For stewardship teams writing empiric guidance
Syndromic antibiogram software that groups your isolates by urinary, bloodstream and respiratory source
A hospital-wide antibiogram answers "how does E. coli do against ceftriaxone". The prescriber in the ICU at 2 a.m. is asking a different question: what covers a bloodstream infection or a ventilator pneumonia on this unit.
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Short answer
A syndromic antibiogram groups isolates by the type of infection they came from, such as urinary, bloodstream or respiratory, instead of pooling every specimen together. Antimicrobe builds it from your lab's CSV export by grouping the specimen source the lab already reported, then lets you cut each syndrome by unit and period with CLSI M39 rules applied. It is part of the Stewardship plan at $749 a month.
Why the hospital-wide antibiogram misleads empiric choices
The traditional cumulative antibiogram puts every first isolate of a species into one row, whatever the specimen. That is the right default for a one-page annual report, and CLSI M39 still recommends it as the baseline. It also hides the differences that matter most when therapy starts before the culture is back.
Urine isolates dominate most hospital datasets, so the E. coli row is mostly urinary E. coli. A drug that looks fine there can perform worse in blood or respiratory isolates from the same building. And the organism mix itself changes by syndrome: Pseudomonas aeruginosa and Staphylococcus aureus matter far more in ventilator pneumonia than in an outpatient bladder infection.
CLSI M39 recognizes this and describes stratifying cumulative data by specimen source, by unit such as the ICU or emergency department, and by patient population. Most hospitals stop at "urine and non-urine" because doing more by hand in Excel means rebuilding the whole report for every cut.
How Antimicrobe builds a syndromic antibiogram
You upload the same line list you already pull for the annual report: patient identifier, collection date, specimen source, unit, organism, antibiotic and the S, I or R your lab reported. Antimicrobe maps your column names once and remembers them.
Each isolate is then placed in a syndrome group from the specimen source the lab wrote, so a urine or catheter urine specimen counts as urinary, blood and line tips as bloodstream, sputum, BAL and tracheal aspirates as respiratory. Sources it does not recognize land in "Other", where they stay visible and countable instead of disappearing.
The de-duplication and the 30 isolate rule are the same ones described on CLSI M39 antibiogram software, and the export columns are listed on laboratory information system exports.
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LIS or instrument export
One CSV for the year with source and unit on every row
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Syndrome grouping
Specimen source mapped to urinary, bloodstream, respiratory and four more groups
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CLSI M39 rules
First isolate per patient, no percentage on fewer than 30 isolates
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Syndromic tables
One table per syndrome, cut by unit and period, printable
- Urinary, from urine, midstream and catheter urine specimens
- Bloodstream, from blood cultures and line tips
- Respiratory, from sputum, bronchoalveolar lavage, tracheal and endotracheal aspirates and pleural fluid
- Skin and soft tissue, from wound, abscess, ulcer and burn specimens
- Central nervous system, from CSF
- Gastrointestinal, from stool, peritoneal fluid and bile
- Bone and joint, from bone, synovial fluid and prosthetic material
Syndrome by unit is where the numbers change
The grouping becomes useful when it is combined with location. Respiratory isolates from the ICU are a different population from respiratory isolates on a medical floor, and bloodstream isolates from the emergency department mostly reflect community onset infection. On the Stewardship plan every syndrome table can be cut by unit, by period and by year, and the cut is printed in the table heading so nobody mistakes an ICU respiratory table for the house-wide one.
Published experience points the same way. At the Children's Hospital of Philadelphia, Simpao and colleagues (Applied Clinical Informatics, 2018) built an electronic antibiogram around nine clinical scenarios, including community-acquired blood, urine and wound infections and separate ICU views. They found 90 percent of MRSA wound isolates from the emergency department susceptible to clindamycin against 79 percent hospital-wide, a gap a single house-wide row would never show.
Unit-level work for critical care is covered in more depth on ICU antibiogram software, and the urinary view on UTI antibiotic resistance in your own isolates.
Syndromic antibiogram vs WISCA
A weighted-incidence syndromic combination antibiogram (WISCA) goes one step further. Instead of a table of organisms against drugs, it gives one coverage estimate per regimen for a whole syndrome, weighting each pathogen by how often it causes that syndrome and counting polymicrobial infections. Randhawa and colleagues (Critical Care, 2014) built WISCAs for ventilator-associated pneumonia and catheter-related bloodstream infection at a Toronto ICU and found that no single agent covered more than 85 percent overall, while meropenem plus vancomycin reached 93 percent.
