For Altera Paragon and Paragon Denali hospitals
Paragon EHR antibiogram software that turns an Altera Paragon lab export into a CLSI M39 antibiogram for a community hospital
Paragon stores every culture and susceptibility result your lab releases, and it already sends your AU and AR files to NHSN. The yearly antibiogram your prescribers actually read is still built by hand, usually by one pharmacist in January.
Try the builder on the sample data, or drop in your own CSV. It is parsed in your browser and never uploaded.
Short answer
Paragon EHR antibiogram software takes a delimited export of finalized susceptibility results from Altera Paragon, Paragon Denali or the lab system beside it, and builds the cumulative antibiogram from that file. Antimicrobe keeps the first isolate per patient per period, flags organisms under 30 isolates as CLSI M39 recommends, pools years when one year is too thin, and prints the rules it applied with counts. The Lab plan is $249 a month for one facility, bought by card, with no interface to build.
What a Paragon hospital already has
Paragon has always been the small hospital EHR in its family. McKesson built it, Allscripts bought it with McKesson Enterprise Information Solutions on October 2, 2017 for $185 million and said it would keep Paragon for the small hospital segment and Sunrise for larger institutions. In May 2022 Allscripts sold that hospital business for $670 million in cash to a Constellation Software subsidiary that now trades as Altera Digital Health.
Altera sells the current version as Paragon Denali, which it unveiled at HIMSS24 in March 2024 as a cloud-native EHR on Microsoft Azure for rural, critical access and community hospitals. The four community systems Altera named as early Denali sites in February 2025, including 50-bed Columbus Community Hospital in Nebraska, were all existing Paragon customers.
Lab results reach Paragon in one of two ways. Altera describes Paragon Laboratory Management as automating the processing of orders, charges and results inside the EHR. Some hospitals run a separate laboratory system instead, such as Altera Lab, which Altera sells as an EHR-agnostic LIS with discrete microbiology results and which the CAP TODAY November 2025 LIS survey lists at 31 US sites. Either way the finalized susceptibility results an antibiogram needs are already stored as data, not as paper.
Where a Paragon antibiogram usually falls short
Altera does not publicly describe a CLSI M39 cumulative antibiogram report in Paragon, Paragon Denali or Altera Lab, and its user documentation sits behind a customer login. So the report is usually a line list from the lab or a report writer, finished in Excel. The same handful of problems shows up every year.
How small hospitals handle thin counts, pooled years and regional data is compared on critical access hospital antibiogram software.
- Repeat cultures counted as new isolates. A patient with three positive urines in a month is one isolate under M39, and in a denominator of 60 the extra two move the percentage by several points
- Preliminary results in the file. A report that pulls every result, not only final ones, counts susceptibilities that were later corrected
- Small counts printed as percentages. A community hospital reaches 30 isolates for E. coli and Staph aureus and for little else, so most cells need pooled years or a count
- Settings mixed together. Emergency, inpatient, swing bed and clinic cultures land in one table unless someone filters them on purpose
- Nobody remembers last year. The formulas live in one spreadsheet that one person built, and the rules change with whoever rebuilds it
How to export antibiogram data from Paragon
Ask whoever writes reports for the lab, usually the lab manager, the Paragon system analyst or the lab system administrator, for one delimited file of finalized microbiology susceptibility results for the analysis period. If your hospital runs a separate LIS beside Paragon, take the file from the LIS, because that is where the microbiology results are verified.
One row per organism and drug works, and so does one row per isolate with a column per drug. Include a patient identifier (hashed is fine), collection date, location or patient type, specimen source, organism, antimicrobial and the released interpretation. Keep the location column, so emergency, inpatient, swing bed and clinic cultures can be split or pooled by choice and not by accident.
WHONET users should not expect a Paragon template in BacLink. The WHONET guide to laboratory information system exports gives detailed templates only for MEDITECH Magic and Cerner Classic and asks every other system for a delimited text export. That is the same file Antimicrobe reads.
A column-by-column example of a good export is on laboratory information system exports.
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1
Paragon or LIS report
Finalized susceptibility results for the year, with location and specimen source
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2
CSV file
One delimited export, plus a reference lab line list if some cultures were sent out
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3
Antimicrobe
First isolate per patient, 30 isolate flag, years pooled when one year is too thin
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4
Antibiogram
House-wide, urine and unit tables with counts and a rule receipt for the committee
Paragon reports, WHONET and Antimicrobe compared
WHONET is the free route and suits a lab with time to learn it. The practical differences are on the WHONET alternative page.
| Question | Paragon report and Excel | WHONET with BacLink | Antimicrobe |
|---|---|---|---|
| First isolate per patient | Only if built into the sheet | Yes, if configured | On by default, counts shown |
| Final results only | Depends on the report | Depends on the export | Final results only, by rule |
| Under 30 isolates | Manual | Configurable | Flagged, years pooled on request |
| Unit and source cuts | A new sheet per cut | Yes, after setup | Any column in the file |
| Runs on | Excel on one PC | Windows desktop | Any browser, with seats |
| Cost | Staff hours | Free, paid in staff hours | $249 a month on the Lab plan |
Does a Paragon antibiogram follow CLSI M39?
