Best antibiogram software for hospitals, compared by who does the work, M39 fit and cost
There are eight realistic ways for a US hospital to produce its cumulative antibiogram, from a free WHO program to a six-figure surveillance platform. Here is what each one asks of your staff, how well it follows CLSI M39, and what it costs.
9 min read
The best antibiogram software for most US hospitals is the option that applies the CLSI M39 rules for you and puts the report in front of pharmacy without a lab analyst rebuilding it each year. WHONET and Excel are free but cost staff hours. Instrument and LIS reports are included but hard to audit. Enterprise platforms do far more and cost far more. A dedicated tool sits in between, from $249 a month.
This comparison is written for the pharmacy director, stewardship pharmacist or lab manager who has been told the antibiogram is late again and has to decide what to change. Each option is described from its maker's published material or a peer-reviewed paper, named inline so you can check it.
What separates good antibiogram software from the rest
Every option on this list can print a table of percent susceptible. The differences show up in four places, and they are the questions a CAP inspector, a new infectious diseases physician or a stewardship committee eventually asks.
The full rule set, rule by rule, is on CLSI M39 antibiogram software.
- The first isolate rule. CLSI M39 counts the first isolate per patient per species in the period, whatever the specimen source. Removing repeats by accession or by susceptibility pattern instead gives different numbers, by minus 11 to plus 25 percent on the same data in one study (White and colleagues, Diagnostic Microbiology and Infectious Disease, 2001)
- Small counts. Species with fewer than 30 isolates should not get a printed percentage, or should be clearly marked
- Cuts done properly. A urine, ICU or outpatient table has to be de-duplicated inside that cut, not filtered from the house-wide list
- A reader outside the lab. Pharmacy and infection prevention need to open it, and ideally see how it was built
Antibiogram software options compared
| Option | Who does the work | M39 rules | Cost |
|---|---|---|---|
| Excel by hand | A pharmacist or lab analyst, every year | Only if the builder applies them | Staff hours |
| WHONET | A trained analyst on a Windows PC | Analysis options, set by the user | Free, plus conversion time |
| Instrument software (EpiCenter, MYLA, LabPro) | The lab, inside the vendor system | Depends on report setup | Included with the instrument |
| LIS or EHR report (Epic, Oracle Health, MEDITECH) | An analyst or report writer | Depends on the build | Analyst hours |
| Power BI or another BI tool | A data analyst with SQL and DAX | Built in by the analyst | BI license plus build time |
| Enterprise platform (Sentri7, TheraDoc, VigiLanz) | The vendor feed, then pharmacy | Check the module | Quoted, not published |
| Antimicrobe | The software, from an export | On by default, with a rule receipt | From $249 a month |
The options one by one
Excel is where most small hospitals start, and plenty stay there. It works when one person knows the method and has the time in January. It breaks when that person leaves, when someone asks for an ICU table, or when the medical staff asks how repeats were removed and nobody wrote it down.
WHONET is free desktop software from the WHO Collaborating Centre, and it is the most capable free option. It applies the first isolate rule as an analysis option and handles any data you can convert with its BacLink utility. The cost is the analyst: learning it, converting the export each year and rebuilding the layout the committee expects. It runs on Windows only.
Instrument software comes with the AST system. BD EpiCenter, bioMérieux MYLA and OBSERVA, and Beckman Coulter LabPro all print antibiogram reports, and Beckman also offers a free Excel Antibiogram Export Tool. They see only the results that ran on that vendor's instruments, and their report settings are often configured once and never checked again.
LIS and EHR reports pull every released result, which is their advantage. Epic hospitals usually build one in Beaker Reporting Workbench or Clarity, and Oracle Health and MEDITECH hospitals in their own report tools. The duplicate logic is whatever the report writer built, so it needs a check against M39 before anyone relies on it.
Power BI is a growing route at hospitals with a data team. A group presenting at SHEA Spring 2023 (Dauphin and colleagues, Antimicrobial Stewardship and Healthcare Epidemiology) built a dynamic CLSI-compliant antibiogram in Power BI from SQL feeds, using DAX and M code, and validated it against OBSERVA. Updating it each year became a refresh. Their validation also found discrepancies from cascade reporting that had to be resolved first, which is the hidden cost of building it yourself.
Enterprise surveillance platforms such as Wolters Kluwer Sentri7, Premier TheraDoc and VigiLanz do real-time alerting, intervention tracking, infection surveillance and NHSN reporting, and an antibiogram is one module among many. They are priced as platforms, by quote, with an implementation project. Nobody buys one only for the antibiogram.
