FAQs: Antimicrobial Resistance (AR) Option

General Submission Requirements

Q1: What does NHSN require for AR data submission?

If not already enrolled in NHSN, follow the 5-step process here: 5-Step Enrollment for Acute Care Hospitals/Facilities. If your facility is enrolled in NHSN and now wants to participate in the AR Option by submitting AR data to NHSN, then your facility must have an Admission Discharge Transfer (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.

NHSN does not allow manual entry 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 several self-identified vendor systems supporting AR Option submission listed on the Society for Infectious Disease Pharmacistsexternal icon 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 leverage internal IT/informatics resources to report these data. However, this does take specialized knowledge of coding and data aggregation. For this reason, NHSN does not recommend this option for most facilities.

You can find the details on what data are required to be reported on our NHSN AUR Module webpage within the AUR 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 Submission Support Portal website.

 

Q2: Do I need Secure Access Management Services (SAMS) credentials to view or submit AR data to NHSN?

Yes, you will need SAMS credentials to submit and/or view AR data. If you are new to NHSN, a user with administrative rights at your facility, such as the facility administrator, must first add you to the NHSN AR Option following the steps in question #3. After being invited to NHSN, review and accept the NHSN Rules of Behavior and complete the SAMS enrollment process pdf icon[PDF – 542 KB]. All NHSN users must follow these steps before using the application. While waiting for your SAMS credentials, you can complete the training in the AUR Educational Roadmap. After you receive your SAMS credentials, you’ll be able to log into your NHSN facility. You can find more information about SAMS on the About SAMS webpage.

 

Q3: How do I add a user to view/upload data into the AR Option?

A user with administrative rights, such as the facility administrator, must follow these steps to add users to the NHSN AR Option:

  1. From the NHSN Homepage, navigate to Users on the left-hand side menu.
  2. Select Add User.
  3. Complete all fields marked with a red asterisk (*) and select Save.
    1. Consider whether you should designate this new user as an AU Option and/or AR Option contact. The NHSN AUR Team will use this information to target notifications for AUR related content like AU and AR quarterly users calls, updates regarding AUR resources, and data quality related outreach.
  4. On the next screen, assign user rights and select Save. Users need rights to the Patient Safety Component to view and submit AR data. If the user will submit AR data, NHSN recommends Administrator-level user rights. You can use the Custom Rights option to limit user rights to just AR data and no other patient safety modules. Be careful when assigning Custom Rights, as certain settings will prevent users from accessing AR data.

For complete details and instructions, please refer to the NHSN AUR User Rights document pdf icon[PDF – 350 KB].

 

Q4: How do I create a Monthly Reporting Plan for the AR Option?

NHSN requires a Monthly Reporting Plan 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. Do not list individual inpatient locations 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.  List the outpatient locations 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.

 

Q5: 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.

 

Q6: What qualifies as an AR Event?

An AR event contains isolate level antimicrobial susceptibility results for a specific organism. An isolate is defined as a population of a single organism observed in a culture obtained from a patient specimen. The isolate must meet the three criteria below:

  1. Must be collected from an eligible specimen type: blood, cerebrospinal fluid, urine or lower respiratory
  2. Must be an eligible organism (see Q8)
  3. Must have had antimicrobial susceptibility testing performed for at least one drug.

Please note, your facility should report all eligible isolates that meet the reporting guidelines outlined in the NHSN AUR Module Protocol pdf icon[PDF – 1 MB] to NHSN regardless of the antimicrobial resistance of the isolated organism. This means that even isolates that are susceptible to all required antimicrobials are eligible to be reported to the AR Option.

 

Q7: What specimen sources are acceptable for AR reporting?

Your facility can report all specimen sources included in the Specimen Source tab of the Information Data Model (IDM) spreadsheet with an “X” in the “Valueset: ARSpecimenSource” column to 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 = Cerebrospinal Fluid

The IDM is found within the AR Toolkit located on the CDA Submission Support Portal website.

