FAQs: Antimicrobial Resistance (AR) Option

General Submission Requirements

Q1: What is required for AR data submission?

For the AR Option, your facility must have an ADT system and an electronic Laboratory Information System (LIS) or electronic access to the required data elements. Your facility also should have the ability to package the data into the standardized format of Clinical Document Architecture (CDA) for upload into NHSN.

Manual entry is not allowed due to the amount of data submitted each month. As a result, many facilities use a vendor system to package and submit the AR data via CDA. There are a number of self-identified vendor systems listed on the Society for Infectious Disease PharmacistsExternal website. You may already use one of these vendors currently for the submission of other types of data to NHSN so start there to see if 1) your facility has the capability to submit these data already using your current vendor or 2) your current vendor offers this capability with an “add on” feature. Some facilities are able to leverage internal IT/informatics resources to report these data. However, this does take specialized knowledge of coding and data aggregation and is not recommended for most facilities.

You can find the details on what data are required to be reported on our NHSN AUR Module web page within the training slides and protocol.

If your facility is interested/considering taking up this work internally, you’ll find the AU and AR CDA toolkits which contain the sample CDA files, link to the CDA Implementation Guide, helpful hints, etc. on the CDA Portal website.

 

Q2: How do I create a Monthly Reporting Plan for the AR Option?

A Monthly Reporting Plan is required for every month that you plan to submit AR data.

  • From the NHSN Homepage, select “Reporting Plan” from the left side menu.
  • To add a new monthly reporting plan, click “Add”.
  • Select the month and year for the AR data submission.
  • Then scroll down to the “Antimicrobial Use and Resistance Module” section of the plan.
  • See example screen shot and details below for guidance in selecting the Locations on Monthly Reporting Plan:The Monthly Reporting Plan screen shot is an example of the Antimicrobial Use and Resistance Module section of a Monthly Reporting Plan with the Antimicrobial Resistance boxes checked next to the following locations: facility-wide inpatient, 24-hour observation area, and Emergency Department
    • Select FacWideIn and check the AR box to submit AR Option data for inpatient locations. Individual inpatient locations do not need to be listed in the AR Option plan.
    • If applicable, select an allowed outpatient location type (specifically Emergency Department, Pediatric Emergency Department, and 24-hour Observation Area) and check the AR box to submit for that specific outpatient location. The outpatient locations will be listed as separate lines in the monthly reporting plan as shown in the above example screenshot.
  • Click the Save button at the bottom of the screen.

 

Q3: Can we submit AR Option data if we’re not submitting Antimicrobial Use (AU) data?

Yes. Facilities can submit AR Option data separately without submitting AU Option data.

 

Q4: What specimen sources are acceptable for AR reporting?
All specimen sources included in the Specimen Source tab of the Information Data Model (IDM) spreadsheet with an “X” in the “Valueset: ARSpecimenSource” column can be reported for the AR Option. The Specimen Source tab in the IDM provides further breakdown of the specimen sources into the specific categories outlined in the AR Option Protocol:

  • Specimen category = Non-invasive
    • AR_LRI Specimen = Lower Respiratory
    • AR_Urine Specimen = Urine
  • Specimen category = Invasive
    • AR Blood Specimen = Blood
    • AR_CSF Specimen = Cerebral Spinal Fluid

The IDM is found within the AR Tool Kit located on the CDA Portal website.

 

Q5: I’m from a state health department. Could you tell me the names and NHSN OrgIDs of the facilities submitting AR and AU data from my state?

The NHSN team is not permitted to share identifying facility information such as NHSN OrgID or facility name with state health departments. We can provide you with the number of facilities submitting AU/AR data within your state. However, if you’d like facility-specific information, you can provide us with an email requesting this information, including your contact information, which we can forward to your state’s AU/AR submitters. Facilities can then contact you directly if they so choose but are not obligated to do so.


CMS Reporting

Q6: Is reporting into the Antimicrobial Resistance Option required by CMS?

