Richard, Erin*

Erin Richard – DLX account application

Research overview:

Our research is interested in the role of Waste Water Treatment Plants in the adaptation of Staphylococcus aureus (SA), specifically the acquisition of mobile genetic elements (MGEs) that can increase virulence and confer resistance. Community-acquired, Methicillin-Resistant SA (CA-MRSA) infections have supplanted hospital-acquired Methicillin-Resistant SA (HA-MRSA) to become a dominant cause of infectious disease morbidity and mortality in the USA. CA-MRSA is now endemic, yet its fate and transport is not well defined. SA transmission is thought to require close contact with infected people or contaminated fomites but with increased environmental persistence of SA documented and recent discovery of MRSA in wastewaters, it seems engineered sewage systems could serve as genetic reservoirs and adaptive hot-spots for MRSA. This research could help to define the link between clinical and epidemiological findings and microbial ecology from activated sludge and could help us to rethink engineering waste water treatment processes to protect health and the environment. We have isolated 17 S. aureus strains from two treatment plants in the Lexington area at various points in the treatment process and performed whole genome sequencing. We plan to compare the genomes of these strains to determine if differences in virulence and resistance genes exist between strains from different plants and from different points in the treatment process. The research proposed lies along the intersections of several disciplines, a factor that tends to be associated with maximal impact and opportunity to create fundamental change in how we view our environmental systems.

Assembly of 17 S. aureus strain genomes and gene calling:

Each of the S. aureus genomes are currently in ~20-30 contigs and need to be assembled into whole genomes for further analysis. We plan to use the assembled whole genomes to identify genetic changes in the clones that may be related to sewage source or to the treatment process itself.

Personnel:

Erin Richard, Aetena Amirsoleimani, Gail Brion

Computational methods:

Read processing, genome assembly

Software:

Fastx_toolkit, Velvet, Maker, Augustus, GeneMarkES, Discovar de novo, Samtools, NCBI BLAST, SNAP

Visualization of S. aureus strain genomes:

Visualization of S. aureus strains will enable comparison of these genomic datasets and identification of areas of homology and difference between them.

Personnel:

Erin Richard, Aetena Amirsoleimani, Gail Brion

Computational methods:

Genome visualization, generate coverage maps, generate heat graphs

Software:

Integrative Genmics Viewer, Bedtools, QIIME, TopHat, Cufflinks

Software availability: All programs should be available for free online