Multi-provincial Salmonellosis Outbreak Related to Newly Hatched Chicks and Poults: A Genomics Perspective

Conclusions This was the first outbreak in Canada to provide direct evidence of how genome sequencing can perform source attribution and provide improved data for targeted outbreak investigations salmonellosis. This multi-discipline, multi-jurisdictional, and collaborative investigation also highlighted the importance of timely integrated surveillance based on the farm-to-fork continuum and a One Health concept. While this outbreak investigation was completed without genome sequence analysis, SNV-based clustering was effective for source-tracking of SE during an outbreak associated with exposure to live chicks and poults, while also identifying potentially related clinical isolates that were not epidemiologically investigated. Additionally, other clusters were identified that contained either multi-provincial SE isolates, or clinical isolates with agricultural isolates, illustrating the ability of genome sequencing to provide more information than PT or PFGE for epidemiological investigation. Genome sequencing in provincial public health laboratories on a routine basis has the potential for significant savings to the health care system, agricultural/food industries, and to the Canadian economy. Given the challenges and limitations of conventional typing methods such as PFGE and phagetyping, and the worldwide success and resolution genome sequence analysis, PulseNet Canada will be ceasing phagetyping and PFGE and is moving towards genome sequencing as the gold standard for sur...
Source: PLOS Currents Outbreaks - Category: Epidemiology Authors: Source Type: research