For VITEK 2, MYLA and OBSERVA labs
VITEK 2 antibiogram software that turns MYLA and OBSERVA exports into an M39 antibiogram the pharmacy can cut by unit
Your VITEK 2 already produced every MIC and interpretation the antibiogram needs. The hard part is the year-end report: repeat isolates, results that never ran on the VITEK, and a stewardship pharmacist asking for urine and ICU tables before the committee meets.
Try the builder on the sample data, or drop in your own CSV. It is parsed in your browser and never uploaded.
Short answer
VITEK 2 antibiogram software takes the susceptibility results your bioMérieux VITEK 2 instruments store in MYLA or OBSERVA and turns them into a cumulative antibiogram that follows CLSI M39. Both data managers can print statistical reports on their own. Labs add a dedicated tool when the report has to include results the VITEK never produced, be cut by unit and specimen source, or show the medical staff which rules were applied. Antimicrobe builds it from a MYLA, OBSERVA or LIS export for $249 a month, bought by card.
What MYLA and OBSERVA already do for your antibiogram
bioMérieux sells two data managers that sit behind the VITEK 2. OBSERVA is the older one. bioMérieux describes it as an information management system that stores the test data generated by the VITEK 2 or VITEK 2 Compact and formats it into epidemiology and statistical reports. It is not offered on the VITEK 2 Compact 15, which matters for small labs that bought the smallest instrument.
MYLA is the current middleware. It runs in a browser, connects several bioMérieux instruments (VITEK 2, VITEK MS, BACT/ALERT VIRTUO) and the LIS, and includes a Statistical Reporting Module. bioMérieux also sells MYLA Lab Analytics, an add-on that layers business intelligence charts over that module, and its brochure talks about institutional surveillance of antimicrobial resistance and tracking resistance trends.
So a VITEK 2 lab is not short of reports. What it is often short of is a report that matches the current CLSI M39 rules, includes every result the lab released, and reaches the people who use it without a login to the lab middleware.
Where a VITEK 2 antibiogram falls short
The VITEK 2 is rarely the problem. The gaps sit where the instrument database meets the rest of the lab.
The full rule set, and how each route handles it, is on CLSI M39 antibiogram software. How labs weigh the instrument data manager against WHONET and Excel is covered in antibiogram software for microbiology labs.
- Results the VITEK never produced. Disk diffusion and gradient strips for fastidious organisms, reference lab send-outs and anything tested on a second AST platform usually exist only in the LIS, so a report run from MYLA or OBSERVA leaves them out
- Instrument results versus released results. The Advanced Expert System flags and corrects implausible results, and technologists edit others before release. The antibiogram has to follow what was released to the chart. If edits are made in the LIS and not in the middleware, the two disagree
- A duplicate rule nobody has checked. M39 keeps the first isolate per patient per species in the period, whatever the specimen source. A statistics report that removes repeats by accession or by susceptibility pattern gives different numbers. White and colleagues (Diagnostic Microbiology and Infectious Disease, 2001) found differences of minus 11 to plus 25 percent on the same data
- Cuts made in the wrong order. A urine or ICU table has to be de-duplicated inside that cut, not filtered from the house-wide list after de-duplication
- Query limits. The WHONET guide for OBSERVA notes a maximum of 4,000 samples per export query, so a full year comes out in monthly pieces that someone has to stitch together
- The reader is outside the lab. Pharmacy and infection prevention want urine, blood and unit tables plus a quarterly trend, and they do not work in MYLA
How to export antibiogram data from VITEK 2
From OBSERVA, the route is documented in WHONET's BacLink guide for the VITEK OBSERVA system. An administrator creates the report once under File, Configuration, Reports, New, as a List Report named WHONET, and adds the fields: accession number, patient identifier, collection date, specimen site, location, organism, antibiotic, final MIC and interpretation. To run it, open Reports, Data Management, Search for Specimens by Data Collected, enter a date range, run the report in that format and export it as a text file. Because of the 4,000 sample limit per query, a busy lab runs it month by month.
