Purpose: The purpose of this study was to characterize by whole genome sequencing the genetic diversity of Salmonella present in irrigation canals in Chile and to identify factors related with the presence of Salmonella.
Methods: A total of 34 isolates of Salmonella were selected for whole genome sequencing with the MiSeq platform (Illumina). These isolates represent 18 different serovars isolated from irrigation canals in the Metropolitan Region, Chile. We characterized the MLST type, the presence of plasmids, prophages, and antimicrobial resistance genes. Spatial analysis was conducted in R to identify variables associated with the presence of Salmonella in the canals.
Results: We found a considerable genetic diversity in the sequenced Salmonella. Diversity was represented by 14 distinct MLST types. Our study sequenced for the first time Salmonella representing serovars Santiago, Corvallis, and Edinburg; which represented newly reported MLST types. We found 8 plasmid incompatibility types, including a 3kb plasmid carrying qnrB19, gene that encode quinolone resistance in isolates of serovars Braenderup, Heidelberg, Mbandaka, and Seftenberg. Identification of prophage content showed isolates of serovar Typhimurium containing up to 5 prophages, versus serovar Corvallis containing none. A mixed model regression analysis found an association on Salmonella presence and climate.
Significance: Our study indicates the importance of understanding the genetic and spatial diversity of Salmonella present in irrigation canals. Presence of closely related plasmids in different serovars might indicate transferable characteristics of this small plasmid.