Antibiogram software for reference labs, producing a separate client antibiogram for every nursing home, clinic and small hospital you serve
Nursing homes, clinics and small hospitals get their cultures from you, so their antibiogram has to come from you too. Here is how a reference or outreach lab can produce one per client without a report writer per facility, and what each route costs.
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A reference or outreach laboratory produces client antibiograms by splitting its susceptibility results by the ordering facility, then running the CLSI M39 rules (first isolate per patient per organism, at least 30 isolates per cell) separately for each client. The work is not the math. It is doing it 20 or 60 times a year, consistently, and handling the many clients whose counts are too small to print a percentage.
This is written for the microbiology director, laboratory manager or outreach and client services lead at a US reference lab, hospital outreach program or regional independent lab whose nursing home, urgent care and small hospital clients keep asking for "our antibiogram". It compares the realistic routes and what each one costs.
Why your clients are asking for their own antibiogram
Skilled nursing facilities have had to run an antibiotic stewardship program since CMS added it to 42 CFR 483.80 (surveyed as F881). CDC's Core Elements for nursing homes ask them to track resistance and feed it back to prescribers, and almost none of them have a laboratory. Their culture results live in your LIS, so when a surveyor or a consultant pharmacist asks what their resistance looks like, the facility calls you.
Some health departments now ask directly. Los Angeles County's Health Officer Order of January 19, 2017 requires annual antibiogram submission from acute care hospitals, long-term acute care hospitals and skilled nursing facilities, due June 1 for the prior calendar year, in the department's Excel template only (PDF is no longer accepted), with percent susceptible and the number of isolates for each organism and drug. Its instructions tell nursing homes to work with their reference laboratories on the submission, and tell labs that serve multiple facilities to prepare a separate report for each facility location.
Outpatient groups have their own reason. Joint Commission ambulatory stewardship standards have applied since January 2020, and an urgent care chain that sends every urine culture to one lab can only get a clinic-level resistance picture from that lab.
What a defensible client antibiogram needs
- One report per client location. Do not hand a nursing home the lab-wide cumulative report with its name on it. The LA County instructions say it plainly: separate report for each facility
- Cut by client first, then de-duplicate. The first isolate per patient per organism has to be counted inside each client's data, or a resident cultured once at the hospital and again at the nursing home disappears from one of the reports
- Suppression for small counts. A 90-bed nursing home may send 150 urine isolates a year, and most organisms other than E. coli will fall under 30. Those cells are shown as counts or pooled over two years, never printed as a confident percentage
- Surveillance cultures excluded. Admission MRSA and CRE screening swabs are removed before the numbers are run
- Source split where volume allows. Most client data is urine, which is useful on its own: a urinary antibiogram is exactly what a nursing home prescriber uses for empiric UTI therapy
- The rule receipt on the page. Breakpoint version, date range, first-isolate rule and suppression threshold printed on each report, so the client's committee and any surveyor can see how it was built
Client antibiogram routes for a reference lab, side by side
| Route | Per-client cut | Who does the work | Cost |
|---|---|---|---|
| Instrument data manager (Observa, EpiCenter, LabPro) | Possible with a location filter, one report at a time | A technologist per report | Included with the instrument, staff hours per client |
| LIS report writer (custom query) | Yes, once someone builds it | LIS analyst, then validation after every upgrade | Analyst weeks up front, upkeep each year |
| Excel pivot per client | Yes, by hand | Whoever drew the short straw, each client, each year | No license, days of work at 20 or more clients |
| WHONET | Yes, by location in the analysis | One person on a Windows PC, after BacLink setup | Free software, your hours |
| Antimicrobe Network | Each client a facility, compared side by side | Lab staff in a browser, scheduled export ingest | $2,400 a month, up to 12 facilities |
| Client buys Antimicrobe Lab from your export | The client's own data only | The client, from a CSV you send each quarter | $249 a month, paid by the client |
What the instrument data manager already gives you
Your AST instrument probably ships with an antibiogram. bioMerieux says VITEK 2 data management allows generation of epidemiology reports and antibiograms, and Observa stores VITEK 2 results for statistical reports and export. BD EpiCenter generates antibiograms on demand from Phoenix data, and Beckman offers an Antibiogram Export Tool that turns LabPro Information Manager data into an Excel template.
