genome sequencing emerging as the preferred method for the characterization of enterococci. A scoping review was designed to determine how the use of whole genome sequencing in the surveillance of Enterococcus spp. adds to our knowledge of antimicrobial resistance in Enterococcus spp. Scoping review design was guided by the PRISMA extension and checklist and JBI Reviewer's Guide for scoping reviews. A total of 72 articles were included in the review. Of the 72 articles included, 48.6% did not state an association with a surveillance program and 87.5% of articles identified Enterococcus faecium. The majority of articles included isolates from human clinical or screening samples. Significant findings from the articles included novel sequence types, the increasing prevalence of vancomycin-resistant enterococci in hospitals, and the importance of surveillance or screening for enterococci. The ability of enterococci to adapt and persist within a wide range of environments was also a key finding. These studies emphasize the importance of ongoing surveillance of enterococci from a One Health perspective. More studies are needed to compare the whole genome sequences of human enterococcal isolates to those from food animals, food products, the environment, and companion animals.

Keywords: Enterococcus; One Health; antimicrobial resistance; nosocomial infection; scoping review; surveillance; whole genome sequencing.

Figure 1

PRISMA flow diagram indicating number of articles screened and identified for inclusion in the scoping review (29).

Figure 2

Country of affiliation of corresponding author for included articles.

Figure 3

Proportion of articles included in scoping review identifying resistance to each antimicrobial class (GLY, glycopeptides; PEN, penicillins; MAC, macrolides; AMG, aminoglycosides; OXA, oxazolidinones; TET, tetracyclines; FLQ, fluoroquinolones; PHE, phenicols; LIN, lincopeptides; STR, streptogramins; LIC, lincosamides; ANS, ansamycins; GCY, glycylcyclines; NIT, nitrofurans; SUL, sulfonamides; POL, polypeptides).

Figure 4

Proportion of articles included in scoping review finding an AMR gene or gene type.

Figure 5

Proportion of articles included in scoping review finding different sequence types (NA, no sequence type described).