FHIR Chat · Test results · Covid-19 Response

Stream: Covid-19 Response

Topic: Test results

John Moehrke (Mar 25 2020 at 16:17):

Is there a profile available for Observation on the lab results of the set of covid-19 tests?

David Pyke (Mar 25 2020 at 16:19):

Is a profile needed or can the Observation current structure handle the values?

John Moehrke (Mar 25 2020 at 16:21):

I hope Observation is fine. I just want consistency so that a population-health (broad) query can discover all the results. Yes, I see the set of codes (Grahame's blog), but looking for consistency on the other elements use within Observation

John Moehrke (Mar 25 2020 at 16:22):

for example, if these results are shared into an XDS (and XCA), then a population query (MPQ) can discover statistics

Rob Hausam (Mar 25 2020 at 16:26):

I'm not sure that a specific profile is needed for it. But certainly one can be created (don't know if anyone has done that).

John Moehrke (Mar 25 2020 at 16:27):

we have in US-Core all kinds of profiles of things that I would agree shouldn't need to have been defined... lesson learned, some will not act until all is defined.

Mritunjay Dubey (Apr 05 2020 at 12:45):

Hello People! Reopening this thread. Is there a specific reason we did not use DiagnosticReport (https://www.hl7.org/fhir/diagnosticreport.html) for test results? The DiagnosticReport.Result can be used to carry the observations.

CC: @John Moehrke @David Pyke @Rob Hausam

Abbie Watson (Apr 05 2020 at 13:57):

Logica has just released a very preliminary Covid19 profile, which basically just includes coverage of the Observation resource in regards to oxygen saturation and pulse oximetry data. Basically, they've formalized that we aught to use LOINC code 59408-5, I suppose?

https://covid-19-ig.logicahealth.org/?mc_cid=15d567de77&mc_eid=d82de02680

Not to bash on profiling, but it seems like a lot of infrastructure to specify some value sets. I've always found profiles to appeal to academics a bit more than they're useful in real life. But sure, if we want the structure definitions and everything to be machine readable, why not. When it gets fleshed out with all the testing codes, and procedure codes, and device codes, and such, maybe it will be a comprehensive resource.

Abbie Watson (Apr 05 2020 at 14:12):

So here's my question... should a Covid19 profile be at the beginning of the research and regulatory review process or at the end? Or do we have separate profiles for each? Like... how should we handle LOINC prerelease codes? Or medications that haven't been FDA approved? If the medication has an RxNorm code but the use is off-label, do we include it in the profile? As something optional?

Andrea Pitkus, PhD, MLS(ASCP)CM, CSM (Apr 05 2020 at 20:41):

Logica model was reported on CIMI call, but they were focused on clinical reporting first. Reviewing the Logica model. They list the pulse ox LOINC 59408-5 which would not be used for pos COVID-19 results. (It might be used to report pulse ox data on COVID-19 patients with respiratory symptoms.)

Each performing laboratory should be mapping their COVID-19 results (and same may be mapping orders) to the appropriate LOINC PreRelease terms reflecting the specimen(s), methods, test info involved in their COVID-19 testing. Most current US COVID-19 testing is qualitative PCR based testing, so some Pulse Ox FHIR modeling may not apply like units of measure, UCUM, etc.

Recommend a COVID-19 specific model be created with observations bundled into a Diagnostic Report Resource to capture how these test results are modeled and mapped already in LIS and public health systems for those laboratories performing the testing. It can be expanded to include antibody test reporting as those are just entering the US market now with Mayo and Ortho Clinical Diagnostics methods. A LIVD map is forthcoming with the LOINCs mapped to IVD vendor tests that are currently available.

That said, much may need to be developed for FHIR (extension and/or implementation guide) with regard to lab testing. Normally, specimen type and source would be required along with test order and result and result value information for modeling reporting of the performing laboratory data, such as for ELR. However, given the FEMA/HHS report wants a summary of orders and results and result values that are pos versus neg, along with specimen rejection information (which would come from the performing laboratory per CLIA law and lab accreditation requirements), may wish to address the scenarios below on the source of the all the required data elements first needed to fulfill the reporting requirements.

