Catherine D. Carrillo

This study compares the limit of detection of Salmonella ser. Enteritidis using culture-based and culture-independent methods, finding comparable LOD50 for qPCR and shotgun sequencing, but false positives in unspiked samples and lower LOD50 in feed than caecal contents.

The paper develops a bioinformatic pipeline to detect Salmonella in metagenomic datasets with high sensitivity and specificity by optimizing software parameters and database choices.

The paper develops a multi-locus typing scheme for a plasmid mediating flagella transfer in Salmonella, identifies its homologs in 154 genomes, and demonstrates its utility in tracking plasmid lineages.