CMS has not included Antimicrobial Use (AU) and Antimicrobial Resistance (AR) Module reporting in the Hospital Inpatient Quality Reporting Program. However, the submission of data into the NHSN AU and AR Options via Clinical Document Architecture (CDA) is part of Meaningful Use Stage 3 for Public Health Registry reporting for eligible hospitals as outlined on the CDA Submission Support Portal website. Submitting AUR Module data into NHSN will be the only part of NHSN reporting that qualifies for Stage 3 participation. Additional details are located on the CDC Meaningful Use website.

 

Q7: If my facility voluntarily submits data into the Antimicrobial Resistance (AR) and/or Antimicrobial Use (AU) Options, will those data be shared with CMS?

No. At this time submission of data into the AR and AU Options are not included in any CMS Quality Reporting Program. Therefore, any AR and AU data that are submitted to NHSN will not be shared with CMS.

 

Q8: We are currently only submitting AR Option data into NHSN, can we participate in Meaningful Use Stage 3 (MU3)? Does submitting only AR Option data meet MU3 submission requirements?

In order to participate in Meaningful Use Stage 3 (MU3), both AR and AU Option data are required to be submitted. Keep in mind that submitting AR and AU Option data is just one option to satisfy the Public Health Registry reporting requirement for MU3.


Data Import

Q9: When should AR Summary and AR Event CDA files be uploaded in NHSN?

The AR Summary CDA file is a summary of the entire month and should not be submitted to NHSN any earlier than the first day of the subsequent month. For example, October AR Summary data may be uploaded beginning November 1. An AR Event CDA file represents a specific specimen with one organism and its antimicrobial susceptibility data. Once susceptibility testing has been finalized, those AR Event CDA files can be uploaded into NHSN even before the month has ended.

NHSN recommends that both AR Summary and AR Event data files be submitted to NHSN for a given calendar month by the end of the subsequent calendar month in order to make the data most actionable by your facility.

 

Q10: Can we submit AR and AU CDA files together in the same CDA zip file?

Yes, but for manual upload all of the files in the zipped file must be from one facility. If submitting files via DIRECT CDA Automation, the zipped file can contain CDA files for multiple facilities. For both manual and DIRECT CDA Automation submission, the zipped CDA file can contain up to 1000 files or be 2 MB in size, whichever comes first. Please note, only alphanumeric, hyphen, and underscores are allowed in the CDA file names and zip file names. No special characters are allowed.

 

Q11: How far back can we submit AR Option data?

A facility can submit AR Option data as far back as January 2012, if they have existing Monthly Reporting Plans during that time, or January of the previous calendar year (if no Monthly Reporting Plans previously existed).

Below are two scenarios to help explain this:

  • Facility A has existing NHSN Monthly Reporting Plans going back to January 2016. They can edit the Monthly Reporting Plan to add AUR Module locations for back to January of 2016 and hence submit AR Option data back to January 2016.
  • Facility B does not have any Monthly Reporting Plans in NHSN (meaning they didn’t even have reporting plans for HAI data). They can add Monthly Reporting Plans going back to the January of the year they enrolled in NHSN or back to the January of one calendar year in the past, whichever comes first.
    • If the facility enrolled in January 2017 and it’s December 2017: they can add Monthly Reporting Plans with AUR Module locations back to January 2017 and hence submit AR Option data back to January 2017.
    • If the facility enrolled in January 2015 and it’s December 2017: they can add Monthly Reporting Plans with the AUR Module locations back to January 2016 and hence submit AR Option data back to January 2016.

 

Q12: When trying to import an AR Event CDA file I received the following error: Unable to determine panel drug size. What does this mean?

Depending on the organism reported, there are specific drugs that need to be included in the CDA file. The list of drugs for each organism is called the drug panel and each panel varies with the number of drugs included. The organism and corresponding drug panel can be found in Appendix E of the AUR Module Protocol Cdc-pdf[PDF – 1 MB]. Work with your vendor to ensure all required drugs are accounted for in the CDA file. All drugs in the specific panel must be included in the CDA file regardless of whether they were tested by the lab.


Data Deletion

Q13: We noticed a mistake in our AR Summary record. Can I just resubmit the file?

