Using SNP addresses for Salmonella Typhimurium DT104 in routine veterinary outbreak detection

Area of Science:

• Veterinary epidemiology
• Microbial genomics
• Public health surveillance

Background:

• Single Nucleotide Polymorphism (SNP) addresses, derived from whole-genome sequences (WGSs), are a pathogen typing method.
• Current public health surveillance utilizes SNP addresses for gastrointestinal infections.
• This study explored SNP addresses for Salmonella outbreak detection in veterinary surveillance.

Purpose of the Study:

• To trial the use of SNP addresses in veterinary surveillance for Salmonella outbreak detection.
• To compare temporal and spatio-temporal cluster detection models using SNP addresses versus phage type.
• To evaluate the effectiveness of SNP addresses in early warning systems.

Main Methods:

• Utilized historical datasets of Salmonella cases.
• Compared temporal and spatio-temporal cluster detection models.
• Defined cases by SNP address and by phage type for comparative analysis.
• Analyzed cluster detection timing, size, and characteristics.

Main Results:

• Both temporal and spatio-temporal models effectively detected SNP-based Salmonella clusters.
• Spatio-temporal models consistently detected clusters earlier than temporal models.
• SNP addresses showed spatial and temporal limitations, aiding in differentiating cluster types.
• Spatio-temporal models detected clusters with fewer cases (2-3) compared to phage type models (median 7).

Conclusions:

• SNP addresses are a valuable tool for early detection in veterinary surveillance.
• Spatio-temporal models enhance early outbreak detection capabilities.
• Automation is needed for routine implementation due to the high number of SNP addresses.
• Further research is required on temporal changes and host species impact.