A WISCA needs patient-level infection episodes, which means someone has to decide which positive cultures belong to a true case. That is a research build, usually done in R with the AMR package or in SAS, and it is redone for each syndrome. Antimicrobe does not calculate WISCA. It produces the syndrome-grouped cumulative tables that most stewardship programs actually publish, and its empiric view ranks single agents by the share of all isolates in the selected syndrome they cover.
| Question | Traditional antibiogram | Syndromic antibiogram | WISCA |
|---|---|---|---|
| Unit of analysis | First isolate per patient, all sources | First isolate per patient, within a syndrome group | Infection episode, possibly several organisms |
| Output | Percent susceptible, organism by drug | Percent susceptible, organism by drug, per syndrome and unit | One coverage percent per regimen |
| Data needed | LIS export | LIS export with specimen source and unit | Linked episodes, often chart review |
| Usual tool | Excel, instrument software, WHONET | Excel rebuild per cut, or Antimicrobe | R (AMR package), SAS, research build |
| Who maintains it | Lab, once a year | Stewardship pharmacist, quarterly or yearly | Analyst or researcher |
| Cost with Antimicrobe | $249 a month (Lab) | $749 a month (Stewardship) | Not offered |
Who buys a syndromic antibiogram
The empiric ranking that sits on top of these tables is explained on empiric antibiotic therapy by your antibiogram.
- Stewardship pharmacists rewriting the empiric guidance for sepsis, pneumonia or UTI order sets
- ICU pharmacists and intensivists who want a critical care respiratory and bloodstream table separate from the house
- Emergency department teams that discharge most UTI and skin infection patients home on an oral drug
- Infectious diseases physicians who present local data to the pharmacy and therapeutics committee
- Microbiology lab leaders asked for "a pneumonia antibiogram" on top of the annual report
How much does syndromic antibiogram software cost?
Syndrome and unit cuts are on the Stewardship plan, $749 a month for up to three facilities, 150,000 isolates a year and eight seats, with quarterly trends and MDRO threshold alerts. Annual billing is half the monthly price. A lab that only needs the traditional annual report can stay on Lab at $249 a month, which cuts by source and period.
Enterprise surveillance platforms bundle antibiogram views with real-time alerts and NHSN reporting and do not publish prices. A WISCA research build costs analyst time rather than a license, and it has to be maintained by the person who wrote the code.
The enterprise platforms are compared on antimicrobial stewardship software for community hospitals. Every plan limit is on the pricing page, and the other routes are priced out in how much antibiogram software costs.
What this does not do
- It does not diagnose infection. The syndrome group comes from the specimen source the lab reported, and every screen says so
- It does not calculate WISCA or combination regimen coverage
- It does not reinterpret MICs. It uses the S, I and R your lab reported, or reads MICs against the breakpoint set you choose
- It does not choose therapy for a patient or replace your institutional guideline
- It does not connect to the LIS over HL7. It reads files you export
Related reading: empiric antibiotic therapy by your antibiogram, ICU antibiogram software, UTI antibiotic resistance in your own isolates, CLSI M39 antibiogram software, antibiogram generator. The four steps from susceptibility testing data to an antibiogram cover the method end to end.
Questions
On this page's topic
What is a syndromic antibiogram?
A syndromic antibiogram reports susceptibility for the organisms that cause one type of infection, such as urinary tract, bloodstream or respiratory infection, instead of pooling all specimens. It shows prescribers what covers that syndrome locally, often cut by unit, and is used to write empiric therapy guidance for order sets and pathways.
How is a syndromic antibiogram different from a traditional antibiogram?
A traditional antibiogram counts the first isolate of each species per patient across all specimen sources in one table. A syndromic antibiogram applies the same counting rules inside each infection group, so urinary E. coli and bloodstream E. coli are reported separately and the organism mix reflects the syndrome being treated.
Does CLSI M39 allow stratified antibiograms?
Yes. CLSI M39 keeps the annual cumulative antibiogram as the baseline and describes stratifying data by specimen source, by unit such as the ICU or emergency department, and by patient population. The same rules apply inside each cut, including the first isolate per patient and no percentage on fewer than 30 isolates.
What is a WISCA antibiogram?
WISCA stands for weighted-incidence syndromic combination antibiogram. It estimates the chance that a regimen, including combinations, covers all likely pathogens of a syndrome, weighted by how often each causes it. It needs linked infection episodes and is usually built in R or SAS. Antimicrobe does not calculate WISCA.
How many isolates does a syndromic antibiogram need?
The same 30 isolates per organism and drug that CLSI M39 recommends for any cumulative antibiogram. Splitting by syndrome and unit thins the counts, so smaller hospitals often pool two or three years for respiratory and bloodstream tables. Antimicrobe flags cells under 30 and labels pooled periods.
Which plan includes syndromic cuts?
Syndrome and unit cuts are part of the Stewardship plan at $749 a month for up to three facilities, with quarterly trends and MDRO alerts. Network at $2,400 and Enterprise at $3,990 include them too. The Lab plan at $249 cuts by source and period only.
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