Genetic analysis of persistent Salmonella Infantis strains in Austrian broiler farms

Salmonella (S.) Infantis is the fourth most common human serovar and strictly associated with broiler chickens. Over the last few years, an increased antimicrobial resistance has been observed in this serovar, which is associated with the presence of the so-called pESI plasmid (plasmid of Emerging S. Infantis). This study focused on selected field isolates derived from 3 Austrian broiler farms that were examined for their antimicrobial resistance (AMR) by microdilution assay and their genetic background including the presence of pESI-like plasmid using Illumina sequencing followed by multi-locus sequence typing (MLST). A total of 25 Salmonella isolates from 3 broiler farms and four human isolates which were provided by the National Reference Center for Salmonella (AGES) in Graz (Austria) were used in this study. The majority of isolates were identified as S. Infantis, with the exception of two that were specified as S. Thompson (one isolate from farm 2) and S. Typhimurium (one human isolate). Illumina sequencing results were compared to AMR results for each isolate. The majority of S. Infantis isolates that were multidrug-resistant (MDR) or extensively drug-resistant (XDR) harboured the pESI-like plasmid. The exception was a MDR isolate from farm 2 that did not carry the pESI-like plasmid. In a phylogenetic tree inferred from core genome MLST allelic profiles, MDR and XDR isolates with pESI-like plasmid formed three monophyletic clades. Each clade was represented either with isolates from a single farm or human isolates. The three S. Infantis isolates lacking the pESI-like plasmid formed a separate cluster together regardless on their AMR profile. S. Thompson and S. Typhimurium did not carry the pESI-like plasmid, showed no or limited antimicrobial resistance, and were shown to be distantly related to S. Infantis isolates in the phylogenetic tree. Using conventional MLST all S. Infantis isolates from farms 1 and 3 were assigned to sequence type (ST) 32 and clonal complex (CC) 31, suggesting their close relatedness. In farm 2, on the other hand, the two S. Infantis isolates lacking the pESI-like plasmid were assigned to ST 32 (CC 31) as well, whereas the remaining S. Infantis isolates carrying the pESI-like plasmid belonged to ST 2283 (CC 31). In conclusion, this study demonstrates that the pESI-like plasmid is largely responsible for the MDR classification of S. Infantis isolates. Furthermore, we were able to document the persistence of pESI-like-carrying S. Infantis genotypes over several years in three Austrian broiler farms.