For one hospital antibiogram a year, that is often enough. For 30 client facilities it runs out quickly: each report is a manual run with its own filter, isolates tested by disk diffusion or sent out are missing, and the first-isolate rule has to be checked by hand for each client. The limit is not the software, it is the number of times a year somebody has to sit down and run it.
The hospital-lab version of this decision, one antibiogram for one facility, is covered in antibiogram software for microbiology labs.
How do you make an antibiogram for a nursing home with too few isolates?
Pool, cut to urine, or show counts. Pooling two or three years usually brings E. coli, Klebsiella and Proteus over 30 isolates for a mid-size nursing home; state the window on the report. Restricting to urine keeps the report focused on the decision the facility actually makes. Anything still under 30 is shown as a count, not a percentage.
Some programs go further and pool clients. Colorado's health department published a 2023 statewide nursing home antibiogram from 196 facilities, and weighted-incidence syndromic antibiograms for nursing homes served by a common reference lab have been studied for exactly this small-count problem. A pooled regional report is a useful benchmark, but it is not the facility's own antibiogram and should be labeled that way.
The facility side of this, including the 30-isolate error table, is on the nursing home antibiogram page. Pooling across facilities is covered in regional antibiogram software.
How much does client antibiogram software cost a reference lab?
Enterprise surveillance platforms price per hospital and do not publish numbers, and they are built for the hospital pharmacy, not for a lab serving outside clients. The free routes cost staff time: at a day per client report, 30 clients is six working weeks a year of a technologist or manager.
Antimicrobe publishes its prices. The Network plan is $2,400 a month for up to 12 facilities, 750,000 isolates a year and 25 seats, with scheduled LIS export ingest, custom breakpoint sets, an audit log and side-by-side comparison. A lab with more clients than that fits Enterprise, which covers unlimited facilities, SSO and a BAA, priced in a conversation. The cheapest pattern for a lab with a handful of engaged clients is often to send each client a quarterly CSV of its own results and let the client run the $249 Lab plan itself.
Every limit is on the pricing page, and the wider market is compared in how much antibiogram software costs.
Getting the client data out of the LIS
The only interface this needs is a flat export. One row per isolate and drug, with a patient key, collection date, specimen source, ordering facility or location, organism, antibiotic and the S, I or R interpretation. Include results suppressed from patient reports by cascade rules, because M39 counts what was tested, not what was released. MIC values help if you want to reinterpret under a newer breakpoint version.
Clients who only have older antibiograms as scanned PDFs from a previous lab can pull the tables out with document data extraction software to compare against the new reports. The column names common LIS products use are listed on the LIS susceptibility export page.
Which route fits which lab
A hospital outreach program with a few nursing home and clinic clients can keep using the instrument data manager, or hand each client its own export and let the client buy the Lab plan. A regional reference lab with 10 to 12 active long-term care or urgent care clients that ask every year fits the Network plan, where each client is a facility and the reports come out the same way every time. A lab serving dozens of skilled nursing facilities in a county with a reporting mandate, like Los Angeles, is an Enterprise conversation, because the value is producing all of them, on template, by June 1.
Urgent care and clinic clients have their own cut, the outpatient urine antibiogram, described on outpatient antibiogram software.
Questions to settle before you offer client antibiograms
- Which clients are asking, and for what: a survey binder, a county submission or empiric UTI guidance?
- Does the LIS carry a clean ordering-facility field for every client, including ones that changed names or merged?
- Which breakpoint version will each report state, and who signs off on it?
- What will you print when a client has fewer than 30 isolates of an organism: counts, a two-year pool or nothing?
- Is the client antibiogram a free service, part of the client contract, or a billable report?
- Who at the lab owns the annual run, and what happens when that person is out in May?
Related on this site: nursing home antibiogram software, antibiogram software for microbiology labs, outpatient antibiogram software, LIS susceptibility export.