Genomic investigation of Staphylococcus argenteus clones in the Northern Territory

Methicillin-resistant Staphylococcus argenteus is a significant causative agent of skin sores and lesions in the Tropical North of Australia. Staphylococcal mediated skin and soft-tissue infections (SSTIs) often lead to invasive bloodstream infection, which is also highly prevalent in these areas. Globally, S. argenteus is not often associated with skin infection but with severe invasive infections.

To investigate how methicillin-resistant S. argenteus diseases in the Tropical North differ from the rest of the world, this study will utilize c.600 whole genome sequence from both the north of Australia as well as global collections (Thailand, Denmark, Sweden, Japan, amongst others). Preliminary analyses show the presence of seven distinct clonal complexes of S. argenteus worldwide. Whilst globally disseminated, the most prevalent complex is ST2250, analysis suggests that two complexes, ST1850 and ST2198, are comparatively high prevalence, and indeed dominant, in the north of Australia.

Using S. aureus as a model organism, we will investigate the differences between these clonal complexes in key hot spots of genetic variation such as the presence of plasmids and mobile genetics elements, the vSa-β genomic island and the Staphylococcal cassette chromosome (SCC). A genome wide association studies (GWAS) will then be performed to analyze the associations between each of these elements, and particular CCs and particular disease presentation.

Using whole genome sequencing we will investigate the genetic and epidemiological differences between the two dominant clonal complexes, and how they are driving S. argenteus evolution and disease prevalence. S. argenteus is a known contributor to community-acquired MRSA in the Tropical North, and appears to be equally involved in nasal carriage as in skin sores.

This study will utilize multiple computational tools including phylogeographical packages in the cross-platform tool Beast2 to investigate the spatial and temporal dynamics of S. argenteus isolates from the Tropical North of Australia. To achieve this, we have a curated dataset of S. argenteus genome sequences isolated across a period of ~10 years, with extensive metadata including community location and time of isolation/infection.  A comparable S. aureus dataset of isolates from similar locations and periods of time which will be used to compare transmission and evolutionary rates to S. argenteus.

This project aims to compare global isolates of S. argenteus to better understand the genetic diversity encoded by this emerging pathogen. Preliminary analysis suggests that there are seven clonal complexes (CC’s) that exist across multiple continents in varying distributions. Using whole genome sequencing (WGS) this project will investigate the genetic diversity of the seven CC’s from approximately 600 whole genome sequence of S. argenteus. From these data we will determine the genetic diversity profiles of each CC and investigate whether there is a geographical or temporal signal within and between each CC.

For example: A large proportion of the isolates in the Tropical North of Australia belong to CC1850 and CC2198 which are uncommon or absent elsewhere in the world. By comparing these CC to the dominant CC in the other regions of the world we seek to identify genetic factors which differentiate these clonal complexes, as well as others around the world. This will also help to elucidate whether northern Australian clonal complexes have unique features which may be linked to differences in disease presentation.

Secondly, this project aims to investigate the movement and migration of local clonal complexes of S. argenteus in the Tropical North. Using multiple years of sampling data, with location metadata, and WGS, this project aims to incorporate the use of the Bayesian phylogenetic analysis of molecular sequences to investigate the mutation rate, emergence and migration of both CC1850 and CC2198 S. argenteus throughout rural communities across Australia. Comparing these analyses to overlapping S. aureus datasets will inform the dynamics of the spread and persistence of S. argenteus throughout the Tropical North and the rest of Australia.

Staphylococcus argenteus, is an emerging bacterial pathogen only described in 2015 and previously misidentified as part of the S. aureus clonal complex 75. Although it was first identified in Northern Australia, S. argenteus has since been isolated throughout the world.

Importantly, S. argenteus was often misidentified as methicillin-resistant S. aureus. S. argenteus has been shown to account for up to 71% of community-acquired MRSA in remote aboriginal communities, with further signs of non-β-lactam resistance have emerged in some recent studies. S. argenteus is responsible for a large burden SSTIs and bacteremia in remote indigenous communities.

This project will investigate the evolution and epidemiology of this emerging pathogen including;

1. the migration and transmission of S. argenteus in the Tropical North

2. charactering the genetic repertoire of the circulating Northern Territory isolates and comparing them to a global collection.