There are two options:

  • Manually delete and re-upload a new file
  • Use Succession Management within vendor software

Manual Deletion: To manually delete the record, log into NHSN, select ‘Summary Data’ from the navigation menu on the left side and then select ‘Delete AUR Data’. Use the Summary Data Type drop down menu to select ‘Antimicrobial Resistance Data.’ Select the default Location Code of FACWIDEIN, and use the Month and Year drop down menus to select the month/year you’d like to delete from NHSN. Then click the ‘Delete’ button to delete the record. See the screen shot below for reference.

The Delete Antimicrobial Use and Resistance Summary Data screen shot shows the four required data elements required in order to delete the data.  These four elements are Summary Data Type, Location Code, Month, and Year


Succession Management
: The AR Summary can be automatically updated in NHSN using succession management from within your vendor software. Many vendors have implemented this feature by allowing users to simply export a new version of the file but be sure to work with your vendor to determine if this approach is appropriate for you.

 

Q14: We noticed a mistake in our AR Event record. Can I just resubmit the file?

There are two options:

  • Manually delete and re-upload a new file
  • Use Succession Management within vendor software

Manual Deletion: To manually delete the event record, log into NHSN, select ‘Event’ from the navigation menu on the left side and then select ‘Find’. Use the Event Type drop down menu to select ‘AR – Antimicrobial Resistance’ and optionally input any other identifying information. Select ‘Find’.

The Find Event screen shot shows how to navigate within NHSN homepage to the Find Event page and highlights the Event Type drop down box in which AR - Antimicrobial Resistance is shown

 

Next locate the AR Event to be deleted on the Event List table. Check the box in the Delete column next to the AR Event to be deleted. Click the ‘Delete’ button at the top of the column to delete the event.

 

The Event List screen shot shows the list of Antimicrobial Resistance event records resulting from a search

 

Succession Management: The AR Event can be automatically updated in NHSN using succession management from within your vendor software. Many vendors have implemented this feature by allowing users to simply export a new version of the file but be sure to work with your vendor to determine if this approach is appropriate for you.


Duplicate Rules

Q15: Do the 14-day (blood & CSF) and 1 per month (urine & lower respiratory) duplicate rules extend across calendar months?

The 14-day duplicate rule for invasive specimens (blood & CSF) does extend across calendar months. Even across calendar months there should be 14 days with no positive culture result from the laboratory for the patient and specific organism SNOMED code before another invasive source AR Event is entered into NHSN for the same patient and specific organism SNOMED code. See the below example to visualize the 14-day duplicate rule for invasive sources:

Table 1 displays an example scenario of when to include and exclude reporting into NHSN using the 14-day duplicate rule for invasive specimens (blood & CSF).
Date Lab Result Reported to NHSN? Justification
January 15 Staph aureus isolated from blood culture Yes Patient’s first blood culture of admission; Staph aureus is isolated; AR event reported
January 28 Staph aureus isolated from blood culture No <14 days since last positive culture (Jan 15) of Staph aureus
February 3 Staph aureus isolated from CSF culture No <14 days since last positive culture (Jan 28) of Staph aureus
February 20 Staph aureus isolated from blood culture Yes >14 days since last positive culture (Feb 3) of Staph aureus; AR event reported

 

The 1 per month duplicate rule for non-invasive specimens (urine or lower respiratory) does not extend across calendar months. For urine and lower respiratory specimen isolates, the first non-invasive source AR Event should be reported per month. No more than 1 non-invasive specimen per patient per organism should be reported to NHSN per calendar month. See the below example to visualize the 1 per month duplicate rule for non-invasive sources:

 

Table 2: 1 per month duplicate rule for non-invasive specimens
Date Lab Result Reported to NHSN? Justification
January 1 Staph aureus isolated from urine Yes Patient’s first non-invasive specimen of the month; Staph aureus is isolated; AR event reported
January 20 Staph aureus isolated from urine No Still same month (Jan) as the non-invasive specimen Staph aureus reported to NHSN
January 31 Staph aureus isolated from lower respiratory culture No Still same month (Jan) as the non-invasive specimen Staph aureus reported to NHSN
February 3 Staph aureus isolated from urine Yes Patient’s first non-invasive specimen of new month (Feb); Staph aureus is isolated; AR event reported

 

Q16: Do the 14-day (blood & CSF) and 1 per month (urine & lower respiratory) duplicate rules extend across patient admissions?

