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BIOMIC V3 antibiogram software for disk diffusion labs that need one M39 report across every AST method

BIOMIC V3 reads the disk diffusion and gradient strip tests your automated panel does not cover. That makes its results the ones most likely to be missing, or counted twice, when the annual antibiogram is put together.

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Short answer

BIOMIC V3 antibiogram software turns the disk diffusion results read on a Giles Scientific BIOMIC V3, together with the results from your automated AST system, into one cumulative antibiogram that follows CLSI M39. BIOMIC V3 has its own Cumulative Susceptibility and epidemiology reports, and they cover what BIOMIC holds. Labs add a dedicated tool when the report has to merge BIOMIC results with VITEK, MicroScan, Phoenix or Sensititre results, apply the first isolate and 30 isolate rules inside each cut, and open in a browser for pharmacy. Antimicrobe does that from a CSV export for $249 a month, bought by card.

Computed from your own isolates, never from a national average.

What BIOMIC V3 already does for your antibiogram

BIOMIC V3 is the Giles Scientific system, made in Santa Barbara, California, that images and reads antibiotic disk diffusion (Kirby-Bauer) plates and interprets them by CLSI or EUCAST. It also reads gradient MIC strips such as Etest, broth microdilution plates, API and RapID identification panels, chromogenic urine screens and colony counts. FDA cleared it in December 1994 under 510(k) K944319, product code KZK for automated zone readers, and Giles Scientific says it is the only automated zone reader to complete the FDA 510(k) review.

For reporting, Giles Scientific lists a set of epidemiology and antibiogram reports: Cumulative Susceptibility, Intrinsic Resistance, trend charts by susceptibility category and by zone diameter, zone diameter distributions, location, specimen and organism counts, and single drug and multi drug organism tracking. Custom report formats can be saved and reused. The expert system carries over 2,500 rules, and the March 2026 update loaded CLSI M100 36th edition and EUCAST v16.0 breakpoints.

So a lab that runs all of its AST on disk diffusion through BIOMIC already has a cumulative susceptibility report. The work starts when it does not, which describes most US hospital labs that own one.

Laboratory manager and pharmacist reviewing a cumulative antibiogram table together

Why BIOMIC results end up outside the hospital antibiogram

In most US hospitals the disk diffusion reader is not the main AST system. A 2016 survey of California clinical labs (Humphries and colleagues, Journal of Clinical Microbiology 2018) found 84 of 89 labs, 94.4%, performed AST exclusively on an automated system, and Giles Scientific itself describes BIOMIC V3 as used as both a primary and a secondary AST system. The secondary role is the common one: disk or strip tests for an agent the panel does not carry, a confirmation on a resistant isolate, or a fastidious organism.

Those are exactly the results a stewardship committee asks about. When the antibiogram is printed from the automated system's software alone, the BIOMIC results are not in it. When both are exported and simply added together, the same isolate counts twice.

How each automated system's own software handles the year is covered on VITEK 2 antibiogram software, MicroScan antibiogram software and BD EpiCenter antibiogram software. Broth microdilution plates run beside the panel have the same problem, see Sensititre antibiogram software.

  • Two databases. VITEK, MicroScan or Phoenix results sit in their own data manager, BIOMIC results in BIOMIC, and only the LIS has both
  • Duplicate isolates across methods. A Klebsiella tested on the panel and again by disk for one drug is one isolate, not two
  • Mixed methods for one drug. A drug read by MIC on most isolates and by zone on a few needs one interpretation per isolate, the one your lab released
  • Small counts. Agents tested only by disk on selected isolates rarely reach 30 isolates a year and must not print as a house-wide percentage

How to export antibiogram data from BIOMIC V3

The cleanest route for a mixed lab is the LIS. Giles Scientific lists a two-way ASTM LIS interface with Epic Beaker, Oracle Health (Cerner), MEDITECH, Sunquest and Data Innovations middleware. If BIOMIC results flow into the LIS, one LIS export for the year carries every AST method with the interpretation your lab released to the chart, and that is what the antibiogram should count.

If some results live only in BIOMIC, export them from BIOMIC as well. Giles Scientific offers custom data export formats and a WHONET export for WHONET 5.0 or later, and WHONET's BacLink lists BIOMIC among the disk diffusion readers it converts. For Antimicrobe, choose a delimited text export with patient identifier, specimen date, source, location, organism and the interpretation for each antibiotic, then save it as CSV. Antimicrobe applies the first isolate rule across both files, so a patient tested on two methods counts once.

Antimicrobe reads comma or semicolon separated files. The patient identifier is hashed before anything is stored, and a pseudonymous key works just as well.

What a good LIS export looks like is on laboratory information system exports.

  1. 1

    LIS or BIOMIC

    Export the year with every isolate, disk diffusion and automated panel results included

  2. 2

    CSV file

    Save as CSV, one file per source if the LIS does not hold both

  3. 3

    Antimicrobe

    Map sources and units once. First isolate, 30 isolate and intermediate rules applied across files

  4. 4

    Antibiogram

    House-wide, urine, blood and unit tables, disk-only agents flagged where counts are small

BIOMIC V3 reports and Antimicrobe compared

WHONET is the free route and works well for a lab with time to learn it. The practical differences are on the WHONET alternative page.

