Antibiogram software for Epic hospitals, when the Beaker antibiogram report is enough, and when to buy a separate tool

An Epic hospital has three ways to get a cumulative antibiogram: the antibiogram report in Beaker's Reporting Workbench if Beaker is your lab system, a custom Clarity or Caboodle report built by your analysts, or a separate antibiogram tool fed by an export from Beaker or the micro instrument. The Epic routes cost no new license. They cost analyst time, and the report is only as good as its de-duplication and suppression logic.

This is written for the stewardship pharmacist or microbiology lead at an Epic hospital who has been told "Epic can do that" and now owns an antibiogram that takes a week of cleanup every year. Epic is described here only from published hospital experience and implementation guidance, because Epic does not publish its build documentation publicly.

What Epic actually gives you for the antibiogram

If your microbiology lab runs on Beaker Clinical Pathology, susceptibility results are stored in Epic with CLSI interpretations, and Beaker implementation guides describe pre-configured Reporting Workbench reports for antibiogram statistics alongside turnaround time and critical value reports. The same guidance adds a warning worth repeating to your lab director: build analysts have to validate that the report queries return accurate data, not only that the reports exist, because a report with the wrong denominator logic produces misleading numbers.

The stewardship side is a separate build. Johns Hopkins described its Epic antimicrobial stewardship module in the American Journal of Health-System Pharmacy in 2021: customized alerts and scoring to triage patients, an intervention database, and workbench reports developed for stewardship needs. Their conclusion was that customizing a stewardship module in an EHR requires significant time and expertise in antimicrobials. Epic's certification page lists Bugsy Infection Control as certified for NHSN antimicrobial use and resistance reporting, which covers AUR, not the annual antibiogram.

If your micro lab runs a different LIS and only sends results into Epic, the antibiogram report in Beaker is not yours to use. The data for the antibiogram lives in the lab system, and the Epic question becomes whether anyone will build a Clarity report on results that arrived by interface.

Whether to build the stewardship alerts in Epic at all, or buy Sentri7, VigiLanz or TheraDoc instead, is covered in Epic antimicrobial stewardship module vs third-party tools. The infection prevention version of that question is in Epic Bugsy alternatives.

Five checks your Epic antibiogram report has to pass

Most complaints about an EHR-built antibiogram trace back to a handful of rules from CLSI M39, the standard for cumulative susceptibility reports. Run your current report against these before deciding whether to rebuild it, replace it or leave it.

• First isolate per patient per organism per period, across specimen types. Counting every positive culture inflates resistance, most visibly in ICU patients cultured repeatedly
• No percentage printed under 30 isolates. A small cell should show the count or be pooled, not a %S that swings 20 points between years
• Cuts that match how people prescribe: urine versus non-urine, inpatient versus outpatient, ICU versus ward
• A stated rule for intermediate results and for organisms tested only on request, so a narrow panel does not look like a sensitive organism
• The breakpoint version printed on the report, because a CLSI revision can move %S with no change in the bugs

Antibiogram options for an Epic hospital, side by side

Routes as a US Epic hospital would compare them. Epic routes described from published hospital experience and implementation guidance; Antimicrobe prices from its pricing page.

Route	Who builds and maintains it	M39 first isolate and suppression	Cost
Beaker Reporting Workbench antibiogram report	Lab and Beaker analysts, validated after go-live	Depends on how the report was built and validated	No new license, analyst hours
Custom Clarity or Caboodle report	Report writers in IT, on the analytics queue	Whatever the specification says	No new license, weeks of analyst time
Epic stewardship module	Pharmacy analysts plus stewardship team	Worklists and use reports, not the cumulative report	Licensed through Epic, significant build time
WHONET fed by a Beaker export	The pharmacist or microbiologist, on one Windows PC	Yes, once configured	Free software, your hours
Antimicrobe fed by a Beaker or instrument export	The stewardship team, in a browser	Yes, applied automatically with counts shown	$249 a month (Lab) or $749 (Stewardship)

Is the Epic antibiogram good enough for CLSI M39?

It can be. An Epic antibiogram meets CLSI M39 when its query keeps the first isolate per patient per organism in the period, suppresses cells under 30 isolates, states how intermediate results are handled, and prints the breakpoint version. Whether yours does depends on how it was built and validated, so ask your analyst to show the de-duplication logic, not the output.

A quick test: pull the report's E. coli urine row, then count unique patients with an E. coli urine isolate in the same year from a line list. If the report's isolate count is much higher than the patient count, it is counting repeats.

How much does it cost to build an antibiogram in Epic?

There is usually no license fee, because the hospital already owns Beaker or Clarity. The cost is analyst time: writing or fixing the query, validating it against a manual count, and redoing that validation after upgrades and breakpoint changes. At a community hospital the bigger cost is the queue. A stewardship report request competes with every clinical build, and a fix requested in March can arrive after the antibiogram was due.

Teams with their own report writers sometimes prototype the Clarity query with a tool that can turn plain-English questions into SQL, then hand the draft to IT for review. That shortens the specification, but the M39 rules still have to be written into it and maintained. For the full cost picture across routes, see how much antibiogram software costs.

Running a separate antibiogram tool beside Epic

The pattern that avoids the build queue is simple. Keep Epic for what it does well: orders, alerts, stewardship worklists and AUR. Take a susceptibility line list out of Beaker or the instrument data manager once a quarter or once a year, and build the antibiogram in a tool whose only job is applying the M39 rules the same way every time.

With Antimicrobe that line list is a CSV with one row per isolate and antibiotic: patient or MRN, collection date, specimen source, unit, organism, antibiotic and S, I or R. Common export column headings are recognized automatically. The patient identifier is hashed on upload and never stored, because the first-isolate rule only needs a consistent key. The builder at the top of this page runs the same engine on sample data, so the committee can see the output format before anyone signs anything.

The export mechanics for Beaker and other lab systems are on the LIS integration page, and the finished report format on the hospital antibiogram page. Hospitals comparing this with a full surveillance platform should read the Sentri7 alternatives comparison, since several of those platforms interface with Epic as well.

Which route fits which Epic hospital

A large academic center with Beaker, an analyst assigned to the lab and a microbiologist who owns the report should keep the antibiogram in Epic and invest in validating it. That is the cheapest route when the people exist.

A 100 to 400 bed community hospital on Epic, often on a Community Connect instance run by a larger partner, usually does not control the build queue. For that hospital a $249 a month tool fed by a quarterly export is cheaper than the analyst hours, and the report comes out the same way every year. A multi-hospital Epic system that wants every facility on one rule set is a Network plan conversation.

Community hospitals building a full shortlist can start with the best antimicrobial stewardship software for community hospitals, and critical access hospitals on a partner's Epic instance with the critical access hospital antibiogram page. Hospitals on MEDITECH face the same queue with a SQL Server Data Repository instead of Clarity, covered in antibiogram software for MEDITECH hospitals, and Oracle Health hospitals with a Discern Explorer queue in antibiogram software for Cerner hospitals.

Questions to ask your Epic analyst before buying anything

• Is our micro lab on Beaker, or does another LIS send results into Epic?
• Does the antibiogram report keep the first isolate per patient per organism, and in what period?
• Does it suppress cells under 30 isolates, or print every percentage?
• Which CLSI breakpoint version does it apply, and who updates it?
• When was it last validated against a manual count, and how long would a change request take?
• Can it export a line list we could use elsewhere if the answer to the last question is months?

---

Related on this site: LIS susceptibility export, hospital antibiogram software, CLSI and EUCAST breakpoints, critical access hospital antibiogram.