Comparison of the genetic content and arrangement between Salmonella enterica serovars Senftenberg and Infantis

Authors: BRADSHAW II, DAVID - Oak Ridge Institute For Science And Education (ORISE); Anderson, Christopher; Bearson, Bradley - Brad; Bearson, Shawn

Submitted to: Conference Research Workers Disease Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 10/15/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: OBJECTIVE: The prevalence of poultry-associated Salmonella enterica subsp. enterica serovar Infantis (Infantis) has steadily increased since 2017. A concern associated with Infantis is the concurrent rise in the percentage of Infantis isolates carrying a megaplasmid known as pESI (plasmid for Emergent Salmonella Infantis). The genetic content of pESI varies but can encode multiple virulence, metal tolerance, and antimicrobial resistance genes (ARGs) which may lead to increased virulence or multidrug resistance in human infections associated with contaminated food. pESI has recently been identified in other Salmonella serovars including Agona, Muenchen, Schwarzengrund, and Senftenberg. Due to its concurrent increase in prevalence in poultry, this study focused on Senftenberg to determine its pESI carriage rate and the similarity of the genetic content and arrangement of Senftenberg pESI in comparison with Infantis pESI. METHODS: Assemblies of 2,029 Senftenberg genomes from the NCBI Isolates Browser were assessed for pESI carriage by requiring the presence of the pESI-associated repA gene encoding the RepB family plasmid replication initiator along with at least two out of five “core” pESI genes. Because publicly available complete Senftenberg pESI genomes are not available, six Senftenberg isolates predicted to contain (n=3) and lack (n=3) pESI underwent Oxford Nanopore MinIon long read sequencing. Trycycler assembled the reads while polypolish/polca polished the assemblies with publicly available short reads. Complete genomes of the three Senftenberg pESI were compared to the complete genomes of four Infantis pESI using MAUVE alignments in Geneious. RESULTS: Thirty-one Senftenberg isolates from 2019-2023 in the United States were predicted to have pESI, of which 29 isolates were from turkey-associated sources. In 2022, the carriage rate of pESI in turkey-associated Senftenberg isolates was 43%. Long read assembly of the six Senftenberg isolates confirmed the presence of the pESI megaplasmid in the predicted three (+)pESI isolates with sizes ranging from 300-321 kb. The three isolates containing pESI had 4-6 classes of ARGs (aminoglycoside, beta-lactam, phenicol, sulfonamide, tetracycline, and/or antifolate) encoded on the megaplasmid. Comparisons between the three Senftenberg pESI did not identify genetic rearrangements but did reveal regions of insertion/deletions. Of note was a ~18kb region present in two of the Senftenberg pESI isolates that conferred resistance to multiple ARG classes. This region was also present in three of the four complete Infantis pESI references analyzed and had variable insertions/deletions in comparison to the Senftenberg pESI megaplasmids. CONCLUSIONS: Infantis acquisition of pESI may have contributed to the serovar’s enhanced prevalence and outbreak status in poultry over the last decade. With the detection of pESI in Senftenberg, this study provides a preliminary look into the carriage status of pESI in Senftenberg and comparisons of complete Senftenberg pESI genomes to one another and to Infantis pESI genomes. While pESI from the analyzed Senftenberg and Infantis isolates were generally similar in terms of genetic content, regions of insertions and deletions both within the Senftenberg serovar and between serovars were observed that led to a loss or gain of ARG classes.