 

Q8: What organisms are eligible for AR Option reporting??

Facilities and vendors should refer to the AR Option Pathogen Roll-up Workbook found in the Antimicrobial Resistance Toolkit for organisms eligible for AR Option reporting and the complete list of their associated SNOMED codes. All organisms in the Workbook are eligible for reporting. Refer to the AR Option Pathogen Roll-up Reference Guide, also found in the AR Toolkit, for guidance using the workbook and determining which SNOMED codes are accepted into NHSN.

 

Q9: What locations are eligible for AR Option Event reporting??

NHSN strongly encourages reporting specimens from all NHSN defined inpatient locations (including inpatient procedural areas like operating rooms) and three select outpatient locations: Emergency Department, Pediatric Emergency Department, and 24-hour Observation Area at each facility.

 

Q10: How can I remove missing AR Event data alerts?

The NHSN Alerts tell you that you haven’t yet submitted data for something listed in your Monthly Reporting Plan. The Missing Event alert is specifically telling you that you have reported AR Option summary data for those location/month(s), but you have not yet reported AR Events. Missing Event alerts will appear on the Missing Events tab of the alert screen as shown in the screenshot below:

A screenshot of the Missing Event alert screen that can appear.

 
To clear the Missing Event alerts, you will need to submit the AR event CDA files for the month(s) listed on your alerts screen. If you thought you had already uploaded these data, there is a good chance an error occurred during the original upload process and these specific files failed to import. During the re-submission process, make sure you pay special attention to any errors that may show up on the PDF submission report. Once you have uploaded these data, be sure to generate new datasets.

Alternatively, if there were no isolates that met the definition of an AR event for the given month(s) (see Q6 for AR Event criteria), you can click the “Report No Events” box for the month(s) in question on the Alerts screen. View our guide for more information on how to report no events pdf icon[PDF – 395 KB].

If you do not yet have AR event reporting from your vendor software set up, we request that instead of clicking the “Report No Events” box, you remove the AR Option check boxes on your Monthly Reporting Plan for the time being. Clicking the “Report No Events” box, tells NHSN that your facility identified no specimens that met the criteria for an AR event (in other words, a “true zero”). It would not be appropriate to “Report No Events” just because you were not quite ready to report AR events from your vendor software. See Q4 for how to edit the Monthly Reporting Plan.

 

Q11: How can I remove missing AR Summary data alerts?

The Missing Summary Data alert is specifically telling you that you have not yet reported AR summary records for those location(s)/month(s) listed in your Monthly Reporting Plan. Missing Summary alerts will appear on the Missing Summary tab of the alert screen as shown in the screenshot below:
 

A screenshot of the Missing Event alert screen that can appear.

 
To clear the Missing Summary Data alerts, you will need to submit the AR summary records (also known as the “denominator” data) for the month(s) listed on your alerts screen. If you thought you had already uploaded these data, there is a good chance an error occurred during the original upload process and these specific files failed to import. During the re-submission process, make sure you pay special attention to any errors that may show up on the PDF submission report. Once you have uploaded these data, be sure to generate new datasets.

Of note, beginning with January 2021, facilities should report AR Option summary records for their outpatient locations (Emergency Department, Pediatric Emergency Department, and 24-hour Observation Area) as applicable. These summary records report the number of patient encounters for each location/month. This feature was rolled out in the summer of 2021 and this functionality was backdated to apply for January 2021 forward. Facilities will notice AR Option Missing Summary Data alerts for these location types for 2021 and forward until the summary records have been uploaded. Since this is a newer feature, please reach out to your vendor to determine: 1) if these files are available for 2021 (some vendors are not supporting 2021 submission of AR Summary data for outpatient locations) and 2) if available, where they can be found. If your vendor confirms that these files will not be available for 2021, please edit your 2021 Monthly Reporting Plans to remove the check box in the AR Option column on the rows for the outpatient locations. See Q4 for how to edit the Monthly Reporting Plan. If these files are available, please upload them to clear the alerts.