Both the 14-day duplicate rule for invasive specimens (blood & CSF) and 1 per month duplicate rule for non-invasive specimens (urine & lower respiratory) extend across patient admissions. See the examples below for clarification.

Invasive specimen (blood & CSF) example of the 14-day rule for a specific organism from a single patient across admissions:

 

Table 3: Duplicate rule for invasive specimens across admissions
Date Lab Result Reported to NHSN? Justification
July 1 Escherichia coli isolated from blood culture in Medical Ward Yes Patient’s first blood culture of inpatient admission; Escherichia coli is isolated; AR Event is reported into NHSN.
July 4 Patient discharged from facility
July 7 Escherichia coli isolated from blood culture in Emergency Department No It has been less than 14 days since the last positive culture (July 1) from the patient isolating E. coli.
July 17 Escherichia coli isolated from blood culture in Medical Ward No It has been less than 14 days since the last positive culture (July 7) from the patient isolating E. coli.

 

Non-invasive specimen (urine & lower respiratory) example of the 1 per month rule for a specific organism from a single patient across admissions:

 

Table 4: Duplicate rule for non-invasive specimens across admissions
Date Lab Result Reported to NHSN? Justification
July 1 Escherichia coli isolated from urine in Medical Ward Yes Patient’s first urine specimen of inpatient admission; Escherichia coli is isolated; AR Event is reported into NHSN.
July 15 Patient discharged from facility
July 31 Escherichia coli isolated from urine in Emergency Department No Still same month (July) as the non-invasive specimen E. Coli reported to NHSN
August 3 Escherichia coli isolated from urine in Medical Ward Yes Patient’s first non-invasive specimen of new month (Aug); E. coli is isolated; AR event reported

 

Q17: Do the duplicate rules apply to specimens collected while the patient was at another healthcare facility?

No. The 14-day duplicate rule for invasive specimens (blood & CSF) & 1 per month duplicate rule for non-invasive specimens (urine & lower respiratory) apply only to those specimens collected in the reporting facility. Specimens obtained while the patient was at another healthcare facility should not be included in the 14-day (blood & CSF) or 1 per month (urine & lower respiratory) calculations.


Laboratory Testing Results

Q18: Should preliminary antimicrobial susceptibility test results be reported to NHSN?

No. Only final or corrected susceptibility testing results should be reported to NHSN. No preliminary laboratory results should be used for NHSN AR Option reporting.

 

Q19: If I’m not able to send susceptibility data for specific tests (MIC, E-Test, KB), can I still participate in AR reporting?

Yes, facilities can still participate as long as they are still able to send the final interpretation provided by the lab for the given drug. The specific test result interpretations for MIC, E-Test, and KB are required to be included in the AR Event CDA file. However, in the event that these data cannot be sent, the tests should be reported as “Not Tested” in the CDA for that specific test’s interpretation.

 

Q20: My laboratory suppresses some susceptibility test results. Can I still participate in the AR Option if I’m unable to send all susceptibility results?

Every effort should be made to report all antimicrobial resistance data that meets the NHSN protocol requirements regardless of whether those data are supposed from clinical end users. However, in the event that suppressed data cannot be obtained and/or sent to the NHSN AR Option, NHSN will accept the data your facility is able to provide. Because the AR Event CDA files will not be accepted without containing all of the required drugs for a given organism, please be sure that your vendor is using ‘Not Tested’ for the specific tests/drugs unable to be obtained.

 

Q21: Are all drugs required to be included in the file even if they were not tested by the lab?

No. Isolates in which all of the NHSN required antimicrobials were not tested, should not be reported to NHSN unless there was at least one non-required drug tested. For example, if a Staphylococcus aureus isolate was tested for the non-required drug, oritavancin, and none of the other 23 NHSN required antimicrobials were tested, that isolate would still be considered eligible for reporting to the AR Option. In this case, a facility would report “Unknown” or “Not Tested” for the required drugs.

