Using SNP addresses for <i>Salmonella Typhimurium</i> DT104 in routine veterinary outbreak detection.

ABSTRACT: SNP addresses are a pathogen typing method based on whole-genome sequences (WGSs), assigning groups at seven different levels of genetic similarity. Public health surveillance uses it for several gastro-intestinal infections; this work trialled its use in veterinary surveillance for salmonella outbreak detection. Comparisons were made between temporal and spatio-temporal cluster detection models that either defined cases by their SNP address or by phage type, using historical data sets. Clusters of SNP incidents were effectively detected by both methods, but spatio-temporal models consistently detected these clusters earlier than the corresponding temporal models. Unlike phage type, SNP addresses appeared spatially and temporally limited, which facilitated the differentiation of novel, sta

SUBMITTER: Bettridge JM 

PROVIDER: S-EPMC10644063 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature