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.

Genetic and Virulence Profiles of Enteroaggregative Escherichia coli (EAEC) Isolated From Deployed Military Personnel (DMP) With Travelers' Diarrhea

“…To compute a SNP-based phylogeny for the sampled EAEC, we used a custom-built core genome (cg) SNP discovery pipeline described in more detail in Eppinger et al (2010Eppinger et al ( , 2011Eppinger et al ( , 2014, Rusconi et al (2016), and Hau et al (2018), which is implemented on the open-source web-based bioinformatics platform Galaxy (Goecks et al, 2010). This high-resolution SNP discovery and typing strategy allowed us to put the sampled EAEC strains into a phylogenomic context and determine their individual phylogenetic relationships.…”

“…The resulting SNP panel for each of the query genomes was used for further processing; (ii) SNP validation and filtering. We used several SNP curation strategies as described previously (Eppinger et al, 2010(Eppinger et al, , 2011(Eppinger et al, , 2014Rusconi et al, 2016;Hau et al, 2018). Briefly, cataloged SNPs from each genome were merged into a single SNP panel and SNPs located within excluded regions were removed along with low quality alignments or misalignments, non-uniformly distributed regions and InDels, as previously described (Myers et al, 2009;Morelli et al, 2010;Eppinger et al, 2014).…”

Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes

“…To compute a SNP phylogeny, we used a custom-built core genome (cg) SNP discovery pipeline described in more detail in Eppinger et al (2010Eppinger et al ( , 2011bEppinger et al ( , 2014, , and Hau et al (2018), which is implemented on the open-source webbased bioinformatics platform Galaxy (Goecks et al, 2010). The chromosomal core was defined as the set of genic and intragenic regions that are not repeated, do not contain prophages, IS elements, GIs, or other mobile genome elements (MGEs), which evolve at different rates and therefore are not indicative of evolutionary relationships.…”

“…The majority rule consensus SNP tree was visualized in Geneious (Kearse et al, 2012) and decorated with EvolView (Zhang et al, 2012;He et al, 2016;Subramanian et al, 2019). Calculation of the consistency index (CI) in Mesquite (Maddison and Maddison, 2016) for each SNP allowed us to identify parsimony informative SNPs and flag homoplastic SNPs, as described in our previous works (Eppinger et al, , 2011bHau et al, 2018). This strategy was also used for the discovery of plasmidborne SNPs referenced to closed pO157 and pSFO157 plasmids of strains EC4115 (Eppinger et al, 2011b) and 3072/96 (Brunder et al, 2006), respectively.…”

“…Further structural analysis of FliK in E. coli including diverse bacteria suggests functional conservation at this particular position (Marchler-Bauer et al, 2017). To determine the genetic relationships of the individual isolates at a higher level of phylogenetic accuracy and resolution, we performed a cgSNP analysis using a custom developed SNP discovery and validation pipeline described in detail in our previous works (Eppinger et al, , 2011bHau et al, 2018). Comparison of the chromosomes yielded a total of 7,673 high-quality SNPs, of which 4,109 were parsimony informative.…”