Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium

Abstract

Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated clade A1, and that plasmids are major contributors to the emergence of nosocomial E. faecium. Here we further explored the adaptive evolution of E. faecium using a genome-wide co-evolution study (GWES) to identify co-evolving single-nucleotide polymorphisms (SNPs). We identified three genomic regions harbouring large numbers of SNPs in tight linkage that are not proximal to each other based on the completely assembled chromosome of the clade A1 reference hospital isolate AUS0004. Close examination of these regions revealed that they are located at the borders of four different types of large-scale genomic rearrangements, insertion sites of two different genomic islands and an IS30-like transposon. In non-clade A1 isolates, these regions are adjacent to each other and they lack the insertions of the genomic islands and IS30-like transposon. Additionally, among the clade A1 isolates there is one group of pet isolates lacking the genomic rearrangement and insertion of the genomic islands, suggesting a distinct evolutionary trajectory. In silico analysis of the biological functions of the genes encoded in three regions revealed a common link to a stress response. This suggests that these rearrangements may reflect adaptation to the stringent conditions in the hospital environment, such as antibiotics and detergents, to which bacteria are exposed. In conclusion, to our knowledge, this is the first study using GWES to identify genomic rearrangements, suggesting that there is considerable untapped potential to unravel hidden evolutionary signals from population genomic data.

Keywords: Enterococcus faecium; genome-wide co-evolution analysis; genomic rearrangement.

Fig. 1.

(a) All 17 236 epistatic links of the genes contained in region-1, region-2 and region-3. (b) Genomic organization and annotation of genes from regions 1–3 in E. faecium AUS0004.

Fig. 2.

Genome comparisons using strain E0139 (non-clade A1) as a reference. (a) E0139 compared to type 1 strain E1334; (b) E0139 compared to type 2 strain E8202; (c) E0139 compared to type 3 strain E6055; (d) E0139 compared to type 4 strain E7098. ‘n’ indicates the number of isolates with a similar genomic organization and for which a complete chromosome was available. Same-strand DNA similarity is shaded red, while reverse similarity is shaded blue. Blue bar, position of the pot operon; green bar, position of the ABC transporter; red arrow, insertion site for the phosphotransferase system (PTS)-encoding genomic island [24]; brown arrow, insertion site for the carbohydrate transport system-encoding genomic island [23].

Fig. 3.

Core-genome tree based on 1644 strains with the 3 metadata panels: (i) distribution of genomic rearrangements types among 38 complete chromosomes, (ii) indication of strains lacking a genomic rearrangement among 10 complete chromosomes and draft genomes and (iii) indication of strains with insertion of a carbohydrate transport system encoding genomic island, orange [23], or a phosphotransferase system (PTS) encoding genomic island, purple [24]. Black cross, indication of clade A1 dog isolates that lack the insertions/inversion or non-clade A1 dog isolates that do contain insertions/inversion.

Fig. 4.

(a) Genomic organization of the most predominant type 2 genomic rearrangement in strain E8202 with indication of insertion and inversion sites. (b) Genomic organization for reference strain E0139.