 

Q12: How should date of admission be defined?

For the AUR Module, the number of admissions is defined as the aggregate number of admissions to any of the inpatient locations within the facility (facility-wide inpatient) starting on the first day of each calendar month through the last day of the calendar month. An admission is counted when the patient arrives in an NHSN designated inpatient location regardless of patient status (for example, inpatient, observation). Further, an admission to an inpatient unit is counted even if the patient is discharged that same calendar day. Please note, the admissions definition used in the AUR Module is different than the definition used in the NHSN MDRO/CDI Module.

Within the AR event file, the date of admission is the calendar date that the patient physically locates to an inpatient location. If the specimen was collected in an outpatient location (for example, Emergency Department), use the date of the patient arrives the outpatient location (date of encounter) for the admission date field in the AR event file.

 

Q13: I’m from a state health department. Could you tell me the names and NHSN OrgIDs of the facilities submitting AR data from my state?

Yes. NHSN’s updated Agreement to Participate and Consent allows the NHSN Team to share specific information with State & Local Health Departments for prevention purposes such as the NHSN OrgIDs and facility names of those submitting AU and/or AR data into NHSN. Please send your request to NHSN@cdc.gov.

For the purposes of disease surveillance and prevention, state, local, and territorial health departments can have a special Data Use Agreement (DUA) with the CDC, which allows them to gain access to NHSN data from the facilities in their jurisdiction. Facilities in your jurisdiction are automatically added to a Group through the DUA process and health departments do not have to wait for facilities to accept Confer Rights Template. You can find more information about the DUA process in the DUA Announcement.


CMS Reporting

Q14: Is reporting into the Antimicrobial Resistance Option required by Centers for Medicare and Medicaid Services (CMS)?

CMS has not included AUR Module reporting in the Hospital Inpatient Quality Reporting Program. However, the submission of data into the NHSN AU and AR Options via CDA is a part of the CMS Promoting Interoperability Program (formally known as Meaningful Use Stage 3, or MU3) for eligible hospitals as outlined on the NHSN Promoting Interoperability Program website. Currently, submitting data into the AUR Module is the only part of NHSN reporting that qualifies for Promoting Interoperability Program participation.

 

Q15: If my facility voluntarily submits data into the AR and/or AU Options, will NHSN share those data with CMS?

No. There are no CMS Quality Reporting Programs that include data submitted into the AR and AU Options. NHSN does not and will not share any AR and AU data your facility submits to NHSN with CMS.

 

Q16: We are currently only submitting AR Option data into NHSN, can we participate in the Promoting Interoperability Program (formally Meaningful Use Stage 3)? Does submitting only AR Option data meet submission requirements?

To get credit for participation in the CMS Promoting Interoperability Program, CMS requires facilities to submit data for both AR and AU Options. Keep in mind that for the calendar year of 2022, submitting AR and AU Option data is a bonus option for the Public Health Registry reporting requirement for the Promoting Interoperability Program.


Data Import

Q17: When is the deadline to upload AR Summary and AR Event CDA files into NHSN each month?

The AR Summary CDA file is a summary of the entire month and, as such, facilities should not submit the AR Summary CDA file to NHSN any earlier than the first day of the subsequent month. For example, a facility may upload October AR Summary data beginning November 1. NHSN recommends that facilities submit both AR Summary and AR Event data files to NHSN for a given calendar month by the end of the subsequent calendar month to make the data most actionable by your facility. However, facilities should wait at least seven calendar days following the end of the month before submitting AR Event data to ensure the lab completed all susceptibility testing and reported results to the electronic health record (EHR).

 

Q18: Can we submit AR and AU CDA files together in the same CDA zip file?

