Statewide antibiogram software for health departments that pool hospital and lab data into one report every year
State HAI/AR programs in Oregon, Nebraska, Tennessee and New York City now publish statewide and regional antibiograms. Here is how they build them, where the work goes, and what software for a statewide antibiogram costs.
8 min read
Statewide antibiogram software takes isolate level susceptibility data from many hospitals and labs, applies one set of CLSI M39 rules to all of it, and prints a state table plus regional tables that clinicians can use when their own facility has too few isolates. Antimicrobe does this from CSV files, from $2,400 a month for up to twelve facilities.
This post is for the healthcare associated infections and antimicrobial resistance (HAI/AR) program at a state health department, the stewardship pharmacist or epidemiologist who owns the antibiogram there, and large local health departments that want a regional report for their own jurisdiction.
How state health departments build statewide antibiograms today
Several states now publish one, and their own descriptions show how varied the plumbing is. The common thread is that the report is built once a year by a small team, with whatever tool the analyst already knows.
Earlier rounds were harder. A University of Maryland stewardship webinar on the Maryland statewide antibiogram described submissions arriving in different formats, with different drug and organism lists, as PDF, Word, Excel and fax. Colorado's first statewide antibiogram, built from 2016 data, ran into the same problem: facilities track their data in different ways. If your program is still collecting finished facility antibiograms, that is the stage you are in. Health systems with the same pooling problem inside one network are covered in regional antibiogram software for health systems.
| Program | Where the data comes from | How it is built | What clinicians get |
|---|---|---|---|
| Oregon Health Authority | Hospital AR data reported to NHSN, 84% of hospitals (31 acute care, 18 critical access) | Tableau Public dashboard, updated yearly | Statewide antibiogram dashboard |
| Nebraska DHHS | 46,065 Gram-negative isolates from the state electronic disease surveillance system | SAS 9.4, first isolate per patient per organism | Statewide table plus 18 local health department tables and heat maps |
| NYC Health Department | Regional antibiogram data, by borough, age group and setting | Built with the Firstline decision support platform | An app on iOS, Android and the web |
| Tennessee Department of Health | Statewide and regional antibiograms | Published on the TDH data site | Tables and resistance trends over time |
Should a statewide antibiogram pool isolates or facility antibiograms?
Pool isolates whenever you can. A statewide antibiogram built from isolate level rows can apply the first isolate rule across the whole dataset, count each organism correctly, and cut the data by region, setting or specimen source after the fact. Averaging finished facility percentages cannot do any of that, and a patient seen at two hospitals is counted twice.
Facility antibiograms are still useful as a first step, especially when they carry the isolate count behind each percentage, because a weighted average is better than none. But the programs that publish regional tables, like Nebraska with its 18 local health department reports, work from isolate data. That is also the only format statewide antibiogram software can check for you.
In practice the isolate data comes from one of three places: the AR Option data hospitals report to NHSN (see NHSN AUR reporting software for what that involves on the hospital side), electronic laboratory reporting already flowing into your surveillance system, or a direct CSV export from each participating lab.
What statewide antibiogram software has to do
A state report is read by thousands of prescribers who never see the method, so the rules have to be applied identically for every facility and printed under the table. These are the jobs that eat analyst time today.
- Apply CLSI M39 once, for everyone. First isolate per patient per organism per period, final results only, no percentage printed on fewer than 30 isolates
- Cut by geography. State, then health department jurisdiction, region or county group, with every pooled table naming what is in it
- Cut by setting and source. Inpatient, outpatient and long-term care, and urine separate from everything else, because urine E. coli rates differ from blood
- Show missing data. Nebraska greys out a result when more than 30% of isolates lack it. Any statewide tool needs a rule like that, because not every lab tests every drug
- Hold the breakpoint version. Labs move to new CLSI breakpoints in different years, and a statewide table has to say which version each result was read under
- Repeat next year without a rebuild. The same column mapping and the same rules, with year over year trends
How much does statewide antibiogram software cost?
Most programs do not see a line item, because the cost is analyst time. A SAS or R workflow is cheap in licenses and expensive in the weeks an epidemiologist spends cleaning files, de-duplicating isolates and formatting tables, and that work starts over when the analyst leaves. A Tableau dashboard adds a publishing layer but not the cleaning. Decision support apps such as Firstline do not publish their pricing.
Antimicrobe publishes its price. Network is $2,400 a month for up to twelve facilities, with side by side comparison, which fits a regional health department or a state pilot. Enterprise is $3,990 a month with unlimited facilities and isolates. Annual billing is half the monthly price on every plan.
Programs usually pay for this kind of work from CDC Epidemiology and Laboratory Capacity (ELC) funding. Nebraska's statewide report was produced with Nebraska Medicine and UNMC through a stewardship program funded by DHHS through the ELC grant.
A full breakdown of what the other routes cost, including staff hours, is in how much antibiogram software costs, and every plan limit is on the pricing page.
Can a health department use Antimicrobe for a statewide antibiogram?
Yes, if you have isolate level data. Antimicrobe reads a CSV export with one row per isolate and drug, keeps the first isolate per patient, flags cells under 30 isolates, and prints a state table and one table per region from any column in the file, such as jurisdiction, county group or setting. Each participating facility counts toward the plan.
It does not replace your surveillance system, your NHSN data access or your electronic laboratory reporting feed. It sits after them, where the analyst currently opens Excel or SAS. It does not reinterpret MICs, it uses the interpretation each lab reported, and it does not receive HL7 messages directly.
Once the tables exist, most programs present them to an HAI/AR advisory council before release, and a presentation maker that turns the PDF report into slides saves the night before that meeting. The rules applied to each table are the same ones described on CLSI M39 antibiogram software, and the regional view is the same one nursing home operators use on nursing home antibiogram software.
Questions to ask before choosing statewide antibiogram software
- Does it read isolate level data from NHSN extracts, ELR and lab CSV files without a custom build for each?
- Does it apply the first isolate rule across all facilities, not facility by facility?
- Can it print a state table and a table per jurisdiction or region from the same upload, naming the facilities pooled?
- How does it show missing results and cells under 30 isolates?
- Can next year's report be produced by someone other than the analyst who built this year's?
- What does it cost at our facility count, and is that price published?
Related on this site: regional antibiogram software for health systems, CLSI M39 antibiogram software, NHSN AUR reporting software, how much antibiogram software costs, Antimicrobe pricing.