Microbial Source Tracking
The food and beverage industry is intimately tied to one or more biological processes which may be susceptible to microbial contamination. The resulting downtime and recalls can be costly and is often a recurring event. The source of the contamination often remains elusive, preventing timely and effective preemptive strategies from being implemented.
To facilitate the timely implementation of effective counterstrategies, DNASense offers a state-of-the-art source contamination tracking service. Forward us your contaminant and isolates (e.g., isolates on agar-plates) and let us resolve their relatedness. It is a complete sample-to-answer workflow involving cutting-edge whole-genome sequencing and de novo genome assembly. The resulting genomes can be compared to each other and to strains isolated during previous outbreaks. This spatiotemporal sample trajectory provides a high-resolution foundation for minimizing costly downtime and for optimizing internal standard operating procedures.
The workflow is similar to that used for the surveillance of SARS-CoV-2 variants. Specifically, we compare the number and position of DNA nucleotide changes in each of the isolated strains and place them in a “family tree”. Depending on the species of concern, we offer either multi-locus sequence typing (MLST or cgMLST) or an analysis of the core genome single-nucleotide polymorphisms.
The team behind DNASense has extensive experience within the fields of (meta)genomics and variant tracking. Our active involvement in state-of-the-art methods and sequencing platforms (read about it in Nature Methods) ensures that customers obtain valuable insight from our tailored bioinformatic analyses.
Our standard package includes: Optional pre- and post-project meetings with a DNASense specialist, DNA extraction, library preparation, sequencing, pre- and post-sequencing quality control, de novo assembly, taxonomic profiling, cgSNP analysis, online access to raw data and results files and a detailed project report.
Add-on services (non-exhaustive list): Structural variant (SV) analysis, multi-locus sequencing typing (MLST), on-site sequencing, fast turn-around time.
In several ways:
- By not blindly trusting that isolates are pure cultures! In our experience, 10-50+ % of all isolates contain background contaminants that may provide ambiguous biochemical responses and potentially pollute SNP calling.
- Using state-of-the-art long read sequencing and de novo assembly. Using this approach, we can more efficiently remove unwanted contaminants.
- Our SNP calling workflow is not based on crude read mappings. Instead, our SNP calling workflow starts from the contamination-filtered, error-corrected genomes.
- By flexibility. We can scale our capacity to meet your demands. Even our reports can be customized to meet your need and expertise.
All who might be interested, but mainly larger companies within the Food and Beverages segment.
We can scale our sequencing capacity to meet your demands. If you are very time-sensitive and depending on the number of samples, we can provide warp-speed answers within 24 hours (upon receiving the samples). We charge an additional fee for this service. This also applies to our ultra-fast (TAT up to 3 work days) and our fast track (TAT up to 5 work days) options. The standard turnaround time is 15 work days.
Generally, we guarantee complete discretion. We are always open to signing NDAs (non-disclosure agreements).
Yes, we can handle biomass in almost any form. For shipment, refer to our general shipping guidelines.
Yes, we are often able to isolate (bin) different genomes from a sample. However, increased sequencing may be required to generate the recommended 100x coverage of the target genome.
Yes, we offer an add-on service for so-called metagenomic sequencing and genome extraction directly from a contaminated product.
Yes, we offer customer-specific genome databases for ongoing surveillance.
Yes, for an additional fee we offer an on-site service involving the identification of the contaminant.
We have access to Oxford Nanopore and Illumina. For rapid contamination source tracking involving prokaryotes we use the Oxford Nanopore R10.4.1 pore (kit V14)
We recommend/target 100x when using Oxford Nanopore R10.4.1 chemistry. This is more than sufficient for generating error-corrected genomes (read about it in Nature Methods).
For relatively complete prokaryotic genomes with little or no contamination, we use the Genome Taxonomy Database (GTDB), which potentially provides species-level resolution. Our standard service also includes rDNA extraction and classification against the Silva SSU database (genus level for both prokaryotes and eukaryotes). Custom databases can be included (add-on service).
The raw read accuracy of Nanopore sequencing is slightly lower than Illumina but we use state-of-the-art Q20+ chemistry which achieves comparable consensus accuracies and handles homopolymers found in prokaryotes (see Nature Methods).