Some laboratory administrators have indicated they have begun pulling custom reports to meet the requirements pulling data from their LIS and EHR systems (not necessarily in FHIR). However, it was indicated on Friday's LIVD call that it's likely not the LIS as we're not aware of LIS vendors supporting FHIR for reporting lab results currently. Yet, the LIS is the source of origin for lab results and has the most granular data. For example specimen rejection information would be in the HL7 v 2.51 SPM 21 segment (as required for ELR)

Andrea Pitkus, PhD, MLS(ASCP)CM, CSM (Apr 05 2020 at 21:17):

A second part of this is the workflow/structure/modeling of laboratory data within a "hospital." Note query of a single hospital EHR unlikely to provide all COVID-19 testing information required for FEMA reporting. Quite a few different scenarios commonly occur and may apply to a particular hospital's reporting counts. If data are only assessed from an EHR, scenarios, 6, 7, and 8 (and maybe 9) could be missed and could be over half of the testing volume performed by a hospital lab. It's vital these reports are accurate!

MD in hospital A orders COVID-19 testing in their EHR, order and specimen sent to their hospital lab, who performs analysis and reports results in their hospital LIS and reports back to the ordering provider in the hospital EHR. (May be LIS and EHR are different vendors and are interfaced, or LIS and EHR are same vendor and interfaced or same vendor with shared database without interfacing the two.) I understand FEMA wants these results.
MD in hospital A orders COVID-19 testing in their EHR, order and specimen sent to their hospital lab. Hospital A doesn't perform COVID-19 testing, so they place an order in hospital B's LIS and sends over specimens to be analyzed in hospital B's lab, performs analysis and reports results in their hospital lab's LIS and reports back to the ordering hospital a lab LIS who sends result to provider in hospital B's EHR. (Again, vendors may be same or different for each LIS and EHR in data flow/ interoperability path). I understand FEMA wants these results.
Scenario 2 can have orders and results sent to a public health lab. I understand FEMA doesn't need these results as they are getting them form public health already.
Scenario 2 can have orders and results sent to a reference laboratory for testing. If performing lab is LabCorp, Quest, Mayo, ARUP, or Bioreference, then FEMA doesn't need these results as they are already receiving from these labs.
Scenario 2 can have orders and results sent to a reference laboratory for testing, not included in the FEMA list. Example would be Sonic Laboratories. I understand FEMA wants these results.
This scenario entails non hospital providers ordering COVID-19 tests on patients in an outpatient scenario (ED and never admitted, urgent care, clinic, drive u collection site, etc.). Many different types of EHRs may be involved in the ordering process or may be the same as the affiliated hospital EHR and be just inpatient and outpatient versions. The providers would have an existing contract/agreement for testing at a hospital laboratory. The order would be sent with the specimen to the hospital lab LIS (and may never exist in the hospital's EHR!), where the laboratory would perform testing, recording results in their LIS and sending results back to the ordering provider's EHR. (Again, many different combinations of EHR and LIS may occur as in scenario #2). Not clear in documentation if FEMA wants these test results, but have heard they do want them. One can interpret they want ANY testing performed by the hospital lab. In this scenario these orders and results would qualify. If they are omitted, it may cause case counts to be falsely low, depending on this testing volume over time even as protocols and guidelines have changed.
This scenario entails non hospital providers ordering COVID-19 tests on patients in an outpatient scenario (ED and never admitted, urgent care, clinic, drive u collection site, etc.) from unaffiliated sites with the hospital lab. Many different types of EHRs may be involved in the ordering process or could be same vendor/different version as hospital EHR. The providers would have an existing contract/agreement for testing at a hospital laboratory. The order would be sent with the specimen to the hospital lab LIS (and may never exist in the hospital's EHR!), where the laboratory would perform testing, recording results in their LIS and sending results back to the ordering provider's EHR. (Again, many different combinations of EHR and LIS may occur as in scenario #2). Not clear in documentation if FEMA wants these test results, but have heard they do want them. One can interpret they want ANY testing performed by the hospital lab. In this scenario these orders and results would qualify. If they are omitted, it may cause case counts to be falsely low, depending on this testing volume over time even as protocols and guidelines have changed.
This scenario entails independent non-hospital providers ordering COVID-19 tests on patients in an outpatient scenario (ED and never admitted, urgent care, clinic, drive u collection site, etc.) from unaffiliated clinic sites with the hospital lab. Many different types of EHRs may be involved in the ordering process or could be same vendor/different version as hospital EHR or LIS. The providers would have an existing contract/agreement for testing at a hospital laboratory. The order would be sent with the specimen to the hospital lab LIS (and may never exist in the hospital's EHR!), where the laboratory would perform testing, recording results in their LIS and sending results back to the ordering provider's EHR. (Again, many different combinations of EHR and LIS may occur as in scenario #2). Not clear in documentation if FEMA wants these test results, but have heard they do want them. One can interpret they want ANY testing performed by the hospital lab. In this scenario these orders and results would qualify. If they are omitted, it may cause case counts to be falsely low, depending on this testing volume over time even as protocols and guidelines have changed.

