Sunquest LIS antibiogram software that turns a Sunquest Laboratory export into an M39 antibiogram without the Crystal Reports cleanup

Where a Sunquest antibiogram usually falls short

The problem is not the data. It is the step between the data and the table. A 2024 paper from Brigham and Women's Hospital (Kanjilal and colleagues, Journal of Clinical Microbiology) put it plainly: Crystal Reports generated in the Sunquest LIS and WHONET can calculate these numbers, but both are limited by the extensive post-processing needed to use the data and the manual, non-automatable nature of the queries.

That post-processing is where antibiograms drift away from CLSI M39 without anyone deciding they should. The same handful of problems shows up in almost every Sunquest lab that builds its report in Excel.

If your lab already has a reliable Crystal Report, keep it as the export. The fix is in what happens to the file afterward, which is the subject of CLSI M39 antibiogram software.

• Duplicate isolates. A query that pulls every culture counts a patient with five positive urines five times. Older published Sunquest searches used one isolate per patient per month, which is not the M39 rule of one per patient per analysis period
• Preliminary and corrected results. A query that does not filter on final, verified results can count interpretations that were later changed
• Cut order. Splitting by unit after de-duplicating house-wide gives different numbers from de-duplicating each unit cut on its own
• One Crystal Report per cut. House-wide, urine, blood and each ICU usually mean separate report runs, separate exports and separate spreadsheets
• Small counts. Organisms under 30 isolates end up printed as a percentage because nobody had time to suppress them by hand
• Readers outside the lab. Pharmacy and infection prevention get a PDF, not something they can filter, so every follow-up question comes back to the lab

How to export antibiogram data from Sunquest

Ask your LIS analyst for one delimited file covering the full analysis period, usually January through December, with one row per organism and drug result or one row per isolate with a column per drug. Either layout works. The columns that matter are a patient identifier (a hashed or pseudonymous key is fine), collection date, ordering location or unit, specimen source, organism, antimicrobial and the released interpretation (S, I, R or SDD).

Filter to final, verified microbiology results and leave surveillance and screening cultures out, or keep a column that marks them, so they can be excluded consistently. If you already run a Crystal Report for the annual antibiogram, its underlying detail export is usually the right starting point. Save it as CSV.

WHONET users should know that BacLink has no ready-made Sunquest template. The WHONET guide to exporting from laboratory information systems gives detailed templates only for MEDITECH Magic and Cerner Classic and asks every other LIS for a delimited text export, because BacLink cannot read an LIS database directly. That is the same file Antimicrobe reads.

What a good LIS export looks like, column by column, is on laboratory information system exports.

1. 1

   Sunquest query

   Final, verified susceptibility results for the year, every instrument and bench method included

2. 2

   CSV file

   One delimited export, long or wide layout, patient key hashed or pseudonymous

3. 3

   Antimicrobe

   Map columns, units and sources once. First isolate, 30 isolate and intermediate rules applied per cut

4. 4

   Antibiogram

   House-wide, urine, blood and unit tables with a rule receipt for the committee

Sunquest reports, WHONET and Antimicrobe compared

WHONET is the free route and works well for a lab with the time to learn it. The practical differences are on the WHONET alternative page.

Does a Sunquest antibiogram follow CLSI M39?

It follows M39 only as far as the query and the spreadsheet do. Sunquest stores the results. It is the report logic that decides whether the first isolate per patient per analysis period is kept, whether results that are not final are excluded, whether species under 30 isolates are suppressed and whether each unit cut is de-duplicated on its own. None of that is guaranteed by the LIS itself.

The College of American Pathologists checklist asks labs that provide primary testing for hospitals to report cumulative susceptibility data to the medical staff at least yearly, and an inspector or a new pharmacy director will ask how the numbers were made. Every Antimicrobe export prints a rule receipt listing the rules applied and the isolate counts before and after de-duplication, so that answer is on paper.

The rule set, rule by rule, and how each common tool handles it, is on CLSI M39 antibiogram software. The finished report your committee signs is described on hospital antibiogram software.

What the Clinisys consolidation means for your annual report

Clinisys now owns several US laboratory systems. It combined Sunquest, HORIZON and Apollo LIMS under one brand in 2022 and acquired Orchard Software in July 2025. For a Sunquest site that means version upgrades, a possible move to newer Clinisys products and, for health systems, sister hospitals that may run a different Clinisys LIS.

An antibiogram that depends on a Crystal Report tied to one Sunquest version has to be rebuilt every time that happens. An antibiogram built from a plain CSV does not, because the rules live in the report tool rather than in the LIS. The same mapping reads an export from Sunquest this year and from whatever replaces it later, and a hospital that joins the system mid-year adds a file rather than a reporting project.

Which plan fits a Sunquest lab

A single hospital lab producing the annual house-wide report with urine and blood cuts 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.

A stewardship program that wants unit cuts, syndrome groups, quarterly trends and MDRO counts uses Stewardship at $749 a month for up to three facilities. A health system or a reference lab reporting for several facilities from one Sunquest instance uses Network at $2,400 a month.

Every limit is on the pricing page. Labs building reports for client facilities will find the setup in antibiogram software for reference labs.

What this does not do

• It does not connect to Sunquest directly or through HL7. It reads exported files, as often as you choose to export them
• It does not reinterpret MICs or zone sizes. It uses the S, I and R your lab released, so breakpoint changes are made in the LIS and the instruments
• It does not replace Sunquest for result entry, verification or reporting to clinicians
• It does not submit to NHSN or any public health system
• It does not send real-time alerts on individual patients