Exploration of Foods and Foodomics

Table 4. Three-tiered adaptive implementation model: investigation stages, methods, and enabling conditions.

Investigation stage	Tier 1: foundational (all settings)	Tier 2: intermediate (moderate-resource)	Tier 3: advanced (high-resource)	Enabling conditions required
Outbreak detection	Passive clinical reporting; basic food inspection	Active sentinel surveillance; food monitoring programs	Integrated molecular surveillance (PulseNet-equivalent); AI-assisted signal detection	T1: Basic lab + reporting. T2: Trained inspectors, national surveillance. T3: Genomic database, IT infrastructure
Pathogen detection	ISO/AOAC culture methods; biochemical confirmation	Culture + PCR/qPCR; ELISA-based rapid assays	WGS (Illumina/Nanopore); metagenomics; proteomics	T1: BSL-2 lab. T2: PCR platform + reagents. T3: Next-gen sequencer, bioinformatics pipeline
Source attribution	Case-control interviews; trace-back of suspect food vehicles	PFGE/MLST typing; trace-forward supply chain mapping	SNP phylogenomics; metagenomics source tracking; GIS-supply chain overlay	T1: Trained epidemiologist. T2: Molecular typing capability. T3: WGS platform + GIS software
Risk assessment	Semi-quantitative risk ranking; HACCP review	Simplified QMRA using published dose-response data	Dynamic QMRA with real-time omics data inputs; stochastic modelling	T1: HACCP competency. T2: QMRA training + software. T3: Biostatistician + MCRA/R integration
Communication & decision	National authority notification; product recall protocol	Multi-agency coordination; stakeholder briefings	Real-time dashboards; GIS risk visualization; AI-assisted decision support	T1: Legal framework. T2: Inter-agency protocols. T3: Data visualization platforms

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AI: artificial intelligence; GIS: geographic information systems; MLST: multilocus sequence typing; PCR: polymerase chain reaction; PFGE: pulsed-field gel electrophoresis; QMRA: quantitative microbial risk assessment; qPCR: quantitative polymerase chain reaction; SNP: single-nucleotide polymorphism; WGS: whole-genome sequencing.

Declarations

Acknowledgments

The authors wish to acknowledge the institutional support of the Indonesian Food and Drug Authority (BPOM) in facilitating this research. No external writing assistance was used. The authors are solely responsible for the content.

Author contributions

AS: Conceptualization, Methodology, Data curation, Writing—original draft, Writing—review & editing, Visualization. WY: Writing—original draft, Writing—review & editing. FUS: Writing—original draft, Writing—review & editing. All authors read and approved the submitted version.

Conflicts of interest

The authors declare that there are no conflicts of interest.

Ethical approval

Not applicable.

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

Not applicable.

Funding

Not applicable.

Copyright

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