9 This scenario involves health workers that are screened for potential exposures and infections. They may be seen by their primary care provider or more likely employee health who may order COVID-19 testing to rule out infection so they can return to work. These may be ordered by an Employee Health physician in an employee health system/module of EHR and may be tested by the health system/hospital laboratory or could be done elsewhere to protect confidentiality or if the health system doesn't offer testing (any of the scenarios above, except #1) The employee name or demographics may be omitted, and a confidential code used to identify their specimen and results may or may not be associated in their regular EHR chart. (Anyone else with employee health experience to provide more details on scenarios?) Results are reported confidentially back to employee health by the performing laboratory. I assume FEMA would be interested in these results too to get a better handle on health worker infection rates as some have inquired about these numbers. If testing is performed by the hospital lab, suspect these would be included in the case counts.

Are there any other scenarios not listed, where folks are aware of testing being performed to ensure they aren't missed, but captured in reporting to FEMA?
Another I thought of is outpatient tested positive (by any performing lab), but then is admitted to the hospital at a later point (such as British PM Boris Johnson), do these impact the hospital results for a particular day (I'd argue no, unless outpatient testing by a hospital lab is excluded for some reason from FEMA scope).
Forgot to mention nursing home patients. Most of those will have an agreement with a reference or nearby hospital lab. Staff would collect specimens and a physician would place the order. A number of these long term care facilities may still be faxing or using paper orders too. When these paper requisitions are received at the performing laboratory with the specimen, electronic orders are placed within the LIS so testing can be performed and reported back electronically (in the LIS). The long term care facility may request results be faxed back. (Personally seen faxed results also hand entered into the Long Term Care Facility EHR as they may not be interfaced with the performing laboratory.) I'd also lump in rehab hospitals, and similar settings.

@Hans Buitendijk @Abigail Watson @Rob Hausam @David Pyke @John Moehrke @Keith Boone**
@Eric Haas which scenarios above does the measure models you're building include?

Hans Buitendijk (Apr 06 2020 at 00:36):

I'd say the measure model could handle these, but the actual measure being defined depends on the party interested in having that measure and the level of precision they define. So far, main focus is on those already defined by CDC and FEMA and their definitions at the level of specificity they have provided. I can see a number of the scenarios raising questions on how the CDC and FEMA could be interpreted, thus could be clarified. But those are then questions that should be raised to either the CDC or FEMA in the context of a specific measure of concern. I understand that for CDC/NHSN spreadsheet the nhsdn@cdc.gov e-mail address (there is no specific, assigned name) would be the place to ask for clarification , or perhaps make suggestions on new/existing measures. I have not figured out yet what/who that contact is for the FEMA set.

Keith Boone (Apr 06 2020 at 05:11):

Other measure requests are coming in ... see https://github.com/AudaciousInquiry/saner-ig/issues?q=is%3Aissue+is%3Aopen+label%3A%22Measure+Proposal%22
I am also expecting a require related to Biosurveillance related to the work that Farzad did in NY

Andrea Pitkus, PhD, MLS(ASCP)CM, CSM (Apr 06 2020 at 23:13):

I've been in contact with multiple people on clarifications on the FEMA/WH/HHS lab data and secnarios shared with the contacts. CDC indicated on today's lab call that FAQs are coming out to assist laboratories on the details regarding the lab test data required by FEMA/WH/HHS. Waiting for an official response while they work on it, but that is also why I shared the scenarios to help folks here be aware of them as they think about how the requirements will be met.
Some major health systems and medical centers have already had their teams craft custom reports pulling data from the LIS and EHR.

Last updated: Apr 12 2022 at 19:14 UTC

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