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Application of Whole‐Genome Sequences and Machine Learning in Source Attribution of Salmonella Typhimurium
Author(s) -
Munck Nanna,
Njage Patrick Murigu Kamau,
Leekitcharoenphon Pimlapas,
Litrup Eva,
Hald Tine
Publication year - 2020
Publication title -
risk analysis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.972
H-Index - 130
eISSN - 1539-6924
pISSN - 0272-4332
DOI - 10.1111/risa.13510
Subject(s) - salmonella , danish , biology , logistic regression , attribution , random forest , artificial intelligence , machine learning , veterinary medicine , computer science , bacteria , genetics , medicine , psychology , social psychology , linguistics , philosophy
Prevention of the emergence and spread of foodborne diseases is an important prerequisite for the improvement of public health. Source attribution models link sporadic human cases of a specific illness to food sources and animal reservoirs. With the next generation sequencing technology, it is possible to develop novel source attribution models. We investigated the potential of machine learning to predict the animal reservoir from which a bacterial strain isolated from a human salmonellosis case originated based on whole‐genome sequencing. Machine learning methods recognize patterns in large and complex data sets and use this knowledge to build models. The model learns patterns associated with genetic variations in bacteria isolated from the different animal reservoirs. We selected different machine learning algorithms to predict sources of human salmonellosis cases and trained the model with Danish Salmonella Typhimurium isolates sampled from broilers ( n = 34), cattle ( n = 2), ducks ( n = 11), layers ( n = 4), and pigs ( n = 159). Using cgMLST as input features, the model yielded an average accuracy of 0.783 (95% CI: 0.77–0.80) in the source prediction for the random forest and 0.933 (95% CI: 0.92–0.94) for the logit boost algorithm. Logit boost algorithm was most accurate (valid accuracy: 92%, CI: 0.8706–0.9579) and predicted the origin of 81% of the domestic sporadic human salmonellosis cases. The most important source was Danish produced pigs (53%) followed by imported pigs (16%), imported broilers (6%), imported ducks (2%), Danish produced layers (2%), Danish produced cattle and imported cattle (<1%) while 18% was not predicted. Machine learning has potential for improving source attribution modeling based on sequence data. Results of such models can inform risk managers to identify and prioritize food safety interventions.