Difficult Diagnoses: Pathogen-Agnostic Advanced Molecular Testing for ID

Infectious disease physicians are usually consulted when specimens from patients with clinical infections are noted to be negative after available diagnostic microbiological testing. In those situations, consultants recommend adjunct testing to rule out rare and difficult-to-detect pathogens and, in some cases, may recommend pathogen-agnostic advanced molecular testing to detect emerging pathogens (NEJM 2019). The frequency of such consultations, the types of infections for which advanced testing is recommended, and the availability and access to laboratories that perform advanced molecular testing on patient samples in routine clinical practice in the US is not well understood (Nature Medicine 2020).

We would like to gain an understanding of how often infectious disease physicians in the US encounter such difficult-to-diagnose patients, where they send samples for pathogen-agnostic advanced testing such as metagenomic sequencing or whole genome sequencing, and how those results are used in their clinical practice.

The purpose of this survey is to better understand how and when ID physicians use pathogen-agnostic advanced molecular testing for patients with difficult-to-diagnose syndromes.

Name EIN ID

What types of advanced molecular diagnostic tests have you ordered/used?      [Select all that apply] Broad range 16S rRNA gene sequencing Whole genome sequencing Metagenomic next-generation sequencing (mNGS) None of the above Other, specify: How often within the past two years have you used advanced molecular diagnostic testing? Often (weekly)     Sometimes (monthly)     Rarely (quarterly or less often)     Once Not at all - STOP HERE and submit survey Within the past two years, advanced molecular diagnostic testing was used for:      [Select all that apply] a. Symptom or illness duration:  Acute (<3 weeks)     Subacute (3 weeks to 3 months)     Chronic (>3 months) b. Specimen type:            Blood CSF Plasma Synovial fluid Bone Tissue from biopsy / aspiration Stool Urine Respiratory tract         Other, specify: Where have molecular diagnostic specimens in your institution been sent for testing?      [Select all that apply] Local / institutional lab Commercial / reference lab Research-only lab State/jurisdictional public health lab Federal public health lab Who pays for this external laboratory testing and associated costs? Patient ----- Never Sometimes Usually Unsure Health insurance ----- Never Sometimes Usually Unsure Hospital / institution ----- Never Sometimes Usually Unsure Lab ----- Never Sometimes Usually Unsure Research funds ----- Never Sometimes Usually Unsure Other, specify: ----- Never Sometimes Usually Unsure Are these advanced molecular test results made available to patients in your institution? Yes     No     Not sure What turnaround time would you find unacceptable and lead to you not using advanced molecular diagnostic testing? >24 hours     >48 hours     >3 days >7 days >10 days   Which of the following barriers have…      [Select all that apply]   …prevented you from requesting molecular diagnostic testing …created difficulty in using molecular diagnostic testing Diagnostic stewardship barriers imposed by my institution Cost or lack of payor coverage Lack of guidelines Lack of CLIA certification (needed for insurance payment) Lack of FDA approval Difficulty interpreting results (e.g. not sure how to interpret a positive test) Determining which laboratory to use Determining how to order Difficulty with specimen collection or transportation Not sharing test results with patients Other, specify: In the following situations, have you found advanced molecular diagnostic tests helpful? In clinical decision making ----- Never used Rarely Occasionally Often To assist with stopping antimicrobials ----- Never used Rarely Occasionally Often During outbreak investigation ----- Never used Rarely Occasionally Often For infection prevention/surveillance ----- Never used Rarely Occasionally Often Confirmation of a diagnostic result ----- Never used Rarely Occasionally Often Any final comments about pathogen-agnostic advanced molecular testing:

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