BIOMIC V3 from Giles Scientific product pages, Antimicrobe from its pricing page. Report behavior depends on how each lab set up BIOMIC.
Question BIOMIC V3 reports WHONET with BacLink Antimicrobe
Which results it sees Tests read on BIOMIC Any file you convert Any CSV you export, from BIOMIC, the LIS or other instruments
Merging several AST methods No Yes, after mapping each format Yes, de-duplicated across files
First isolate per patient Not stated by Giles Scientific, check your setup Yes, if configured On by default, counts before and after shown
Under 30 isolates Not stated Configurable Flagged, not printed as a percentage
Who can open it Staff with BIOMIC access Whoever has WHONET Seats for pharmacy and infection prevention
Cost Not published by Giles Scientific Free, paid in staff hours $249 a month on the Lab plan

Does the BIOMIC V3 cumulative susceptibility report follow CLSI M39?

It can, but check three things before you sign it. First, we found no Giles Scientific page, brochure or paper that says the Cumulative Susceptibility report applies the M39 first isolate rule, one isolate per patient per species per period whatever the source. Confirm how your BIOMIC handles repeat isolates.

Second, M39 asks that species with fewer than 30 isolates are not presented as a reliable percentage, which matters most for agents tested by disk only on selected isolates. Third, the report should use the interpretations your lab released, under current breakpoints. If a technologist edits a result in the LIS after BIOMIC read it, the BIOMIC database and the chart disagree, and the antibiogram should follow the chart.

Every Antimicrobe export prints a rule receipt listing the rules applied and the isolate counts before and after de-duplication, which is the page a CAP inspector or a new stewardship physician asks for.

The full rule set, rule by rule, is on CLSI M39 antibiogram software.

How accurate is BIOMIC V3 compared with manual reading?

The published comparisons are good. Korgenski and Daly (Journal of Clinical Microbiology 1998) found 4 false susceptible and 6 false resistant reads in 3,339 organism and antimicrobial combinations, 0.1% and 0.2%. Fader and colleagues (Journal of Clinical Microbiology 2013) compared BIOMIC disk reading with MicroScan WalkAway panels at hospital labs in Texas, Michigan and Ontario and reported category agreement of 98.4% for Gram-negative and 98.7% for Gram-positive organisms.

Reader accuracy is not the antibiogram's weak point. Counting is. The same accurate result becomes a wrong percentage when it is counted twice, counted under a repeat culture, or printed for a species with 12 isolates.

Which plan fits a BIOMIC V3 lab

A single hospital lab producing the annual house-wide report and source cuts needs the Lab plan, $249 a month for 1 facility, 25,000 isolates a year and 2 seats, with cuts by source and period, CLSI breakpoints and CSV and print exports. It is bought by card and there is no implementation fee.

A stewardship program that wants unit cuts, syndrome groups, quarterly trends and MDRO counts uses Stewardship at $749 a month for up to three facilities. A reference or public health lab that reads plates on BIOMIC for client facilities fits Network at $2,400 a month for up to 12 facilities.

Every limit is on the pricing page. Labs reporting for outside facilities will find the per-client setup in antibiogram software for reference labs.

What this does not do

  • It does not connect to BIOMIC V3 directly. It reads exported files, as often as you choose to export them
  • It does not read zone diameters or MIC values or reinterpret them. It uses the S, I and R your lab released, so breakpoint changes are made in BIOMIC and the LIS
  • It does not replace BIOMIC for plate reading, the expert rules or QC
  • It is for human clinical antibiograms, not veterinary breakpoints
  • It does not submit to NHSN or any public health system

Related reading: CLSI M39 antibiogram software, Sensititre antibiogram software, MicroScan antibiogram software, VITEK 2 antibiogram software, WHONET alternative. The four steps from susceptibility testing data to an antibiogram cover the method end to end.

Questions

On this page's topic

Can BIOMIC V3 generate an antibiogram?

Yes. BIOMIC V3 includes a Cumulative Susceptibility report and other epidemiology reports, and custom formats can be saved for reuse. They cover the tests read on BIOMIC, so check the duplicate isolate setting and the 30 isolate threshold before you publish, and merge in your automated panel results if BIOMIC is not your only AST method.

How do I get BIOMIC results into my hospital antibiogram?

Export the year from the LIS if BIOMIC results are interfaced there, because one file then holds every AST method. If they live only in BIOMIC, export them separately as delimited text and combine both files in a tool that de-duplicates patients across files, so an isolate tested two ways counts once.

Is BIOMIC V3 FDA cleared?

Yes. The BIOMIC Microbiology Data Management System was cleared by FDA in December 1994 under 510(k) K944319, product code KZK for automated zone readers. Giles Scientific says it is the only automated zone reader to complete the FDA 510(k) review.

Can I use WHONET with BIOMIC V3?

Yes. BIOMIC V3 exports results to a file that WHONET 5.0 or later opens, and WHONET's BacLink lists BIOMIC among the disk diffusion readers it converts. WHONET is free on Windows. The cost is the setup time and rebuilding the report layout each year.

Which breakpoints does BIOMIC V3 use in 2026?

The March 2026 update loaded CLSI M100 36th edition and EUCAST Breakpoint Tables v16.0. The antibiogram should still count the interpretation your lab released, so a breakpoint change made in BIOMIC but not in the LIS shows up as a mismatch.

How much does antibiogram software for a BIOMIC lab cost?

Antimicrobe's Lab plan is $249 a month for one facility, bought by card with no implementation fee, and it reads BIOMIC, LIS and other instrument exports. Unit cuts and up to three facilities are on the Stewardship plan at $749 a month.

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