BD EpiCenter antibiogram software that turns your Phoenix results into an M39 antibiogram the pharmacy can cut by unit

Where an EpiCenter antibiogram falls short

The gaps are rarely inside the software. They sit at its edges, where the instrument database meets the rest of the lab and the people who read the report.

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 EpiCenter never saw. Disk diffusion and gradient strips for fastidious organisms, reference lab send-outs and anything run on a second AST platform usually live in the LIS, not in the instrument database, unless someone entered them into EpiCenter. The PLUS configuration supports manual testing, but only if the bench uses it
• Instrument results versus released results. The antibiogram should reflect the interpretations the lab released after technologist review and expert rules. If edits are made in the LIS and not in EpiCenter, the two databases disagree, and the antibiogram follows the wrong one
• A duplicate rule nobody has opened in years. EpiCenter lets the lab define its own duplicate removal. M39 keeps the first isolate per patient per species in the period, whatever the specimen source. A rule that removes repeats 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
• Patient matching depends on the interface. First isolate logic needs a stable patient identifier on every result. If demographics arrive late from the LIS or are keyed by hand at the instrument, repeat isolates slip through as new patients
• Cuts made in the wrong order. A urine or ICU table has to be de-duplicated inside that cut, not taken from the house-wide list after de-duplication, or it keeps whichever isolate happened to be first hospital-wide
• The reader is outside the lab. Stewardship pharmacists want urine, blood and unit tables and a quarterly trend, and they do not log into the EpiCenter workstation

How to export antibiogram data from BD EpiCenter

The export route is documented step by step in WHONET's BacLink guide for BD EpiCenter and BD Phoenix, which requires EpiCenter version 6.60 or later. Open the DataView reporting module, choose the predefined filter under Predefined, WHONET Data Export, set the date range and any other filter criteria, and run it. From Print Preview, export the result as a tab separated text file.

That file, or any DataView query that returns the same fields, is what Antimicrobe reads. It needs a patient identifier, collection date, specimen source, location or unit, organism, antibiotic and the S, I or R interpretation. Open the tab separated file in Excel and save it as CSV before you upload it. 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.

If a meaningful share of your results never passes through Phoenix, export from the LIS instead. What that file looks like is on laboratory information system exports.

1. 1

   EpiCenter DataView

   Run the WHONET Data Export filter, or your own query, for the full year

2. 2

   Tab separated file

   Open it in Excel and save it as CSV

3. 3

   Antimicrobe

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

4. 4

   Antibiogram

   House-wide, urine, blood and unit tables, each with a rule receipt

EpiCenter, WHONET and Antimicrobe compared

WHONET is free and many Phoenix labs keep it for exactly this job. The practical differences, including running it on a Mac, are on the WHONET alternative page.

Does BD EpiCenter follow CLSI M39?

It can, if it is configured to. BD's brochure says EpiCenter meets the M39 guideline as it was then proposed and lets the lab define its own rules, including duplicate removal, so the answer for your lab sits in the report definition. Check three settings: first isolate per patient per species regardless of source, no percentage printed on fewer than 30 isolates, and intermediate results kept out of percent susceptible.

If nobody in the lab can say how those three are set, that is the finding. It is also the question a CAP inspector or a new stewardship physician will eventually ask, and the rule receipt that prints with every Antimicrobe export exists to answer it on paper.

What changes now that BD diagnostics is part of Waters

On February 9, 2026, BD completed the spin-off of its Biosciences and Diagnostic Solutions business and its combination with Waters Corporation. The former BD diagnostics business now sits in a Waters division called Waters Advanced Diagnostics. BD's newer microbiology informatics product, BD Synapsys, belongs to the same family.

BD Synapsys is worth a sentence of its own, because labs often assume it takes over the EpiCenter antibiogram. BD announced it on April 19, 2018 as a browser-based microbiology informatics solution, initially supporting BACTEC FX blood culture systems, Kiestra lab automation and, in the United States, Veritor Plus. That announcement does not list Phoenix susceptibility results or cumulative antibiogram reports, so ask your BD (now Waters) representative which EpiCenter epidemiology reports exist in Synapsys before you plan to retire EpiCenter.

None of that changes the Phoenix on your bench this year. It is, though, the kind of moment when a lab reviews service agreements and asks whether the annual antibiogram should depend on one instrument vendor's reporting module. An antibiogram built from a plain export survives an instrument change, a second platform after a merger and a move to a new LIS, because the rules live in the report tool rather than in the instrument software.

Which plan fits a Phoenix 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 Phoenix 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 EpiCenter or Phoenix 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 reported, so breakpoint changes are made in the lab system
• It does not replace EpiCenter for instrument management, critical result alerts or epidemiology queries at the bench
• It does not submit to NHSN or any public health system