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Title: Genomes of Salmonella with diverse patterns of antibiotic resistance (AR) revealed the dynamics of AR gene organization and detected resistance gene families found in Salmonella

Author
item Frye, Jonathan
item DESAI, P - University Of California
item PORWOLLIK, S - University Of California
item LONG, F - University Of California
item CHENG, P - University Of California
item CHU, W - University Of California
item WEINSTOCK, G - Washington University School Of Medicine
item Guard, Jean
item Hiott, Lari
item Barrett, John
item Humayoun, Shaheen
item Williams, Laura
item Jackson, Charlene
item MCCLELLAND, M - University Of California

Submitted to: American Society for Microbiology Conference
Publication Type: Abstract Only
Publication Acceptance Date: 8/26/2014
Publication Date: 10/5/2013
Citation: Frye, J.G., Desai, P.T., Porwollik, S., Long, F., Cheng, P., Chu, W., Weinstock, G.M., Guard, J.Y., Hiott, L.M., Barrett, J.B., Humayoun, S.B., Williams, L.E., Jackson, C.R., Mcclelland, M. 2013. Genomes of Salmonella with diverse patterns of antibiotic resistance (AR) revealed the dynamics of AR gene organization and detected resistance gene families found in Salmonella. American Society for Microbiology Conference. October 5-9, 2013. Boston, Massachusetts.

Interpretive Summary:

Technical Abstract: We produced and assembled high quality draft genomes (~100X coverage) for 305 Salmonella from a diverse a group of over 100 serovars and diverse sources. Of these isolates, 119 were selected to capture a wide variety of different AR patterns. In our subsequent analyses we included 285 additional publicly available genomes, for a total of 590 annotated genomes. In total, 247 families of AR genes were identified by applying OrthoMCL to 7828 manually curated protein sequences in the Antibiotic genes database (ARDB) and resistance genes in GenBank. We observed 40 exogenous resistance gene families in Salmonella. Homologs of these 40 families were found in a total of 298 other species in GenBank. Comparison of the gene trees of these 40 families and the 16S RNA gene tree revealed the details of the extensive horizontal gene transfer within Salmonella and with other species. At least twenty endogenous genes, present in all or almost all strains of Salmonella, can confer AR when mutated or over-expressed. Examples include gyrase, some components of the ribosome, and parts of multi-drug efflux systems. Ongoing studies will identify the mutations in endogenous genes that result in AR. In summary, high-throughput genomics allows a better understanding of AR gene organization and flow in Salmonella. Ultimately, knowing the sequences of the AR genes present in Salmonella will assist in the development of rapid methods to determine AR profiles for immediate selection of appropriate antibiotics, and may help identify targets for mitigating or slowing the spread of resistance.