Staphylococcus aureus ST59: Concurrent but Separate Evolution of North American and East Asian Lineages

Jo-Ann McClure; Sahreena Lakhundi; Amani Niazy; George Dong; Osahon Obasuyi; Paul Gordon; Sidong Chen; John M Conly; Kunyan Zhang

doi:10.3389/fmicb.2021.631845

Staphylococcus aureus ST59: Concurrent but Separate Evolution of North American and East Asian Lineages

Front Microbiol. 2021 Feb 10:12:631845. doi: 10.3389/fmicb.2021.631845. eCollection 2021.

Authors

Jo-Ann McClure¹, Sahreena Lakhundi², Amani Niazy², George Dong², Osahon Obasuyi², Paul Gordon³, Sidong Chen⁴, John M Conly^{1

2

5

6

7}, Kunyan Zhang^{1

2

5

6

7}

Affiliations

¹ Centre for Antimicrobial Resistance, Alberta Health Services/Alberta Precision Laboratories/University of Calgary, Calgary, AB, Canada.
² Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB, Canada.
³ Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada.
⁴ Department of Epidemiology and Health Statistics, Guangdong Pharmaceutical University, Guangzhou, China.
⁵ Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
⁶ Department of Medicine, University of Calgary, Calgary, AB, Canada.
⁷ The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.

Abstract

Despite initially being described in North America, Staphylococcus aureus (SA) sequence type ST59 is the most commonly isolated sequence type in Eastern Asia. The origins and evolution of this strain type remains unclear and therefore we gathered a collection of ST59 isolates from Canada and mainland China for a detailed genetic analysis of the lineage. Bayesian inference phylogenomic analysis of our isolates, along with previously published ST59 sequences indicated that the lineage could be divided into 6 distinct subgroups (WGS-1 thorough 6), each having distinct molecular characteristics. Analysis also demonstrated the concurrent but separate evolution of North American and East Asian lineages, as well as the extensive diversification of the East Asian lineage. The presence of a mobile element structure (MES) was found to be the major difference between these two continental lineages, absent in all North American isolates, and present in all East Asian ones. Other mobile genetic elements, such as the Immune Evasion Complex (IEC), Panton Valentine Leukocidin (PVL), and Staphylococcal Cassette Chromosome mec (SCCmec), showed significant variability within each sub-group and likely represents local selective pressures rather than major characteristics defining the groups. Our analysis also demonstrated the existence of a more ancient ST59 sub-lineage from North America, which was MES negative and contained some of the earliest reported ST59 isolates. Combined with the existence of a MES negative isolate from Taiwan, predicted to have appeared prior to diversification of the East Asian lineages, these results hint at the possibility of a North American origin for the lineage, which gained hold in Eastern Asia following acquisition of MES, and subsequently diversified.

Keywords: Staphylococcus aureus; evolution; mobile element structure; mobile genetic element; multilocus sequence type ST59; phylogeny; virulence; whole genome sequences.