Single Nucleotide Polymorphism Analysis Indicates Genetic Distinction and Reduced Diversity of Swine-Associated Methicillin Resistant Staphylococcus aureus (MRSA) ST5 Isolates Compared to Clinical MRSA ST5 Isolates

Abstract

Livestock associated methicillin resistant S. aureus (LA-MRSA) are lineages adapted to livestock species. LA-MRSA can be transmitted to humans and public health concerns exist because livestock may be the largest MRSA reservoir outside of hospital settings. Although the predominant European (ST398) and Asian (ST9) lineages of LA-MRSA are considered livestock adapted, North American swine also harbor ST5, a globally disseminated and highly pathogenic lineage. This study applied whole genome sequencing and single nucleotide polymorphism (SNP) typing to compare the population structure and genetic relatedness between swine associated and human clinical MRSA ST5 isolates. The established high-resolution phylogenomic framework revealed that LA-MRSA and human clinical MRSA ST5 are genetically distinct. LA-MRSA isolates were found to be clonal within farms, while greater genome diversity was observed among sampled clinical MRSA ST5. Analysis of the accessory genome demonstrated that LA-MRSA ST5 isolates and clinical MRSA ST5 isolates harbor different AMR genes and virulence factors, consistent with the SNP analysis. Collectively, our data indicate LA-MRSA and clinical MRSA ST5 isolates are distinct and the swine reservoir is likely of minimal significance as a source of clinical MRSA ST5 infections.

Keywords: LA-MRSA; Staphylococcus aureus; agriculture; mobile genetic elements; phylogenetic analysis; single nucleotide polymorphism (SNP) typing; swine; whole genome sequence (WGS).

FIGURE 1

Genomic distribution of SNPs. The position of the 761 identified SNPs were plotted on the Mu50 chromosome using a sliding window of 1,000 bp. SNPs were distributed throughout regions included in the analysis and did not indicate any locations for mutational hotspots. Regions lacking SNP predictions are associated with locations of mobile genetic elements and repeat regions that were excluded from the SNP discovery and encode elements such as the SCCmec element and the β-hemolysin converting bacteriophage.

FIGURE 2

Maximum parsimony SNP tree of ST5 MRSA isolates. Comparison of 156 genomes, including 153 MRSA ST5 isolates, Mu3, ED98, and Mu50, yielded a total of 764 SNPs, of which 247 were parsimony informative. The tree shown is a majority-consensus tree of 4,440 equally parsimonious trees with a consistency index of 0.9428. Trees were recovered using a heuristic search in Paup 4.0b10 (Wilgenbusch and Swofford, 2003). This tree is broken into clades, with Clade I representing clinical MRSA ST5 isolates from humans with no swine contact and Clade II representing LA-MRSA ST5 isolates. Clade IIa–d are subsets of LA-MRSA ST5 isolates and each subclade represents an individual farm or production system.

FIGURE 3

Maximum parsimony SNP tree of ST5 MRSA isolates with MGE analysis. The SNP tree developed for Figure 2 was decorated using Evolview (He et al., 2016). The tree shows the MGE complement of these isolates, specifically describing the SCCmec element, the β-hemolysin converting bacteriophage (harboring virulence factors involved in innate immune evasion), and antimicrobial resistance genes involved in tetracycline resistance (tetT/tetL) and macrolide resistance (ermA and ermC).