From MYLA, use the Statistical Reporting Module or ask your MYLA administrator for a line-level export of AST results for the year. WHONET's BacLink also lists a MYLA format, which tells you the data is exportable at line level. If a meaningful share of your results never runs on the VITEK, export from the LIS instead.
Antimicrobe reads the file once it is saved as CSV. It needs a patient identifier, collection date, specimen source, unit, organism, antibiotic and the S, I or R your lab released. The patient identifier is hashed before anything is stored, and a pseudonymous key works just as well. If the export has one column per antibiotic rather than one row per result, the mapping is set up once during onboarding.
What a good LIS export looks like, including wide files from Epic Beaker and Cerner, is on laboratory information system exports.
-
1
MYLA or OBSERVA
Run the line-level AST export for the year, month by month on OBSERVA
-
2
Text or Excel file
Combine the months and save as CSV
-
3
Antimicrobe
Map sources and units once. First isolate, 30 isolate and intermediate rules applied
-
4
Antibiogram
House-wide, urine, blood and unit tables, each with a rule receipt
MYLA, WHONET and Antimicrobe compared
WHONET is free and many VITEK labs keep it for this job. The practical differences, including running it on a Mac, are on the WHONET alternative page. Labs with BD Phoenix instruments will find the same comparison on BD EpiCenter antibiogram software, and MicroScan labs on MicroScan antibiogram software.
| Question | MYLA or OBSERVA reports | WHONET with BacLink | Antimicrobe |
|---|---|---|---|
| Which results it sees | bioMérieux instruments connected to it | Whatever you export and convert | Whatever you export, from the middleware or the LIS |
| First isolate per patient | Depends on the report definition, check it | An analysis option | On by default, counts before and after shown |
| Fewer than 30 isolates | Depends on the report definition | You filter the output | Suppressed and marked, threshold is a setting |
| Unit and source cuts | Filters in the statistics module | Yes, set up by hand | Each cut de-duplicated on its own |
| Who can open it | Lab users with middleware access | A Windows PC with WHONET installed | A browser, with seats for pharmacy and infection prevention |
| Cost | Inside the bioMérieux agreement, Lab Analytics is an add-on | Free, paid in staff hours | $249 a month on the Lab plan |
Does the VITEK 2 antibiogram follow CLSI M39?
It can, but the instrument does not decide that. The report definition in MYLA or OBSERVA does. Check three settings: the first isolate per patient per species regardless of specimen source, no percentage printed for fewer than 30 isolates, and intermediate results kept out of percent susceptible. Then confirm the report uses released interpretations, not raw instrument calls.
If nobody in the lab can say how those are set, that is the finding. It is also the question a CAP inspector or a new stewardship physician eventually asks, and the rule receipt that prints with every Antimicrobe export answers it on paper.
Where the Advanced Expert System fits
The VITEK 2 Advanced Expert System checks each result against a knowledge base of MIC distributions and resistance phenotypes, flags results that look biologically implausible and suggests corrections. bioMérieux describes a knowledge base built from over 100,000 references with more than 2,000 phenotypes. It works on one isolate at a time, before release.
The antibiogram works on the year. The two are complementary: AES makes each released result more trustworthy, and the antibiogram has to count those released results once per patient and present them in a form a prescriber can use for empiric choices. Neither replaces the other.
What about bioMérieux stewardship software
bioMérieux bought out LUMED, a Canadian clinical decision support company, in January 2024, taking its stake from 16 to 100 percent. LUMED APSS supports antimicrobial prescribing and infection prevention at the bedside, and bioMérieux announced its CE marking in April 2025. It is a prescribing tool, not a lab antibiogram tool, and US availability is a question for your bioMérieux representative.
Whatever a hospital chooses for bedside decision support, the annual cumulative antibiogram is still the lab's report. An antibiogram built from a plain export also survives an instrument change, a second AST platform after a merger and a move to a new LIS, because the rules live in the report tool rather than in instrument software.
