Salmonella enterica subsp. enterica serovar Typhimurium Raw sequence reads. Salmonella enterica subsp. enterica serovar Typhimurium

The number of sporadic salmonellosis cases attributable to outbreak sources is usually unknown. We used multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS) to reveal the likely number of sporadic isolates related to an outbreak source. Using the predominant MLVA pattern of isolates linked to the source, we categorized 1655 clinical Salmonella Typhimurium Phage type 9 isolates from 2009-2015 into MLVA categories according to similarity to that pattern. We randomly sequenced isolates from each MLVA category and projected the number of historic isolates likely to be related to the outbreak source. MLVA group and genotype was moderately correlated (Cramer’s V 0.49). WGS demonstrated that sporadic salmonellosis attributable to the outbreak source significantly outnumbered cases identified in outbreak investigation. We project up to 30% (400/1585) of sporadic isolates may be attributable to the outbreak source, highlighting the value of genomics and the need for boosting trace back and intervention