What is FORC DB?

Food-borne illness is any types of illness resulting from the consumption of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food, as well as chemical or natural toxins. One of the main causes of food-borne illness is pathogenic bacteria (pathogens) such as Salmonella, Vibrio, Bacillus and Staphylococcus. In the United States, using FoodNet data from 2000–2007, the CDCP(Centers for Disease Control and Prevention) estimated there were 47.8 million foodborne illnesses per year (16,000 cases for 100,000 inhabitants) with 9.4 million of these caused by 31 known identified pathogens. In Korea, 141 cases (40.4%) are reported for foodborne illness caused by pathogenic bacteria in 2014.

Virulence factors are molecules produced by pathogens that contribute to the pathogenicity of the organism and enable them to achieve the following: (ⅰ) colonization of a niche in the host (ⅱ) immunoevasion, evasion of the host's immune response (ⅲ) immunosuppression, inhibition of the host's immune response (ⅳ) entry into and exit out of cells (ⅴ) obtain nutrition from the host. Pathogens commonly induce several symptoms related to food-borne illness by the virulence factors they produce. These products are encoded by specific genes and expressed in the form of transcript. Therefore, the investigation of food-borne pathogen omics data including genome, transcriptome, and metagenome can provide the information for the mechanisms of food-borne illness occurrences and will be crucial to the food-borne illness researches.

FORCDB is a freely available database of omics data produced by NGS sequencing. Genomic data have been produced by sequencing pathogens which were retrieved from the outbreak of food-borne illness. Transcriptomic data have been produced by sequencing pathogens which were exposed to different food sources. Food sources known to be major sources of food-borne illness have been sequenced and stored as metagenomic data. All these types of data can be accessed and retrieved by user-friendly interface in FORCDB. Additionally, FORCDB allows users to search virulence factors or drug resistance by keywords, genomes or sequences. In the results of search, users can easily check the information for gene producing the virulence factor as well as related KEGG pathways and horizontal gene transfer (HGT) events. Especially, sequence search provides the result of prediction using the Hidden Markov model constructed by virulence factor/drug resistance sequence database.

Data processing

Omics Data Production
Omics data production
Construction of VF/DR Prediction Model and Connection with HGTree
Construction of VF/DR prediction model and connection with HGTree

Summary statistics of FORCDB

Omics Data
Type of dataNumber of casesNumber of samples
Genome 33 33
Transcriptome 11 13
Metagenome 9 128
Virulence Factor Genes
SourceNumberUsed in HMM
Newly sequenced 1,274 638
Pubmed 15,335 34
Patric DB 1,573 1,333
VFDB 2,447
Victors 4,994
Drug Resistance Genes
SourceNumberUsed in HMM
Pubmed 30,912 29
ARDB 7,825 154
CARD 1,841

References

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