Comparative genomics of MRSA strains from human and canine origins reveals similar virulence gene repertoire

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen associated with a wide variety of infections in humans. The ability of MRSA to infect companion animals has gained increasing attention in the scientific literature. In this study, 334 dogs were screened for MRSA in two cities located in Rio de Janeiro State. The prevalence of MRSA in dogs was 2.7%. Genotyping revealed isolates from sequence types (ST) 1, 5, 30, and 239 either colonizing or infecting dogs. The genome of the canine ST5 MRSA (strain SA112) was compared with ST5 MRSA from humans-the main lineage found in Rio de Janeiro hospitals-to gain insights in the origin of this dog isolate. Phylogenetic analysis situated the canine genome and human strain CR14-035 in the same clade. Comparative genomics revealed similar virulence profiles for SA112 and CR14-035. Both genomes carry S. aureus genomic islands νSAα, νSAβ, and νSAγ. The virulence potential of the canine and human strains was similar in a Caenorhabditis elegans model. Together, these results suggest a potential of canine MRSA to infect humans and vice versa. The circulation in community settings of a MRSA lineage commonly found in hospitals is an additional challenge for public health surveillance authorities.

Figure 1

Pulsed-field gel electrophoresis (PFGE) of the SmaI-fragmented genomic DNA of MRSA isolates recovered from healthy and infected dogs in the state of Rio de Janeiro (red circles). (A) Dog isolates from Rio de Janeiro city and (B) dog isolates from Campos de Goytacazes city. USA100, USA300, USA400, WB45 and WB69 (USA1100), and BMB9393 and HU25 (BEC) were representatives of the MRSA international clones used for comparison purposes (blue circle). Dendrograms were generated from the PFGE patterns using GelCompar II software version 6.5.

Figure 2

A time-calibrated Bayesian phylogeny for MRSA strains of the lineage ST5-SCCmec II from canine (SA112) and human origins obtained from 116 core genome alignments. Values at nodes indicate the posterior probabilities for each node. The tree is drawn to a time-scale indicated in years. Blue bars indicate the 95% credibility intervals (CI) for some node ages. The 95% CI for all nodes can be seen at Supplementary Figure S1. The year of 2015 was used as a reference point for chronological estimates, which corresponds to the isolation year of the most recent strain used for the tree construction.

Figure 3

Genome alignments using blast ring generator (BRIG) and multiple alignment of conserved genomic sequence (MAUVE). (A) Overview of the completely closed genomes of the analyzed ST5 MRSA using BRIG. The color circles represent the genomes of each sequenced strain. The outer black circle represents the GC content and the inner the reference genome of the archetypal CA-MRSA strain MW2. Circular maps of ST5 genomes obtained from ST5 MRSA strains collected from canines (SA112—red circle) and humans (CR14-035—blue circle). The reference genome was the genome of the SA112. (B) Alignment between whole genomes of ST5 MRSA strains SA112 (from canine) and CR14-035 (from human) using MAUVE. Note that only four local collinear blocks were identified, with a translocation of the smallest block (represented by the green line).

Figure 4

Regions of genomic plasticity corresponding to bacteriophages and important genomic islands. (A) Schematic representation of the position of bacteriophages in the ST5 genomes of the MRSA strains SA112 (from canine) and CR14-035 (from human) sequenced in this study. (B) Alignment of the genomic island carrying important virulence genes in the genome of the strains SA112 (from canine) and CR14-035 (from human). In νSAα the set genes are highlighted in pink and lpl genes are highlighted in blue. The splABCDF operon in νSAβ is highlighted in purple. In νSAγ, set genes are highlighted in red and psmβ is highlighted in green.

Figure 5

Comparison of survival curves of C. elegans to assess the virulence of the isolates. (A) The nematodes were separately infected with strain SA112, obtained from a dog and CR14-035, obtained from humans. (B) No significant difference was found. The set of strainsNY19335—an Agr-functional CC5 clinical isolate—and MNY19335∆agr::tetM—the isogenic agr knockout mutant—was used to control the experiments. Ns not significant; **p < 0.01.