Salmonella Detection and Characterization

A second 10 g aliquot from each package of meat was sterilely inoculated into 90 mL of buffered peptone water (BPW; Becton Dickinson) and incubated overnight at 37 °C. We transferred a 100 µL aliquot of the meat/BPW homogenate to 10 mL of Rappaport-Vassilidis R10 (RV; Becton Dickinson) broth that was then incubated overnight at 42 °C. RV broth was subsequently inoculated onto xylose-lysine-Tergitol 4 agar (XLT-4; Becton Dickinson) for the differentiation of Salmonella suspect isolates. Characteristic black colonies on XLT-4 agar were tested for lactose fermentation on MacConkey agar and agglutination with polyvalent antisera O. Lactose negative, agglutinating isolates were speciated using MALDI-TOF, and confirmed Salmonella underwent whole genome sequencing (MiSeq, Illumina, San Diego, CA). Reads were assembled using the SPades assembler version 3.9 and post-processed with MisMatch corrector available online from the Center of Genomic Epidemiology (CGE)^{52 (link)}. We confirmed Salmonella genus and species, identified Salmonella serotype, and determined acquired antimicrobial resistance genotype using the KmerFinder, SeqSero, and ResFinder online databases available at CGE^{53 (link)–55 (link)}.