Yes, but for manual upload into the NHSN application, all 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, the application only allows alphanumeric, hyphen, and underscores in the CDA file names and zip file names. The application does not allow special characters in file or zip file names.

 

Q19: How do I know if all the CDA files I am submitting together in the same zip file were successfully uploaded into NHSN?

Sometimes, when you are batch uploading multiple AR files, some files will successfully upload, and others will not. Here is a screenshot of what it looks like when you submit files together and you have some records pass and others fail. Note that both the Error Report and Submit buttons are enabled:
 

Screenshot of when submitting files together and some records pass and others fail when batch uploading multiple AR files

 
If you click on the Events tab in the Validation Results table, you can see the files that passed and failed validation by looking in the Status column. In this instance, 13 records were submitted. Four passed validation and nine failed. When you click the Submit button, the application will only accept the four files that successfully passed validation. The PDF report generated after you click the Submit button will also show the file(s) that successfully imported and the files that did not pass NHSN validation and were therefore not imported.

Please view and save the PDF report for your records each time you import data into the AR Option. The NHSN Help Desk requires information from the PDF report to assist users with inquiries related to data import errors.

 

Q20: When I try to upload my AR files, I get an error message that says, “Antimicrobial Use and Resistance Module not followed for this month, year, and location.” What does that mean and how do I fix it?

If you receive this error for a specimen collected in an inpatient location, it means that you have not included FacWideIN for this month and year in the Antimicrobial Resistance portion of your Monthly Reporting Plan. If you receive this error for a specimen collected in a 24-hour Observation Unit, Emergency Department or Pediatric Emergency Department then you have not included that location for that month and year in the Antimicrobial Resistance portion of your Monthly Reporting Plan. Therefore, you’ll need to add the location(s) (either FacWideIN or the specific outpatient location) to the Antimicrobial Resistance portion of your Monthly Reporting Plan for every month you plan to submit AR data. NHSN will not accept any data that is out of plan. To edit your Antimicrobial Resistance monthly reporting plan, follow the steps in Q4. After you have edited your monthly reporting plan to include the AR data you are wanting to upload, NHSN should accept the CDA file for that month, year, and location.

If you have verified FacWideIN or the specific 24-hour Observation Unit, Emergency Department or Pediatric Emergency Department is on your monthly reporting plan, incorrect location information in your CDA file could be the cause of this error. See Q21 for details on location errors.

 

Q21: When I try to upload my AR files, I get an error message that says my location does not exist and I need to add it to my NHSN facility. I know my location is already in NHSN. What does this error mean?

The location in the CDA file must be the exact match of the “Your Code” value, “NHSN HL7 code” and location type of the values in the NHSN Location Manager. This error message is telling you that the location name used in your CDA file does not match a location currently mapped in your NHSN facility.

To see how your locations are mapped within NHSN, select Facility in the left-hand navigation bar and then Locations and Find. We suggest you reach out to your vendor to verify the location information in NHSN matches the information in the CDA files you are uploading.

 

Q22: 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, the NHSN application requires you to include specific drugs 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 F of the AUR Module Protocol pdf icon[PDF – 1 MB]. Work with your vendor to ensure the CDA file includes all required drugs. The CDA file must include all drugs in the specific panel regardless of whether the lab tested them.

 

Q23: How far back can we submit AR Option data?

Retrospective data submission is always encouraged! 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 2021 and it’s December 2021: they can add Monthly Reporting Plans with AUR Module locations back to January 2021 and hence submit AR Option data back to January 2021.
    • If the facility enrolled in January 2020 and it’s January 2022: they can add Monthly Reporting Plans with the AUR Module locations back to January 2021 and hence submit AR Option data back to January 2021.

Data Deletion

Q24: We noticed a mistake in our AR Summary record. Can I just resubmit the file?

There are two options for correcting AR Summary files:

  • 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 Location Code (for example, FACWIDEIN, Emergency Department), 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: Your vendor software may be able to automatically update AR summary files in NHSN using succession management. 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.

