Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges

Carleton, Heather; Besser, John M.; Williams-Newkirk, Amanda Jo; Huang, Aiping; Trees, Eija; Gerner‐Smidt, Peter

doi:10.1089/fpd.2019.2636

Cited by 30 publications

(17 citation statements)

References 33 publications

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“…However, the error rate of Oxford Nanopore Technologies is still relatively high and might impact the level of details obtained in the analysis, as observed by Hyeon et al [ 14 ]. Another important drawback for the implementation of metagenomics in routine is the need for adapted bioinformatics pipelines [ 60 ]. This has been improving in the last years with the development of new specialized tools that can be proposed in workflows such as the one presented in this study.…”

Section: Discussionmentioning

confidence: 99%

A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine

et al. 2020

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The management of a foodborne outbreak depends on the rapid and accurate identification of the responsible food source. Conventional methods based on isolation of the pathogen from the food matrix and target-specific real-time polymerase chain reactions (qPCRs) are used in routine. In recent years, the use of whole genome sequencing (WGS) of bacterial isolates has proven its value to collect relevant information for strain characterization as well as tracing the origin of the contamination by linking the food isolate with the patient’s isolate with high resolution. However, the isolation of a bacterial pathogen from food matrices is often time-consuming and not always successful. Therefore, we aimed to improve outbreak investigation by developing a method that can be implemented in reference laboratories to characterize the pathogen in the food vehicle without its prior isolation and link it back to human cases. We tested and validated a shotgun metagenomics approach by spiking food pathogens in specific food matrices using the Shiga toxin-producing Escherichia coli (STEC) as a case study. Different DNA extraction kits and enrichment procedures were investigated to obtain the most practical workflow. We demonstrated the feasibility of shotgun metagenomics to obtain the same information as in ISO/TS 13136:2012 and WGS of the isolate in parallel by inferring the genome of the contaminant and characterizing it in a shorter timeframe. This was achieved in food samples containing different E. coli strains, including a combination of different STEC strains. For the first time, we also managed to link individual strains from a food product to isolates from human cases, demonstrating the power of shotgun metagenomics for rapid outbreak investigation and source tracking.

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Section: Discussionmentioning

confidence: 99%

A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine

et al. 2020

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“…The unknown regions surrounding these AMR genes can thus be characterized, as previously performed for unknown and unauthorized GM plants [25][26][27][28][29] . For metagenomics, even if no prior knowledge is required similarly to WGS, this promising approach is still currently in its infancy mainly due to the following bottlenecks that are challenging its implementation 26, [41][42][43][44][45][46] . Indeed, the low abundance of DNA of interest present in the total DNA extract, as frequently encountered with GMO contamination, complicated its identification.…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, metagenomics requires significant development at both wet-and dry-lab levels as well as important computational capacities for such type of complex bioinformatics analysis. However, all these limitations are expected to be overcome in the near future as successfully illustrated by pioneer studies in other problematics, including foodborne pathogen detection [41][42][43][44][45][46] .…”

Section: Resultsmentioning

confidence: 99%

Identification of an unauthorized genetically modified bacteria in food enzyme through whole-genome sequencing

Fraiture

Bogaerts

Winand

et al. 2020

Sci Rep

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Recently, the unexpected presence of a viable unauthorized genetically modified bacterium in a commercialized food enzyme (protease) product originating from a microbial fermentation process has been notified at the European level (RASFF 2019.3332). This finding was made possible thanks to the use of the next-generation sequencing technology, as reported in this study. Whole-genome sequencing was used to characterize the genetic modification comprising a sequence from the pUB110 shuttle vector (GenBank: M19465.1), harbouring antimicrobial resistance genes conferring a resistance to kanamycine, neomycin and bleomycin, flanked on each side by a sequence coding for a protease (GenBank: WP_032874795.1). In addition, based on these data, two real-time PCR methods, that can be used by enforcement laboratories, specific to this unauthorized genetically modified bacterium were developed and validated. The present study emphasizes the key role that whole-genome sequencing can take for detection of unknown and unauthorized genetically modified microorganisms in commercialized microbial fermentation products intended for the food and feed chain. Moreover, current issues encountered by the Competent Authorities and enforcement laboratories with such unexpected contaminations and the importance of performing official controls were highlighted. In the food and feed industry, enzymes, additives and flavourings are frequently produced through fermentation processes involving genetically modified microorganisms (GMM) harbouring antimicrobial resistance (AMR) genes as selection markers 1-10. Even though viable GMM, or associated recombinant DNA, should be absent in the commercialized microbial fermentation products 11-14 , such accidental contaminations on the European (EU) market have already been reported in

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“…Before 2020, reflex culture of specimens positive for Campylobacter , Salmonella , Shigella , and Yersinia increased in FoodNet sites, augmented by CDC funding. Until metagenomic CIDTs are developed, culture is necessary to identify pathogen subtypes, antimicrobial resistance patterns, and whole-genome sequences ( 4 ). Fewer cultures decrease the ability to detect and investigate outbreaks and sporadic cases of emerging pathogens, which relies on sequencing.…”

Section: Discussionmentioning

confidence: 99%

Decreased Incidence of Infections Caused by Pathogens Transmitted Commonly Through Food During the COVID-19 Pandemic — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2017–2020

Ray¹,

Collins²,

Griffin³

et al. 2021

MMWR Morb. Mortal. Wkly. Rep.

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Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges

Cited by 30 publications

References 33 publications

A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine

A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine

Identification of an unauthorized genetically modified bacteria in food enzyme through whole-genome sequencing

Decreased Incidence of Infections Caused by Pathogens Transmitted Commonly Through Food During the COVID-19 Pandemic — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2017–2020

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