Antibiogram software for microbiology labs, instrument data managers, WHONET, Excel and a dedicated report compared
Most microbiology labs already own something that can print an antibiogram: the data manager that came with the AST instrument. Whether that is enough depends on where your results live, who has to read the report, and how many hours the annual build takes.
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Antibiogram software for a microbiology lab comes in four forms: the data manager sold with your AST instrument (bioMerieux Observa for VITEK 2, BD EpiCenter for Phoenix, the LabPro Antibiogram Export Tool for MicroScan), WHONET, an Excel workbook, or a dedicated antibiogram tool that reads an export from the LIS. Instrument software is already paid for but only sees what that system tested. A dedicated tool such as Antimicrobe works from the full LIS export and starts at $249 a month.
This is written for the microbiology supervisor or lab manager who owns the annual cumulative antibiogram and is deciding whether to keep building it the current way. Vendor capabilities come from each vendor's own public product pages, read in September 2026.
Antibiogram software for microbiology labs, side by side
The useful comparison is not features in the abstract. It is which isolates each option can see, whether it applies CLSI M39 rules for you, and who ends up doing the work every spring.
| Option | Isolates it sees | Antibiogram output | Who does the work | Cost |
|---|---|---|---|---|
| bioMerieux VITEK 2 with Observa | Results stored from VITEK 2 and VITEK 2 Compact | Epidemiology and statistical reports, data export | Lab staff, inside the instrument software | Bundled with the instrument contract |
| BD Phoenix with EpiCenter | BD systems; the PLUS configuration adds manual testing | On-demand antibiogram generation, custom alerts for CPO, VRSA, ESBL | Lab staff | Bundled with the instrument contract |
| Beckman MicroScan with LabPro | LabPro Information Manager data | Antibiogram Export Tool: an Excel template you finish yourself | Lab staff, in Excel | Tool downloadable for customers |
| WHONET | Whatever you import through BacLink | Full antibiogram analysis | The one person who learned WHONET | Free, Windows 10 and 11 only |
| Excel | Whatever you paste in | Whatever you build | A microbiologist or pharmacist, by hand | Staff hours |
| Antimicrobe | Every row in the LIS susceptibility export | M39 style antibiogram, source and unit cuts, trends, empiric rankings | Whoever runs the export | $249 to $2,400 a month, published |
What the instrument data manager already gives you
Start with what you own. bioMerieux says the VITEK 2 data management software, with its bidirectional LIS interface, allows generation of epidemiology reports and antibiograms, and that Observa stores VITEK 2 test data and formats it into epidemiology and statistical reports, with export for analysis elsewhere. BD says EpiCenter interfaces with the Phoenix M50 and provides on-demand antibiogram generation, plus custom alerts for critical results such as CPO, VRSA and ESBL. Beckman Coulter gives MicroScan customers an Antibiogram Export Tool, an Excel template for data transferred out of the LabPro Information Manager, which you then turn into your own report and charts.
For a lab where nearly every susceptibility result comes off one instrument and the antibiogram goes to one committee once a year, that can be enough. It costs nothing extra, the data never leaves the lab, and the techs already know the software.
Phoenix labs that want the EpiCenter export steps and the settings to check before trusting its antibiogram report will find them on BD EpiCenter antibiogram software. VITEK labs will find the MYLA and OBSERVA equivalent on VITEK 2 antibiogram software, and MicroScan labs the LabPro export and Excel template comparison on MicroScan antibiogram software.
Where instrument software stops being enough
Problems show up at the edges of what the instrument saw. Disk diffusion and gradient strip results for fastidious organisms, reference lab send-outs, and anything run on a second platform after a lab consolidation are usually in the LIS but not in one instrument's database. EpiCenter's PLUS configuration handles manual testing, but a lab running VITEK in one building and Phoenix in another still has two databases and one antibiogram to publish.
The second gap is the reader. Stewardship pharmacists want the report cut by unit, by specimen source and by quarter, and they want the ICU and urine numbers separated from the facility-wide table. Instrument reports are built around the lab's view of its own results. When the pharmacy asks for a urine-only table for 4 West, the request usually ends in an export and an Excel afternoon.
The third gap is M39 discipline. First isolate per patient per organism per period, and suppressing or flagging cells with fewer than 30 isolates, are the two rules that most change the numbers. Check how your data manager applies them, and whether anyone outside the lab can see that it did.
Is WHONET good enough for a US hospital lab?
WHONET is capable and free, and many labs produce a correct antibiogram with it. The costs are practical: it runs only on Windows 10 and 11, it is a single-user desktop program, and BacLink has to be configured to your LIS export and reconfigured whenever that export changes. In most labs one person knows how it works, which makes the annual report a single point of failure.
We compare the two in detail on the WHONET alternative for the cumulative antibiogram page, including who should keep WHONET.
How a CSV-based antibiogram tool fits the lab
Antimicrobe starts from the export your LIS already produces for the annual report. It needs seven fields: a patient key, the collection date, the specimen source, the unit, the organism, the antibiotic and the S, I or R result. MIC values are used where present and never required. Column names differ between systems, so they are detected and shown back to you for confirmation instead of forcing the export into a template.
From that file it keeps the first isolate per patient per organism per period and shows the count before and after, marks cells under 30 isolates instead of dropping them, and uses your lab's own reported interpretation by default. The output is the facility antibiogram, cuts by source and period (and on the Stewardship plan by unit and syndrome, with quarterly trends), and a print sheet that names every cut applied. Because it reads the LIS export, it sees instrument, manual and send-out results in one table.
The export itself is covered on the laboratory information system integration page, and the breakpoint handling on CLSI and EUCAST breakpoints.
How much does antibiogram software cost for a lab?
Instrument data managers are usually priced inside the instrument, reagent or service agreement, so there is no separate line to compare. WHONET and Excel cost staff hours rather than a license. Dedicated antibiogram software is the one category with a public number: Antimicrobe's Lab plan is $249 a month for one facility, 25,000 isolates a year and two seats, bought by card on the website.
The full breakdown, including enterprise surveillance platforms, is in what antibiogram software costs, and every plan limit is on the pricing page. Labs that also produce reports for nursing homes and clinics they serve should read antibiogram software for reference labs.
Questions to answer before you choose
Run through these with the pharmacy lead in the room, because they are the report's main reader.
Labs that answer yes to the last two usually also have a staffing problem to solve: tracking the CLIA competency assessments each testing person needs is easier with a training and certification platform than with a binder. For the antibiogram itself, try the builder at the top of this page with last year's export, then compare the output with what went to the committee. The finished format is shown on the hospital antibiogram page, and the pharmacy-side view of the same options is in best antibiogram software for hospitals.
- What share of last year's susceptibility results came off the primary instrument, and what share was manual or sent out?
- Does the current report apply first isolate de-duplication, and can a non-lab reader see the before and after counts?
- Who asked for a unit or source cut last year, and how long did it take to produce?
- If the person who builds the antibiogram left in March, could anyone else publish it on time?
- Will a new instrument or LIS in the next two years break the current method?
Related on this site: Sunquest LIS antibiogram software, WHONET alternative for the cumulative antibiogram, laboratory information system exports, antibiogram software cost, hospital antibiogram software.