GENOMIC ANALYSIS TO UNDERSTAND NON-TYPHOIDAL SALMONELLA CARRIAGE: SALMONELLA AGONA – THE BUG THAT WON'T GO AWAY

Abstract

Intro: Salmonella Agona is a non-typhoidal Salmonella known for biofilm production and persistence in the environment and dry food products. S. Agona has been associated with multiple outbreaks and is associated with shedding in pigs, sheep and gulls but little is known about potential carriage in humans or whether large-scale genomic rearrangements play a role in persistent infections. Methods: A review of 2,233 S. Agona isolates from infections in England and associated carriage was undertaken from 2004-2020 in which 1,155 had short read sequencing data available. A representative set of 221 isolates of varying carriage status (Acute, n=77, Convalescent carrier, n=86, Temporary carrier, n=36 and chronic carrier, n = 22) were selected for long read sequencing on the Oxford Nanopore MinION, and genomic arrangement analysis using Socru. The sequence data were also interrogated for AMR determinants, plasmid presence and phylogenetic relationships. Findings: Carriage of S. Agona was present in 6.5% of isolates received at UKHSA (n=144/2,233). Investigation into genome structures of S. Agona revealed both the conserved arrangement GS1.0 and GS25.113, an imbalanced rearrangement where the origin and terminus were much closer together than in GS1.0, producing one very short and one very long replicore. All isolates harboured genotypic resistance to at least 1 antimicrobial class, and many were deemed multi-drug resistant (genotypic resistance to at least 3 classes) with Incl1, IncX1 and colRNAI plasmids most commonly found in the most multi-drug resistant isolates. Phylogenetic analysis indicated that isolates associated with carriage were distributed across the phylogeny intermixed with isolates that caused acute infection. Conclusion: This study reveals that human carriage of S. Agona occurs over a range of timeframes and that the levels of AMR detected across the collection are of concern for treatment of persistent infection. We also identified an unusual genome arrangement using long read sequencing which is undergoing further investigation.