Healthy carriage of Salmonella within cattle lymph nodes is a key source of ground beef contamination with strains of clinical significance

This study assessed the genetic relatedness, evolutionary dynamics, and virulence profile of Salmonella isolated from lymph nodes and ground beef from apparently healthy cattle over two years. For this purpose, we used a set of isolates of nine different serovars: Anatum (n=23), Reading (n=22), Typhimurium (n=10), London (n=9), Kentucky (n=6), Fresno (n=4), Give, Muenster, and monophasic 1,4,[5],12:i- (n=1 each). These isolates were subjected to whole genome sequencing, and assembled and annotated genomes were used for downstream bioinformatic analyses. Although lymph nodes and ground beef were collected and analyzed separately, we still observed clonality between isolates from both sources. This finding suggests that some Salmonella circulating in the gut may reach the lymphatic system, creating a dual reservoir for ground beef contamination. We also found evidence of Salmonella persistence across cattle cohorts, as we observed clonality between isolates collected in different years. Variation in the virulence and pathogenicity island profiles was limited, with minor differences that could not be associated with attenuated virulence in the bovine host. Conversely, isolates of all serovars, except Fresno, were genetically close to strains involved in human salmonellosis in different countries, highlighting the risk to public health posed by strains associated with the carrier state in cattle. Further research is needed to reveal the mechanisms by which Salmonella causes subclinical infections in cattle and persists for long periods within farm environments.