 

Q25: 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 you want to delete on the Event List table. Check the box in the Delete column next to the AR Event. 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: Your vendor software may be able to automatically update AR Event files in NHSN using succession management. 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

Q26: Do the 14-day (blood & CSF) and 1 per month (urine & lower respiratory) duplicate rules extend across calendar months?

Yes, 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 your facility can report another invasive source AR Event in 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

 

However, 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, report the first non-invasive source AR Event per month. Report no more than 1 non-invasive specimen per patient per organism 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

 

Q27: 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; Report AR Event 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; Report AR Event 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

 

Q28: Do the 14-day (blood & CSF) and 1 per month (urine & lower respiratory) 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 specimens collected in the reporting facility. Do not include specimens obtained while the patient was at another healthcare facility in the 14-day (blood & CSF) or 1 per month (urine & lower respiratory) calculations.

 

Q29: Do the 14-day (blood & CSF) and 1 per month (urine & lower respiratory) duplicate rules apply to multiple pathogens identified across a 14-day period?

No. The duplicate rules are specific to a single pathogen. If the laboratory identifies another pathogen, regardless of the specimen source or the date the previous pathogen was identified, this is not considered a duplicate event. The subsequent pathogens should be reported as AR events.

See the example below for clarification.

Table 4: Duplicate rule for non-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; Report AR Event into NHSN.
July 3 Escherichia coli isolated from blood culture in Medical Ward No It has been less than 14 days since the last positive culture (July 1) from the patient isolating E. coli.
July 3 Staph aureus isolated from blood culture in Medical Ward Yes Patient’s first blood culture of Staph aureus is isolated; Report AR Event into NHSN.

 


Laboratory Testing Results

Q30: Should I report preliminary antimicrobial susceptibility test results to NHSN?

No. You should report only final or corrected susceptibility testing results to NHSN. Do not report preliminary laboratory results for NHSN AR Option reporting. Facilities should wait at least seven calendar days following the end of the month before submitting data to ensure the lab completed all susceptibility testing and reported results back to the EHR.

 

Q31: If I’m not able to send susceptibility data for specific tests (minimum inhibitory concentration [MIC], E-Test, Kirby-Bauer [KB]), can I still participate in AR reporting?

Yes, facilities can still participate if they are still able to send the final interpretation provided by the lab for the given drug. NHSN requires the specific test result interpretations for MIC, E-Test, and KB are included in the AR Event CDA file. However, if your facility cannot send test-specific data, report these tests as “Not Tested” in the CDA file.

 

Q32: My laboratory suppresses some susceptibility test results. Can I still participate in the AR Option if I’m unable to send all susceptibility results?

Make every effort to report all antimicrobial resistance data that meets the NHSN protocol requirements regardless of whether those data are suppressed from clinical end users. However, if your facility cannot obtain and/or send suppressed data to the NHSN AR Option, NHSN will accept the data your facility is able to provide. Please be sure that your vendor is using ‘Not Tested’ for the unavailable tests/drugs. The NHSN application will not accept AR Event CDA files that do not contain all the required drugs for a given organism.

 

Q33: Should I report an isolate to the AR Option if all drugs tested were Susceptible?

Yes. Include all drugs in the specific organism’s drug panel in the AR Event file regardless of susceptibility results.

 

Q34: Should I report an isolate to the AR Option if my laboratory did not test for all required antimicrobials but did test at least one non-required drug?

Yes. Isolates where the laboratory did not test for all NHSN required antimicrobials but did test for at least one non-required antimicrobial are eligible for NHSN AR Option reporting. For example, if your laboratory tested a Staphylococcus aureus isolate for the non-required drug oritavancin, but not for any NHSN required antimicrobials, that isolate would still be considered eligible for reporting to the AR Option. In this case, your facility would report “Not Tested” for the required antimicrobials. 