Which plan fits a VITEK 2 lab
A single hospital lab producing the annual house-wide report and a few 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 also wants unit cuts, syndrome groups, quarterly trends and MDRO counts, or up to three facilities, uses Stewardship at $749 a month. A VITEK lab that produces antibiograms for outreach clients such as nursing homes and urgent care groups fits Network at $2,400 a month for up to 12 facilities.
Every limit is on the pricing page. Labs with outreach clients will find the per-client setup in antibiogram software for reference labs.
What this does not do
- It does not connect to the VITEK 2, MYLA or OBSERVA directly. It reads exported files, as often as you choose to export them
- It does not read raw MIC values or reinterpret them. It uses the S, I and R your lab released, so breakpoint changes are made in the lab system
- It does not replace MYLA for instrument management, workflow or result release
- It does not submit to NHSN or any public health system
Related reading: Sensititre antibiogram software, BIOMIC V3 antibiogram software, CLSI M39 antibiogram software, BD EpiCenter antibiogram software, antibiogram software for microbiology labs, WHONET alternative, MicroScan antibiogram software. The four steps from susceptibility testing data to an antibiogram cover the method end to end.
Questions
On this page's topic
Can VITEK 2 generate an antibiogram?
Yes, through its data management software. bioMérieux says OBSERVA formats VITEK 2 data into epidemiology and statistical reports, and MYLA has a Statistical Reporting Module. Whether the output follows the current CLSI M39 edition depends on the report definition, so check the first isolate rule and the 30 isolate threshold.
How do I export data from VITEK 2 OBSERVA?
Create a List Report under File, Configuration, Reports, add the AST and patient fields, then run it from Reports, Data Management, Search for Specimens by Data Collected and export a text file. Each query returns up to 4,000 samples, so export a year month by month and combine the files.
What is MYLA from bioMérieux?
MYLA is bioMérieux's browser-based microbiology middleware. It connects VITEK 2, VITEK MS and BACT/ALERT VIRTUO instruments with the LIS, manages workflow and includes a Statistical Reporting Module. MYLA Lab Analytics is a paid add-on for charts and dashboards on top of that module.
Does the VITEK 2 antibiogram include results not run on the VITEK?
No, unless they were entered into the middleware. Disk diffusion, gradient strips and reference lab results that live only in the LIS are missing from a MYLA or OBSERVA report, which is why many labs build the antibiogram from an LIS export instead.
Can I use WHONET with VITEK 2?
Yes. BacLink supports VITEK OBSERVA and MYLA formats, and the WHONET documentation walks through the OBSERVA export. WHONET is free and runs on Windows. The cost is the conversion time and rebuilding the report layout each year.
How much does antibiogram software for a VITEK 2 lab cost?
Antimicrobe's Lab plan is $249 a month for one facility, bought by card with no implementation fee, and it reads a MYLA, OBSERVA or LIS export. Unit cuts and up to three facilities are on the Stewardship plan at $749 a month.
More on antimicrobial resistance reporting
- hospital antibiogram The annual antibiogram is the most reused document a microbiology laboratory produces, and u...
- antimicrobial resistance surveillance software Resistance surveillance in a US hospital usually means one person, one annual spreadsheet an...
- CLSI M39 antibiogram software Most antibiograms that fail an M39 review fail on the same four things: repeat isolates coun...
- BD EpiCenter antibiogram EpiCenter already holds every Phoenix result your lab produced this year. The work starts af...
- MicroScan antibiogram Your WalkAway already produced every MIC and interpretation the antibiogram needs. The year-...
- Sensititre antibiogram Sensititre is often the plate your lab reaches for when the main AST panel does not carry th...
Start with your own export
See your own resistance picture, cut the way you actually work
Build the antibiogram on the synthetic sample dataset, or drop in your own CSV and watch it parse without leaving your browser. When you want an account, one email address is the whole sign-up.
Your file is parsed in your browser and never uploaded. No card required.