ArticleBMC infectious diseases2020
Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream.
Article in BMC infectious diseases, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 55 citations in OpenAlex.
- Breaking the culture habit: Complementing culture-based veterinary diagnostics with metagenomic data -A case study of feline and canine skin infections.BMC veterinary research · 2026Article
- Food-borne bacterial pathogens: emerging approaches in detection and prevention.Archives of microbiology · 2026Review
- Application of MSB selective enrichment followed by amplicon MinION sequencing for multipathogen detection in smoked salmon.NPJ science of food · 2025Article
- Early detection and population dynamics ofFrontiers in microbiology · 2025Article
- A metagenomics-based workflow for the detection and genomic characterization of GBS in raw freshwater fish.Microbiology spectrum · 2024Article
- Review
- Paired metagenomic and chemical evaluation of aflatoxin-contaminated dog kibble.Frontiers in veterinary science · 2024Article
- Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach.BMC genomics · 2023Article
- Article
- Tunable Magneto-Plasmonic Nanosensor for Sensitive Detection of Foodborne Pathogens.Biosensors · 2023Article
- Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producingFrontiers in microbiology · 2023Article
- bettercallsal: better calling ofFrontiers in microbiology · 2023Article
- Application of MinION sequencing as a tool for the rapid detection and characterization ofFrontiers in microbiology · 2022Article
- The Saprophytic Lifestyle ofFrontiers in microbiology · 2022Review
- Surveillance of Listeria monocytogenes: Early Detection, Population Dynamics, and Quasimetagenomic Sequencing during Selective Enrichment.Applied and environmental microbiology · 2021Article
- Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads.BMC genomics · 2021Article
- Article
- Big Data Impacting Dynamic Food Safety Risk Management in the Food Chain.Frontiers in microbiology · 2021Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe more quickly bacterial pathogens responsible for foodborne illness outbreaks can be linked to a vehicle of transmission or a source, the more illnesses can be prevented. Whole genome sequencing (WGS) based approaches to source tracking have greatly increased the speed and resolution with which public health response can pinpoint the vehicle and source of outbreaks. Traditionally, WGS approaches have focused on the culture of an individual isolate before proceeding to DNA extraction and sequencing. For Listeria monocytogenes (Lm), generation of an individual isolate for sequencing typically takes about 6 days. Here we demonstrate that a hybrid, "quasimetagenomic" approach ie; direct sequencing of microbiological enrichments (first step in pathogen detection and recovery) can provide high resolution source tracking sequence data, 5 days earlier than response that focuses on culture and sequencing of an individual isolate. This expedited approach could save lives, prevent illnesses and potentially minimize unnecessary destruction of food.
methodsNaturally contaminated ice cream (from a 2015 outbreak) was enriched to recover Listeria monocytogenes following protocols outlined in the Bacteriological Analytic Manual (BAM). DNA from enriching microbiota was extracted and sequenced at incremental time-points during the first 48 h of pre-enrichment using the Illumina MiSeq platform (2 by 250), to evaluate genomic coverage of target pathogen, Listeria monocytogenes.
resultsQuasimetagenomic sequence data acquired from hour 20 were sufficient to discern whether or not Lm strain/s were part of the ongoing outbreak or not. Genomic data from hours 24, 28, 32, 36, 40, 44, and 48 of pre-enrichments all provided identical phylogenetic source tracking utility to the WGS of individual isolates (which require an additional 5 days to culture).
conclusionsThe speed of this approach (more than twice as fast as current methods) has the potential to reduce the number of illnesses associated with any given outbreak by as many as 75% percent of total cases and potentially with continued optimization of the entire chain of response, contribute to minimized food waste.
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