 

Q22: Would I report an isolate to the AR Option if all drugs tested were Susceptible?

Yes. All drugs in the specific organism’s drug panel should be included in the AR Event file regardless of susceptibility results.

 

Q23: Would I report an isolate to the AR Option if all of the NHSN required antimicrobials were not tested, but at least one non-required drug was tested?

Yes. Isolates in which all of the NHSN required antimicrobials were not tested, but at least one non-required drug was tested, should be considered eligible to be reported into NHSN. For example, if a Staphylococcus aureus isolate was tested for the non-required drug, oritavancin, and none of the other 23 NHSN required antimicrobials were tested, that isolate would still be considered eligible for reporting to the AR Option.

 

Q24: If the laboratory reports additional information beyond those drugs that are required in the NHSN drug panels, should those drugs be reported to NHSN?

No. Additional drugs should not be reported to NHSN and not included in the CDA file. NHSN will only accept the drugs listed in the specific organism’s drug panel.

 

Q25: If the PBP2a variable is not available from the electronic data for Staphylococcus aureus, should this organism still be reported to NHSN?

Yes. PBP2a is a required variable for Staphylococcus aureus isolates, but if PBP2a-afflutination is not available from the electronic data source, Staphylococcus aureus should still be reported with the PBP2a variable indicated as ‘Unknown’ in the AR Event CDA file.

 

Q26: If the same specific test (E-Test, MIC, KB) is performed on the same isolate but they produce conflicting results, what should be reported for the final interpretation?

Report the final interpretation provided by the laboratory.

If no final interpretation is provided by the laboratory, then report the most resistant interpretation (NS > R > I > S-DD > S > NT). For example, if two E-Tests are performed for the same drug on the same isolate and one produces “Intermediate” and the other produces “Susceptible”, report “Intermediate” as the final interpretation for that specific drug susceptibility.

 

Q27: If multiple specific antimicrobial tests (E-Test, MIC, KB) are performed on the same isolate and they produce conflicting results, what should be reported for the final interpretation?

Report the final interpretation provided by the laboratory. If no final interpretation is provided by the laboratory, then report the most resistant specific test interpretation as the final interpretation (NS > R > I > S-DD > S > NT).

For example, if drug susceptibility results produced MIC = “Resistant” and E-Test = “Intermediate” but no final interpretation was provided, report “Resistant” as the final interpretation for that specific drug susceptibility.

 

Q28: If two isolates from the same day have conflicting susceptibilities to the panel of antimicrobials tested, which isolate should be reported?

Report the isolate with the most resistant final interpretation (NS > R > I > S-DD > S > NT). If a final interpretation was not provided by the laboratory, report the isolate with the higher amount of drug resistance based on the number antimicrobials testing “NS” or “R”. If it cannot be determined which isolate is the most resistant, report the isolate that was the first entered into the Laboratory Information System.

For example, Candida albicans was isolated from two blood specimens collected from the same patient on the same calendar day and no final interpretation was provided by the laboratory. The first isolate tested resistant to three of the eight antimicrobials tested and the second isolate tested resistant to four of the eight antimicrobials tested. Report the second isolate to NHSN since it showed the higher amount of resistance.

 

Q29: Will the D-Test or other testing methods be added for AR Option reporting?

No. At this time, additional laboratory testing methods, such as the D-Test, will not be added to the AR Option requirements.


AR Summary Data

Q30: How do I count patient admissions for AR or AU calculations when a patient’s stay extends from one month to another?

The day a patient enters the door to a facility or a location is the date of their admission to that facility or specific location. If the patient is not discharged, then that stay is all part of that same admission, no matter how long. A stay that continues across multiple months is still only one admission.

If the patient is discharged and then returns at a later time on a separate calendar day, then the patient is counted as a new admission with a new admission date. If the patient is discharged and then returns at a later time on the same calendar day, then the patient is not counted as another admission since a single patient can only attribute 1 admission per calendar day to the monthly total.