The instrument routes are compared step by step on BD EpiCenter, VITEK 2 and MicroScan antibiogram software. WHONET has its own page, WHONET alternative, and the Epic route is covered in antibiogram software for Epic hospitals.
Two more you will come across
Firstline is a clinical decision support app that hospitals use to publish their local guidelines and antibiogram to prescribers on the phone and the web. It distributes an antibiogram well, but the numbers still come from whichever option above your lab uses to calculate them.
The University of Nebraska Medical Center developed an automated, real-time antibiogram that it uses in house and offers for licensing through UNeMed, its technology transfer office. It is a university technology rather than a packaged product, so expect a licensing conversation and your own IT project.
Which antibiogram software is best for a small hospital?
For a hospital under about 200 beds without a data analyst, the best option is usually a dedicated tool or WHONET, not an enterprise platform. Small hospitals have few isolates, so the 30 isolate rule and pooling years matter more than real-time alerts, and the person who builds the report is often also the only stewardship pharmacist.
If that pharmacist has time to learn WHONET, it is free and sound. If not, a dedicated tool removes the yearly rebuild. A critical access hospital meeting the CMS stewardship condition of participation has the same choice with even fewer isolates.
Small and rural hospitals will find pooling options and costs on critical access hospital antibiogram software.
How much does antibiogram software cost?
Antibiogram software runs from free to six figures, but free routes are paid in staff time. WHONET, Excel and instrument reports carry no license fee. Enterprise platforms are quoted per hospital with an implementation fee and are rarely bought for the antibiogram alone. Antimicrobe is the published price in the category: $249 a month for one facility, $749 for up to three with unit cuts.
For a budget request, count the hours. If a pharmacist or analyst spends a few weeks a year building, checking and reformatting the report, that time is the real price of the free routes, and it recurs every year.
The full breakdown by route, including implementation fees and EHR build hours, is in antibiogram software cost.
Where Antimicrobe fits
Antimicrobe builds the cumulative antibiogram from the susceptibility export your lab already produces, from the LIS or from instrument software. It applies the first isolate, 30 isolate and intermediate rules by default, de-duplicates each cut on its own, and prints a rule receipt with the counts before and after. Pharmacy and infection prevention open it in a browser, and it ranks empiric options by local susceptibility.
The Lab plan is $249 a month for one facility, 25,000 isolates a year and two seats, bought by card with no implementation fee. Stewardship, at $749 a month, adds unit cuts, syndrome groups, quarterly trends and MDRO counts for up to three facilities.
It is not an enterprise platform. It does not send real-time alerts, track interventions, run infection surveillance or submit to NHSN. A hospital that needs those needs a platform, and may still use a dedicated tool for the antibiogram itself.
What the full report includes is on hospital antibiogram software, and every plan limit is on the pricing page.
Stewardship is the plan to compare against quotes for antimicrobial monitoring software on the resistance side: the same export, refreshed each quarter, with trends and MDRO counts by unit.
How to choose
That last point is where hospitals often slip. The antibiogram, the annual stewardship report and the committee minutes are separate deadlines with separate owners, and compliance management software that tracks each obligation against the CMS and Joint Commission requirement it satisfies stops the antibiogram from being the item nobody remembered until the survey.
- If you already pay for Sentri7, TheraDoc or VigiLanz, check its antibiogram module against the four M39 points before buying anything else
- If you have a data team and Power BI, building it yourself is realistic, so budget for validation, not just the build
- If one pharmacist owns the report and has no analyst, choose WHONET or a dedicated tool, depending on whether they have time to learn WHONET
- If the antibiogram has to serve several facilities or outreach clients, choose an option that keeps each facility separate and comparable
- Whatever you choose, keep the method written down, because the antibiogram is one of several stewardship obligations a survey will ask about
Questions to ask any antibiogram software vendor
- Which duplicate rule do you apply by default, and can I see the isolate counts before and after?
- What happens to a species with fewer than 30 isolates?
- When I cut by unit or specimen source, is each cut de-duplicated on its own?
- Which results do you see: everything the lab released, or only what one instrument produced?
- Who can open the report outside the lab, and what does a seat cost?
- What is the full first-year cost, including implementation?
Related on this site: CLSI M39 antibiogram software, antibiogram software cost, WHONET alternative, antibiogram software for microbiology labs.