 

Q35: Should I report an isolate if my laboratory did not perform any susceptibility testing?

No. Your facility must perform at least one antimicrobial test for an isolate to be eligible for inclusion in the AR Option. For example, if your facility does not routinely perform susceptibility testing on Candida albicans isolates from non-invasive sites, you would not include Candida albicans isolates from urine specimens in your AR event reporting. However, if a provider requested testing on a Candida albicans isolate and your laboratory performed at least one antimicrobial test, then this specific Candida albicans isolate from the urine specimen would be eligible for inclusion in the AR Option and should be reported regardless of the result of this test. 

 

Q36: If the laboratory reports additional information beyond required drugs in the NHSN drug panels, should I report those drugs to NHSN?

No. Do not report additional drugs to NHSN. NHSN will only accept the drugs listed in the specific organism’s drug panel.

 

Q37: If the penicillin-binding protein 2a (PBP2a) and/or polymerase chain reaction (PCR) mec-gene variables are not available from the electronic data for Staphylococcus aureus, should I still report this organism to NHSN?

NHSN requires that Staphylococcus aureus isolate CDA files include the PBP2a and PCR mec-gene test variables. However, facilities unable to electronically obtain the results of the PBP2a-agglutination and/or PCR mec-gene tests for Staphylococcus aureus may report “Unknown” for these specific tests in the AR Event CDA file.

 

Q38:  If my laboratory performs the same specific test (E-Test, MIC, KB) on the same isolate but they produce conflicting results, what should we report to the NHSN application for the final interpretation?

Report the final interpretation provided by the laboratory. If your laboratory provides no final interpretation, then report the most resistant interpretation (Not Susceptible [NS] > Resistant [R] > Intermediate [I] > Susceptible-Dose Dependent [S-DD] > Susceptible [S] > Not Tested [NT]). For example, if your laboratory performs two E-Tests for the same drug on the same isolate and one produces “Intermediate” (“I”) and the other produces “Susceptible” (“S”), report “Intermediate” (“I”) as the final interpretation for that specific drug susceptibility.

 

Q39:  If my laboratory performs multiple specific antimicrobial tests (E-Test, MIC, KB) on the same isolate and they produce conflicting results, what should we report to the NHSN application for the final interpretation?

Report the final interpretation provided by the laboratory. If your laboratory provides no final interpretation, 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” (“R”) and E-Test = “Intermediate” (“I”) but your laboratory provides no final interpretation, report “Resistant” (“R”) as the final interpretation for that specific drug susceptibility.

 

Q40: If two isolates from the same day have conflicting susceptibilities to the panel of antimicrobials tested, which isolate should I report?

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

For example, suppose the laboratory isolated Candida albicans from two blood specimens collected from the same patient on the same calendar day and provided no final interpretation. 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.

 

Q41: If my LIS does not differentiate between Penicillin G and Penicillin V, how should I report my penicillin susceptibility results?

If the LIS does not differentiate between Penicillin G and Penicillin V, list susceptibility results under Penicillin G and report Penicillin V as not tested.

 

Q42: If my LIS produces meningitis and non-meningitis breakpoint results, which should I report to the NHSN application?

If the LIS produces meningitis and non-meningitis breakpoint results, rely on the specimen source to determine which susceptibility results to report. If the specimen source is CSF, report the meningitis breakpoint susceptibility. If the specimen source is blood, urine, or lower respiratory, report the non-meningitis breakpoint susceptibility.

 

Q43: Will NHSN add the D-Test or other testing methods to the AR Option?

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


AR Summary Data

Q44: How do I count AR Option denominator data?

