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Adam Allred

3:30-3:50 p.m., Tuesday
, PhD
Staff Scientist, Bioinformatics
Animal Health and Food Safety
Thermo Fisher Scientific
2130 Woodward St.
Austin, TX 78744

From bacterial genomes to specific assay targets: A k-mer-based approach

Adam Allred1, Xianghe Yan2, Robert Tebbs1, Gian Marco Baranzoni2, Chobi DebRoy3, Pina Fratamico2

The design of robust genomic assays for detection of microbial pathogens using technologies such as TaqMan® or Ion AmpliSeq™ requires the identification of target sequences that are specific to the microbe(s) of interest. We developed a bioinformatics tool called Jigsaw for identifying highly specific target sequences from whole genomes and other sequences. Jigsaw achieves this by chopping up input genomes into short strings of nucleotides called ‘k-mers.’

We applied Jigsaw independently to two sets of data: (1) A set of 765 Salmonella genomes in order to identify signature sequences for Salmonella servoar Agona and (2) A set of over 170 E. coli O-antigen gene clusters in order to identify signature sequences that would uniquely identify E. coli subtypes. Jigsaw successfully identified signatures for Salmonella Agona and for the vast majority of the O-antigen gene clusters. These results highlight the utility of a k-mer-based approach for capitalizing on large genomic datasets and have implications for increasing the efficiency of assay design for outbreak detection and pathogen-specific surveillance.

1Thermo Fisher Scientific, Austin, TX

2United States Department of Agriculture, Wyndmoor, PA

3The Pennsylvania State University, University Park, PA