Characterization of prophages in Salmonella Typhimurium definitive type 8

Abstract

Background Salmonella Typhimurium DT8 has been associated with human outbreaks. Anderson phage typing scheme has been used for more than four decades for subtyping of Salmonella Typhimurium, but it has shown some limitations. Here, we characterize prophages among Salmonella Typhimurium DT8 strains to test the potential use of prophage sequence profiles for subtyping. Method A total of 54 isolates of Salmonella Typhimurium DT8 were selected for this study which was part of an outbreak study by Ashton et al. (2015)*. Twenty-six isolates were associated with an outbreak in the States of Jersey in 2013 and 28 isolates were non-outbreak-associated isolates. Comparative genomics using a range of bioinformatic tools was carried out including SPAdes for de novo assembly of WGS data. PHASTER was used for characterisation of prophages (http://phaster.ca/). Result All DT8 strains are lysogenic for three prophages (RE-2010, ST64B and Gifsy-2). Moreover, the three prophages showed identical sequence among outbreak and non-outbreak isolates. Interestingly, prophage SSU5 was detected in one non-outbreak isolate. Prophage SSU5 is closely related to cryptic plasmid pHMC2 that infects only rough strains of Salmonella Typhimurium. This study is the first to report the presence of prophage SSU5 in Salmonella Typhimurium DT8. Conclusion It is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation of Salmonella Typhimurium. Prophage profiling might be unsuitable subtyping method. The emerging genetic analysis should be combined with the conventional method for epidemiological surveillance until WGS-based analysis can be improved and standardized. *https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336196/