 

Q31: Are Patient Days and Admissions reported for outpatient locations for the AR Option?

Patient Days and Admissions are not reported for outpatient locations for the AR Option. Additionally, outpatient locations (Emergency Department, Pediatric Emergency Department and 24-hour observation area) are not included in the FacWideIN patient day and admission counts.

 

Q32: Is the number of blood cultures performed in a given month still required for reporting AR Option data to NHSN?

This variable was removed from the NHSN AR Option protocol but the field is still required for valid import of the CDA. Dummy data can be used because that value will not be saved into the NHSN database.


AR Option Analysis

Q33: How do I view my AR Option data once it’s been uploaded into NHSN?

AR Option data can only be viewed using the NHSN Analysis function. Specific details on the AR Option analysis can be found in the protocol or in the Analysis Resources section of the NHSN AUR Module Cdc-pdf[PDF – 1 MB] webpage. Additionally, the Antimicrobial Resistance Event Line List Cdc-pdf[PDF – 1 MB] Quick Reference Guide has been developed to assist with viewing, modifying, and interpreting the AR Option event data.

Remember to generate data sets within your NHSN facility before running your analysis reports so that any newly uploaded data will be included. See question Q34 below for information on generating data sets.

 

Q34: I uploaded AR Option data but I don’t see it when I run my reports within analysis. What happened to my data?

Newly uploaded data won’t appear in the analysis reports until a new data set is generated within NHSN. The data set is a snap shot of the data currently in your NHSN facility at the exact time you click the “Generate New Data Sets” button. Make sure to always generate new data sets after uploading data into NHSN. Also note that each NHSN user has their own data sets.

 

Q35: How do I read the AR Event Line List?

The Antimicrobial Resistance Event Line List report is an organized, detailed list of each record entered into NHSN. You may have to modify the report filtering by month, pathogen, specimen, or other variable as the default settings may produce a report that is too lengthy to be useful and/or displayed. The report can be used to verify the data imported successfully and can also be helpful for data validation.

Below is an example AR Event Line List report and a description of how to read this report:

Antimicrobial Resistance Line Listing Report shows an example report of the pathogen Candida auris and the susceptibility for each drug in it's panel

 

Candida auris was isolated from a patient’s blood specimen collected in the MICU on September 13, 2016. This isolate was non-susceptible to anidulafungin and susceptible to caspofungin, fluconazole, flucytosine, itraconazole, micafungin, posaconazole. Voriconazole was not tested. (Please note that data on this report are fictitious and for example only.)

 

Q36: Could you provide more details on how the NHSN AR Option Facility-Wide Antibiogram is calculated?

The NHSN Facility-wide antibiogram shows the organisms from the specimens reported into the AR Option for a given month. It lists all antimicrobials and the percent of isolates that were non-susceptible (R, I, or NS) to the organism. That calculation is shown below:

(Total isolates R+Total isolates I+Total isolates NS)/Total isolates tested  ×100

The percent non-susceptible is only calculated when there are 30 or more isolates tested for a particular drug.

 

Q37: How do I read an antibiogram?

The antibiogram shows the organisms from the specimens reported into the AR Option for a given month. It lists all antimicrobials and the percent of isolates that were non-susceptible (R, I, or NS) to the organisms.

Below is an example a facility-wide antibiogram and a description of how to read it:

AR Option facility antibiogram

 

The column headers list the specific pathogen while the rows represent each antimicrobial. In this example, 33% of the Acinetobacter species isolates and 0% of the Staphylococcus aureus isolates tested in January 2014 were not susceptible to ciprofloxacin. Or in other words, 67% of the Acinetobacter species isolates and 100% of the Staphylococcus aureus isolates tested were susceptible to ciprofloxacin. Cells with “.” represent organism/drug combinations for which there were less than 30 isolates tested. Cells shaded in grey represent non-valid organism/drug combinations. For the full drug name, see the Antimicrobial Ingredients tab of the Information Data Model (IDM) spreadsheet which is found within the AR Tool Kit located on the CDA Submission Support Portal website.