Report combined denominator data for all inpatient locations within the facility (FacWideIN) monthly. This includes patient days (the number of patients present in the facility at the same time on each day of the month, summed across all days in the month) and admissions (the number of admissions to an inpatient location in the facility each month). A patient is counted in the patient days and admissions count for the facility if they are physically located in an NHSN-defined inpatient location regardless of patient status (for example, inpatient, observation). Further, a patient admitted to an inpatient unit is counted as an admission even if they were discharged that same calendar day. Neither the FacWideIN patient days nor admissions denominators should include the counts from outpatient locations (ED, pediatric ED, and 24-hour observation area).

Beginning in 2021, facilities should also report AR Option denominator data from the outpatient locations included in their AR Option reporting plan (ED, pediatric ED, and 24-hr observation area). The number of outpatient encounters for the month for that location is included in each individual outpatient location AR Summary file. Each patient visit to the outpatient location counts as a single encounter. If the patient’s stay continues into a second calendar day, that patient should still only be counted as one encounter. If the patient is discharged, or leaves, then returns to that outpatient unit during the same calendar day, that patient should be counted as two encounters. If the patient transfers from one outpatient location to another within the same facility, that patient should be counted as one encounter for the first outpatient location and should not be counted as an encounter for the receiving location (specifically, encounters should not be counted more than once when patients transfer between outpatient locations in the same facility).  

 

Q45: How do I count patient admissions for AR 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 location regardless of patient status (for example, inpatient, observation). If the facility does not discharge the patient, then that stay is all part of that same admission, no matter how long. A stay that continues across multiple calendar months is still only one admission.

If the patient discharges and then returns on a separate calendar day, then count the patient as a new admission with a new admission date. If the patient discharges and then returns on the same calendar day, then do not count the patient as another admission since a single patient can only attribute 1 admission per calendar day to the monthly total.

 

Q46: 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. These location types report outpatient encounters only. Additionally, outpatient locations are not included in the FacWideIN patient day and admission counts.


AR Option Analysis

Q47: How do I view my AR Option data once I’ve uploaded it into NHSN?

Users can view AR Option data 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 webpage. Additionally, NHSN developed the Antimicrobial Resistance Event Line List pdf icon[PDF – 323 KB] and Antimicrobial Resistance Denominator Line List pdf icon[PDF – 394 KB] Quick Reference Guides to assist with viewing, modifying, and interpreting the AR Option event and summary data.

Remember to generate data sets within your NHSN facility before running your analysis reports so the data set includes any newly uploaded data. See question Q48 below for information on generating data sets.

 

Q48: 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 you generate a new data set within NHSN. The data set is a snapshot of the data currently in your NHSN facility during the time period specified when 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. See the Generating Datasets Guide pdf icon[PDF – 359 KB] for more information.

 

Q49: How do I read the AR Event Line List?

The Antimicrobial Resistance Event Line List report is an organized, detailed list of each record a facility reports into NHSN. You may have to modify the report by 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. Users can review the report to verify the data imported successfully and can also be helpful for data validation.

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

Screenshot of AR Event Line List report showing fictitious data and a description of how to read this report:

 
The Laboratory isolated Stenotrophomonas maltophilia from a patient’s cerebrospinal fluid collected in the MSICU on October 14, 2021. This isolate was resistant to cefiderocol, ceftazidime, chloramphenicol, levofloxacin, and minocycline. The laboratory did not test for sulfamethoxazole with trimethoprim. (Please note that data on this report are fictitious and for example only.)

You can find more information about the AR Event Line List in the Antimicrobial Resistance Event Line List quick reference guide pdf icon[PDF – 323 KB].

 

Q50: How do I read the AR Summary Line List? 

