Comparative genomic analysis of clinical Enterococcus faecalis distinguishes strains isolated from the bladder

Abstract

Background: Enterococcus faecalis is the most commonly isolated enterococcal species in clinical infection. This bacterium is notorious for its ability to share genetic content within and outside of its species. With this increased proficiency for horizontal gene transfer, tremendous genomic diversity within this species has been identified. Many researchers have hypothesized E. faecalis exhibits niche adaptation to establish infections or colonize various parts of the human body. Here, we hypothesize that E. faecalis strains isolated from the human bladder will carry unique genomic content compared to clinical strains isolated from other sources.

Results: This analysis includes comparison of 111 E. faecalis genomes isolated from bladder, urogenital, blood, and fecal samples. Phylogenomic comparison shows no association between isolation source and lineage; however, accessory genome comparison differentiates blood and bladder genomes. Further gene enrichment analysis identifies gene functions, virulence factors, antibiotic resistance genes, and plasmid-associated genes that are enriched or rare in bladder genomes compared to urogenital, blood, and fecal genomes. Using these findings as training data and 682 publicly available genomes as test data, machine learning classifiers successfully distinguished between bladder and non-bladder strains with high accuracy. Genes identified as important for this differentiation were often related to transposable elements and phage, including 3 prophage species found almost exclusively in bladder and urogenital genomes.

Conclusions: E. faecalis strains isolated from the bladder contain unique genomic content when compared to strains isolated from other body sites. This genomic diversity is most likely due to horizontal gene transfer, as evidenced by lack of phylogenomic clustering and enrichment of transposable elements and prophages. Investigation into how these enriched genes influence host-microbe interactions may elucidate gene functions required for successful bladder colonization and disease establishment.

Keywords: Bladder microbiome; Comparative pangenomics; Enterococcus faecalis genomics; Niche adaptation.

Fig. 1

Enterococcus faecalis strains isolated from diverse body sites do not represent distinct lineages

Fig. 2

Pangenome analysis shows presence of strain-specific genes. Gene presence is denoted by a black bar for each individual strain, represented by a circular bar graph. Sorting based on gene presence and absence is displayed in the dendrogram

Fig. 3

Functional enrichment analysis identifies COG and KEGG hits significantly enriched in bladder strains. Genes significantly enriched in bladder strains (yellow, A-C) fall above the 1.25 y-intercept and to the left of the -0.5 x-intercept. Genes enriched in blood (coral, A), fecal (green, B), and urogenital (purple, C) fall above the 1.25 y-intercept and to the right of the 0.5 x-intercept. Gene labels containing gene names are shared between functional enrichment and machine learning analyses

Fig. 4

Functional enrichment identifies ABRicate hits significantly enriched in bladder strains. Genes significantly enriched in bladder strains (yellow, A-C) fall above the 1.25 y-intercept and to the left of the -0.5 x-intercept. Genes enriched in blood (coral, A), fecal (green, B), and urogenital (purple, C) fall above the 1.25 y-intercept and to the right of the 0.5 x-intercept