It follows M39 as far as the report and the spreadsheet do. Paragon stores the results, but the M39 decisions are made by whoever builds the antibiogram: keeping the first isolate per patient per period, leaving out results that were not final, not printing a percent susceptible on fewer than 30 isolates, and labeling pooled years.
Antimicrobe applies those rules every time and prints a rule receipt with isolate counts before and after de-duplication. When the committee or a surveyor asks how the E. coli number was made, the answer is on the page instead of in someone's memory.
Each M39 rule and how common tools handle it is on CLSI M39 antibiogram software.
Paragon Denali, NHSN AUR and the antibiogram
Paragon already covers NHSN reporting. The CDC Antimicrobial Resistance vendor list, last reviewed May 12, 2026, shows Paragon 24.1, Paragon 25.1 and Paragon Denali 2.0 as validated, and the Antimicrobial Use list, last reviewed June 24, 2026, shows the same three. So a Paragon hospital does not need extra software to send AU and AR files.
The AR file and the antibiogram start from the same finalized susceptibility results, but they go to different readers. The AR file goes to NHSN. The antibiogram goes to your prescribers, your stewardship committee and the order sets. That second job is the one Antimicrobe does, and it does not touch the first.
It also survives a change of EHR. Some Paragon hospitals are moving to Denali and some, by their own comments to KLAS in 2026, are leaving Paragon altogether. An antibiogram built from a plain CSV keeps its rules and its history through either move, because the rules live in the report tool and not in the EHR.
Which AUR products CDC has validated, and what each costs, is compared in NHSN AUR reporting software compared.
Which plan fits a Paragon hospital
A single Paragon hospital producing a house-wide, urine and emergency department antibiogram needs the Lab plan, $249 a month for one facility, 25,000 isolates a year and two seats, bought by card with no implementation fee. Two seats usually means the stewardship pharmacist and the infection preventionist or lab manager.
A hospital that also wants unit cuts, syndrome groups, quarterly trends and MDRO counts, or that reports an attached clinic or nursing home as a separate facility, uses Stewardship at $749 a month for up to three facilities. A multi-hospital Paragon system that wants one regional report plus each hospital's own uses Network at $2,400 a month.
Every limit is on the pricing page. Larger Altera hospitals on Sunrise will find their route in antibiogram software for Altera Sunrise hospitals.
What this does not do
- It does not connect to Paragon directly or through HL7. It reads exported files, as often as you export them
- It does not reinterpret MICs or zone sizes. It uses the S, I and R your lab released
- It does not replace Paragon Laboratory Management or your LIS for result entry, verification or reporting
- It does not submit antimicrobial use or resistance data to NHSN, which Paragon already does
- It does not send real-time alerts on individual patients
Related reading: critical access hospital antibiogram software, CLSI M39 antibiogram software, CPSI EHR antibiogram software, laboratory information system exports, WHONET alternative. The four steps from susceptibility testing data to an antibiogram cover the method end to end.
Questions
On this page's topic
Does Paragon have an antibiogram report?
Altera does not publicly describe a CLSI M39 cumulative antibiogram report in Paragon or Paragon Denali, and its user guides are behind a customer login, so ask your Altera contact what your site has. Most Paragon hospitals export a line list of final susceptibility results and build the antibiogram in Excel or in a separate tool such as Antimicrobe.
How do I export microbiology results from Paragon?
Ask your lab manager or Paragon analyst for a delimited report of finalized susceptibility results for the year, with patient identifier, collection date, location, specimen source, organism, drug and released interpretation. If microbiology is verified in a separate LIS, export from the LIS instead. Save it as CSV and upload it.
Who owns Paragon EHR?
Altera Digital Health owns Paragon. Altera was formed when Allscripts sold its hospital and global business, including Paragon and Sunrise, to a Constellation Software subsidiary for $670 million in cash in a deal that closed on May 2, 2022. Allscripts had bought Paragon from McKesson in October 2017.
Is Paragon EHR validated for NHSN AUR reporting?
Yes. The CDC NHSN vendor lists show Paragon 24.1, Paragon 25.1 and Paragon Denali 2.0 as validated for both the Antimicrobial Use and the Antimicrobial Resistance Options. That covers the files sent to NHSN. The cumulative antibiogram for your own prescribers is a separate report.
What happens to our antibiogram if we leave Paragon?
If it is built from a CSV export, nothing breaks. Export the historical years from Paragon before the cutover, keep building from the new system's export afterwards, and the rules and trends stay the same because they live in the antibiogram tool, not in the EHR.
How much does antibiogram software for a Paragon hospital cost?
Antimicrobe's Lab plan is $249 a month for one facility, bought by card with no implementation fee, and it reads Paragon, LIS and reference lab exports. Stewardship is $749 a month for unit cuts, trends and MDRO counts across up to three facilities, and Network is $2,400 a month for multi-hospital systems.
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