The AR Summary line list is a report summarizing denominator data reported into NHSN for FacWideIN and the individual outpatient locations. For FacWideIN, this includes data on patient days and admissions whereas outpatient encounters are reported for the outpatient locations. By default, this report also includes the “report no AR events” variable. Information on how to modify the AR summary line list, for example filtering by month or changing the variables displayed, is available in our AR Denominator Line List pdf icon[PDF – 394 KB] quick reference guide. NHSN has also developed a guide for more information on how to report no AR events pdf icon[PDF – 394 KB]. Below is an example AR Summary Line List report showing fictitious data and a description of how to read this report:
 

A screenshot of the AR Summary Line List report showing fictitious data and a description of how to read this report

 
This report includes the default variables included in the AR summary line list report. The first line shows that in January 2021 for FacWideIN, there were 5,241 patient days and 264 admissions. The second line shows in July 2021 for EMER, there were 375 patient encounters. The third line shows in July 2021 for FacWideIN, there were 2,350 patient days and 460 admissions reported. In January 2021, the Report No AR Event variable = N, indicating that there are AR Events reported for that calendar month. However, in both rows for July 2021, the Report No AR Event variable = Y, indicating that there were no AR Events to be reported for that calendar month and the facility checked the “Report No Events” boxes for both FacWideIN and EMER. (Please note that data on this report are fictitious and for example only.)

 

Q51: What validation checks should I conduct on my AR Option data?

NHSN provides guidance on recommended AR validation pdf icon[PDF – 400 KB]. Facilities implementing AR Option reporting and those facilities that have undergone a vendor system change can use this guidance. Facilities can also use this guidance on an annual basis for ongoing validation.

Suppression can lead to significant biases in the antimicrobial resistance data available for surveillance or infection control. Facilities should make every effort to report all antimicrobial resistance data that meet the NHSN protocol requirements, regardless of whether those data are suppressed from clinical end users. Review of AR Option data, including the steps outlined in the AR Validation guidance pdf icon[PDF – 400 KB] can be an important step in ensuring data reported to NHSN are complete and accurate.

 

Q52: Could you provide more details on the NHSN AR Option Facility-Wide Antibiogram calculation?

The NHSN Facility-wide antibiogram shows the organisms from the specimens reported into the AR Option for a specified time period of interest. It lists all antimicrobials and the percent of isolates that were susceptible (S) to the antimicrobial. Below is the calculation:

%S= Total # isolates STotal # of isolates tested  ×100

 

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

 

Q53: How do I read the NHSN AR Option Facility-Wide Antibiogram?

The facility-wide antibiogram table displays the calculated percent susceptible (%S) for each organism-antimicrobial combination for the time period of interest. Users can modify the antibiogram table to further customize this output. Additional information on the antibiogram is available in the antibiogram quick reference guide pdf icon[PDF – 537 KB].
Below is an example of a facility-wide antibiogram showing fictitious data and a description of how to read it:

Screenshot of a facility-wide antibiogram showing fictitious data and a description of how to read it

 
The column headers list the organism category and specific pathogen while the rows represent each antimicrobial, sorted by drug class. In this example, 49% of the Candida glabrata isolates tested were susceptible to fluconazole. 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 List of Antimicrobial Agents Eligible for AUR Moduleexcel icon spreadsheet, which is found in the Supporting Materials section of the AUR Module webpage. (Please note that data on this report are fictitious and for example only.)

 

Q54: How are AR events classified as community-onset (CO) or healthcare facility-onset (HO)?

NHSN automatically calculates AR event onset categorization based on the number of hospital days between the date the patient is admitted to the facility and the specimen collection date. Facility admission date is considered Day 1.

  • ≤ 3 days = community-onset (CO)
  • ≥ 4 days = healthcare facility-onset (HO)

The table below indicates the onset of an AR event collected on hospital days one through five.

Table 5: The table below indicates the onset of an AR event collected on hospital days one through five
Specimen collected on hospital day: AR event onset:
ED encounter CO
Day 1 (admission) CO
Day2 CO
Day3 CO
Day4 HO
Day5+ HO

 
Please note: any specimen collected in an outpatient location will be categorized as community-onset (CO).
 
Q55: : Where can I learn more about how to run, modify and interpret AR Option analysis reports?

Please visit the Analysis Resources section of the AUR webpage to access quick reference guides developed for all AR Option analysis reports.