Details:

Alternative Title:
Emerg Infect Dis
Personal Author:
Zhang, Shaokang ; Li, Shaoting ; Gu, Weidong ; den Bakker, Henk ; Boxrud, Dave ; ... More +
Zhang, Shaokang ; Li, Shaoting ; Gu, Weidong ; den Bakker, Henk ; Boxrud, Dave ; Taylor, Angie ; Roe, Chandler ; Driebe, Elizabeth ; Engelthaler, David M. ; Allard, Marc ; Brown, Eric ; McDermott, Patrick ; Zhao, Shaohua ; Bruce, Beau B. ; Trees, Eija ; Fields, Patricia I. ; Deng, Xiangyu Less -
Description:
Increasingly, routine surveillance and monitoring of foodborne pathogens using whole-genome sequencing is creating opportunities to study foodborne illness epidemiology beyond routine outbreak investigations and case-control studies. Using a global phylogeny of Salmonella enterica serotype Typhimurium, we found that major livestock sources of the pathogen in the United States can be predicted through whole-genome sequencing data. Relatively steady rates of sequence divergence in livestock lineages enabled the inference of their recent origins. Elevated accumulation of lineage-specific pseudogenes after divergence from generalist populations and possible metabolic acclimation in a representative swine isolate indicates possible emergence of host adaptation. We developed and retrospectively applied a machine learning Random Forest classifier for genomic source prediction of Salmonella Typhimurium that correctly attributed 7 of 8 major zoonotic outbreaks in the United States during 1998-2013. We further identified 50 key genetic features that were sufficient for robust livestock source prediction.
Subjects:
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Animals Case-Control Studies Disease Outbreaks Epidemiological Monitoring Foodborne Diseases Genomics Humans Livestock Phylogeny Research Retrospective Studies Salmonella Infections Salmonella Typhimurium Whole Genome Sequencing Zoonoses
Source:
Emerg Infect Dis. 25(1):82-91
Pubmed ID:
30561314
Pubmed Central ID:
PMC6302586
Document Type:
Journal Article
Place as Subject:
United States
Collection(s):
Emerging Infectious Diseases
Main Document Checksum:
[+]
urn:sha256:f41d9f8d06835b4b6570370f21adc4b9865e90b15ec1a8a6e1007ce88e93368e
Download URL:
https://stacks.cdc.gov/view/cdc/75848/cdc_75848_DS1.pdf
File Type:

Supporting Files

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