The report
Hospital antibiogram production, from twelve months of isolates to a signed-off report
The annual antibiogram is the most reused document a microbiology laboratory produces, and usually the most expensive one to make.
Short answer
A hospital antibiogram is a periodic summary of susceptibility across all isolates in a period, organism by antibiotic, used to guide empiric therapy. CLSI document M39 describes how to build one: analyse at least a year, include only the first isolate per patient per organism, and do not report an organism and drug combination with fewer than 30 isolates.
The three rules that decide every number on the page
Almost every disagreement about an antibiogram comes down to one of these, and each is a visible setting in the builder rather than something buried in a method note.
- First isolate per patient per organism, so repeat cultures cannot skew the report toward the sickest patients
- A minimum of 30 isolates before a cell is reported, because a percentage on a handful of isolates reads like a fact and is not
- A stated treatment of intermediate results, either excluded from the denominator or counted as resistant
Where the weeks go, and what removes them
The analysis is not the slow part. The slow part is pulling the export, de-duplicating by hand in a spreadsheet, pivoting, checking the suppressed cells, formatting, circulating a draft, and doing it again when someone asks for the intensive care version.
When those steps are one filter combination, the annual report stops being a project and the follow-up questions stop being a negotiation.
Sub-reports worth publishing alongside it
- Intensive care versus non-intensive care, the most requested cut in most hospitals
- Urine only, which usually carries enough isolates to stand alone
- Blood only, for the sepsis guideline, accepting that more cells will suppress
- Paediatric isolates, where they exist in sufficient number
Related reading: the breakpoint set behind the numbers, the program that consumes the report. The four steps from susceptibility testing data to an antibiogram cover the method end to end.
Questions
On this page's topic
How long should the reporting period be?
A year is the convention and the safest default for cell counts. Shorter periods are useful for watching movement, and they will suppress more cells, which is the honest trade.
Should the antibiogram include all isolates or only significant ones?
That is a laboratory decision about what enters the export. The rules here apply to whatever you send, and the receipt states what was applied.
Can I reproduce last year exactly?
Yes, if you keep the export. The same file plus the same settings gives the same matrix, which is what makes a year-over-year comparison meaningful.
More on antimicrobial resistance reporting
- UTI antibiotic resistance Urine is the highest volume specimen most laboratories process, which makes it the one sourc...
- carbapenem resistant organism Carbapenem resistance is the event that changes what a hospital can do next, and it is the l...
- empiric therapy Every empiric decision is a bet placed before the culture is back. The only honest way to im...
- resistance map Public resistance maps are useful for policy and useless for prescribing. The map that chang...
- antibiotic stewardship program A stewardship program lives or dies on whether it can answer questions quickly. Most of the...
- CLSI breakpoints A breakpoint revision can move a susceptibility rate by several points without one organism...
Start with your own export
See your own resistance picture, cut the way you actually work
Build the antibiogram on the synthetic sample dataset, or drop in your own CSV and watch it parse without leaving your browser. When you want an account, one email address is the whole sign-up.
Your file is parsed in your browser and never uploaded. No card required.