whole genome
sequencing
FOR OUTBREAK ANALYSIS
Using high-resolution short read whole genome sequencing, we provide within species comparison to understand relatedness of specific strains. We will provide a report with strain relatedness to help put the nosocomial transmission in context to understand and hopefully eliminate transmission pathways. We can sequence the isolates found in your environmental and patient surveillance samples or you can send us isolates of epidemiologic concern for sequencing directly. We also offer Clostridiodes difficile culturing for sequencing services.
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Phylogenetic tree: Analysis of all sequenced isolates to determine relatedness to each other. The clusters identified will inform outbreak mitigation strategies and acknowledge non-related imports.
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Longitudinal analysis of transmission: Analysis of transmission patterns over time. All of your isolate sequencing data is securely stored and can be re-analyzed against new isolates of concern.
whole genome sequencing
Request A CONSULTATION
Infection prevention groups can send us isolates (patient and/or environmental) and we utilize our advanced, high-quality laboratory services and analytics – including Whole Genome Sequencing (WGS) – to answer the following types of questions for them in a timely manner:
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Are these organisms related?
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Is this infection imported from outside our facility or acquired nosocomially? What is the potential role of the clinical environment?
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Has this specific strain of pathogen been seen in our facility before? Is there an issue in our environment that we need to address?
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How can we identify and manage point sources? How implement a surveillance program?
Your positivity rate for C. difficile toxin PCR has jumped in the past week in your MICU.
Is it an environmental transmission or a result of antibiotic usage?
example scenario:
YOUR CONCERN
HOW WE HELP
Send your C. difficile PCR positive stools to AMR Services and we will provide the answer in a concise usable format.
With WGS and our bioinformatics pipeline, we can help in your understanding if the increase in C. difficile in your hospital is a clonal transmission stemming from a common source or an issue for antimicrobial stewardship.
Request A CONSULTATION
Infection prevention groups can send us isolates (patient and/or environmental) and we utilize our advanced, high-quality laboratory services and analytics – including Whole Genome Sequencing (WGS) – to answer the following types of questions for them in a timely manner:
-
Are these organisms related?
-
Is this infection imported from outside our facility or acquired nosocomially? What is the potential role of the clinical environment?
-
Has this specific strain of pathogen been seen in our facility before? Is there an issue in our environment that we need to address?
-
How can we identify and manage point sources? How implement a surveillance program?