Regional antibiogram software for health systems and health departments, pool isolates across facilities without breaking M39
A regional antibiogram looks like a spreadsheet exercise until the facility reports arrive with different breakpoint versions, different first isolate rules and different drug panels. The fix is to pool isolates, not percentages, and that decides which software can do the job.
8 min read
Regional antibiogram software combines susceptibility data from several hospitals, clinics or long-term care facilities into one cumulative antibiogram, with each facility still visible on its own. The software that works pools isolate-level rows under one rule set. The approach that usually fails is collecting each facility's finished antibiogram and averaging the percentages.
This is written for the stewardship director of a health system with four to twelve hospitals and for state and local HAI and antimicrobial resistance programs building a regional or county antibiogram. Both are asked for the same deliverable and both run into the same wall.
Why pooled facility antibiograms rarely add up
The best documented US example is New York City. The NYC Health Department asked hospitals for their facility antibiograms for 2021, 2022 and 2023, and 45 of the city's 56 hospitals took part, covering 76 percent of hospital beds (Creation and Distribution of 2021 to 2023 New York City Regional Antibiograms, PMC12461460). That is excellent participation. The authors still report that differences in data reporting limited their ability to pool antibiograms across facilities, and they name electronically reported susceptibility data as the route to explore next.
The reasons are predictable once you have seen a few facility reports side by side. One hospital applies the current CLSI breakpoints and another is two revisions behind. One de-duplicates to the first isolate per patient per year and another per admission. One reports urine separately, another folds it in. Cascade reporting means a drug tested on every isolate in one lab is only reported on resistant isolates in the next, which makes its percent susceptible look far worse. And a finished report that gives 88 percent without the denominator cannot be weighted at all.
Pool isolates, not percentages
A regional number is only defensible if every facility's isolates went through the same rules before anything was summed. That means collecting row-level susceptibility results (organism, antibiotic, interpretation, date, source, a patient key) from each facility, applying one breakpoint version and one first isolate rule to the combined file, and only then computing percent susceptible.
Row-level pooling also fixes a problem that summary pooling cannot see at all: patients who move between facilities. A patient cultured in the community hospital and again after transfer to the tertiary center counts twice in two facility antibiograms. With a shared pseudonymous patient key across the system, the first isolate rule removes the duplicate. Without one, the regional table quietly over-represents your sickest, most resistant patients.
The last requirement is keeping facilities visible. A system-wide table hides the one hospital whose E. coli susceptibility to ceftriaxone is ten points below the rest, and that difference is often the reason the regional project was started.
Regional antibiogram options compared
These are the routes health systems and health departments actually use in the US. Vendor and program details come from their own public pages and published reports, read in September 2026.
| Option | What gets pooled | Same rules at every site? | Who does the work | Cost |
|---|---|---|---|---|
| Spreadsheet template from each facility | Finished facility antibiograms | No, each lab uses its own | Health department or system analyst | Staff hours |
| WHONET | Isolate data imported through BacLink | Yes, if every file is mapped | One trained analyst on a Windows PC | Free |
| Firstline | Facility data, compiled by the vendor | Set by the project | Firstline and the sponsoring health department | Not published |
| Enterprise surveillance platform per hospital | Each hospital separately | Only if every site runs the same build | Pharmacy informatics at each site | Quoted, not published |
| Antimicrobe Network plan | Isolate rows from each facility's LIS export | Yes, one breakpoint set and one first isolate rule | Whoever schedules the export | $2,400 a month, up to 12 facilities |
Firstline is a clinical decision support app. NYC used it to distribute the regional antibiogram to prescribers by borough, age group and setting, and its strength is delivery at the point of care rather than the analysis your stewardship team runs. WHONET is covered in depth on our WHONET alternative page.
How do you build a regional antibiogram?
You build a regional antibiogram by agreeing on one method, collecting isolate-level results from each facility in that method's format, pooling them, and publishing both the combined table and each facility's own column. The agreement matters more than the software, but the software decides whether the agreement survives the second year.
- Pick one breakpoint source and version for the regional report, and record it on the output
- Define the first isolate rule (per patient, per organism, per calendar year is the M39 default) and the minimum of 30 isolates per cell
- Agree on a pseudonymous patient key that is stable across facilities, generated on the facility side
- Collect the LIS susceptibility export from each site, with facility, unit and specimen source on every row
- Publish the pooled antibiogram, each facility alongside it, and cells under 30 isolates flagged instead of dropped
What does regional antibiogram software cost?
Most options do not publish a price. Enterprise surveillance platforms are sold with an implementation fee and an annual license, and vendor-run regional projects are scoped per contract. WHONET and spreadsheets cost analyst time instead of a license, and in a regional project that time is usually spent reconciling files rather than analyzing them.
Antimicrobe publishes its numbers. The Network plan is $2,400 a month for up to twelve facilities, 750,000 isolates a year and 25 seats, with cross-facility comparison, scheduled ingest of the export your LIS already produces, an API, custom breakpoint sets and an audit log. A system larger than that, or one that needs SSO, a business associate agreement and invoicing, moves to Enterprise.
Every limit is on the pricing page, and the single-facility view of the same engine is described on the antimicrobial resistance surveillance software page.
Health system or health department, what changes
A health system owns its facilities, so it can mandate the export, the patient key and the schedule. The regional antibiogram becomes a routine report, and the useful output is the side-by-side view: which hospital is drifting, which unit drives the system's carbapenem resistance, whether the smaller sites should use the system table or their own.
A health department can only ask. Participation is voluntary, facilities send what they already have, and the department has to accept files in whatever shape they arrive. Here the software has to tolerate different column names and still apply one rule set, and the department has to be able to show each facility how its own numbers were computed. Long-term care facilities that cannot reach 30 isolates on their own are often the biggest beneficiaries of a regional table.
Nursing homes and their consultant pharmacists are covered on the nursing home antibiogram page, and the facility comparison view on the resistance map across your own facilities.
Questions to settle before the first data call
- Which breakpoint version will the regional report use, and who decides when it changes?
- Will facilities send isolate rows or finished reports, and what happens to a facility that can only send the report?
- Who generates the shared patient key, and does it ever leave the facility in identifiable form?
- Is the output for prescribers, for the stewardship committee, or for publication, and does each need a different cut?
- Who notices when a facility's scheduled export stops arriving or changes format?
That last question is where regional projects quietly degrade: a site upgrades its LIS, a column is renamed, and a quarter of data goes missing without anyone noticing. Teams that already run a warehouse often point a data observability monitor at the incoming files for freshness, volume and schema. For the antibiogram itself, load one facility's export into the builder at the top of this page, then see the LIS export requirements before you write the data call.
Related on this site: antimicrobial resistance surveillance software, resistance map across your facilities, CLSI and EUCAST breakpoints, nursing home antibiogram.