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Abstract
With the increasing application of high-throughput sequencing technologies, there have been growing interest in studying food and food-related microbiomes. In particular, metagenomics of food holds potential in detection and subtyping of foodborne pathogens and comprehensive microbiome profiling of food samples.
In this study, a targeted metagenomics approach was developed for isolation-independent detection and subtyping of foodborne bacterial pathogens in a single workflow. Immunomagnetic separation (IMS) and multiple displacement amplification (MDA) were combined for selective concentration of Salmonella genomic DNA from chicken breasts and shotgun metagenomics was used to sequence the Salmonella-targeted IMS-MDA product. Termed as quasimetagenomics, this approach was shown to be effective in shortening culture enrichment while allowing accurate in silico serotyping and high-fidelity single nucleotide polymorphism (SNP) typing of the pathogen. This approach was further evaluated and successfully applied to other selected food samples including iceberg lettuce, black peppercorns, and romaine lettuce. Rapid detection and subtyping of Salmonella was achieved using nanopore MinION sequencing. Simultaneous detection and subtyping of Salmonella and Escherichia coli O157:H7 from spiked romaine lettuce were successfully achieved using individual IMS-MDA treatment and quasimetagenimic sequencing.
Full metagenomics characterization was then performed by conducting a longitudinal and cross-sectional survey on multiple retail chicken breast products varying in packaging types, processing establishments, antibiotics usage and seasonality. Chicken microbiomes were sequenced and analyzed using shotgun metagenomics. The chicken microbiomes displayed longitudinal consistency over time and cross-sectional distinctiveness associated with processing environments. Packaging type and processing environment significantly influenced composition and diversity of the microbiomes, while antibiotic usage and seasonality showed no significant impact. Low abundances of antimicrobial resistance genes were found on chicken breasts; however, no significant resistome difference was observed between antibiotic free and conventional products. Benchmarked by culture enrichment, shotgun metagenomic sequencing delivered high sensitivity (0.75) and specificity (0.93) for Salmonella detection from chicken breasts.
The application of food metagenomics in detection and subtyping of foodborne pathogens and microbiome profiling can be expanded to other food commodities and may provide further insights into microbiome analysis of food.
In this study, a targeted metagenomics approach was developed for isolation-independent detection and subtyping of foodborne bacterial pathogens in a single workflow. Immunomagnetic separation (IMS) and multiple displacement amplification (MDA) were combined for selective concentration of Salmonella genomic DNA from chicken breasts and shotgun metagenomics was used to sequence the Salmonella-targeted IMS-MDA product. Termed as quasimetagenomics, this approach was shown to be effective in shortening culture enrichment while allowing accurate in silico serotyping and high-fidelity single nucleotide polymorphism (SNP) typing of the pathogen. This approach was further evaluated and successfully applied to other selected food samples including iceberg lettuce, black peppercorns, and romaine lettuce. Rapid detection and subtyping of Salmonella was achieved using nanopore MinION sequencing. Simultaneous detection and subtyping of Salmonella and Escherichia coli O157:H7 from spiked romaine lettuce were successfully achieved using individual IMS-MDA treatment and quasimetagenimic sequencing.
Full metagenomics characterization was then performed by conducting a longitudinal and cross-sectional survey on multiple retail chicken breast products varying in packaging types, processing establishments, antibiotics usage and seasonality. Chicken microbiomes were sequenced and analyzed using shotgun metagenomics. The chicken microbiomes displayed longitudinal consistency over time and cross-sectional distinctiveness associated with processing environments. Packaging type and processing environment significantly influenced composition and diversity of the microbiomes, while antibiotic usage and seasonality showed no significant impact. Low abundances of antimicrobial resistance genes were found on chicken breasts; however, no significant resistome difference was observed between antibiotic free and conventional products. Benchmarked by culture enrichment, shotgun metagenomic sequencing delivered high sensitivity (0.75) and specificity (0.93) for Salmonella detection from chicken breasts.
The application of food metagenomics in detection and subtyping of foodborne pathogens and microbiome profiling can be expanded to other food commodities and may provide further insights into microbiome analysis of food.