Microbiology lab software for culture and sensitivity reporting
Microbiology lab software should let a lab report a culture the way the bench actually works: a preliminary report at 24 hours, then a signed final report with every organism, its colony count and a sensitivity table, and every quarter an antibiogram that tells referring doctors which antibiotics still work locally. PathLab Software does this inside the same LIS that runs your haematology and biochemistry, for Indian pathology labs of every size.
What should microbiology lab software do?
Most lab software treats a culture as one more test with a free-text result box, so the microbiologist ends up typing organism names and antibiotic lists into Word. A culture is different from a glucose result in five ways, and software for a microbiology bench has to handle all five:
- Staged reports. A culture takes 24 to 72 hours or longer. Doctors need a preliminary result ("Gram-negative bacilli isolated, sensitivity to follow") early, and a final report later on the same order.
- Isolates, not parameters. One urine culture may grow nothing, one organism or two. Each organism needs its own name, colony count and comment.
- AST panels. Each organism group is tested against a different list of antibiotics. The lab decides the lists and their order; the software should fill them in rather than make staff type 12 antibiotic names.
- Interpretation rules the lab owns. Zone sizes and MICs are turned into S, I, SDD or R using breakpoints from the CLSI or EUCAST document the lab has adopted. Those tables change every year, so the lab must be able to enter and update them.
- An antibiogram. The cumulative percentage of isolates susceptible to each antibiotic, counted from the lab's own finalised results, is what infection-control teams and referring doctors ask for.
How does a culture move through PathLab Software?
Seven steps, from the barcode scan at reception to a signed report and the quarterly antibiogram. Nothing is retyped between them.
- Receive the specimen. When a sample carrying Urine C&S, Blood C&S, Pus C&S or Sputum C&S is marked received, a culture appears on the microbiology worklist with its specimen type and the lab's default incubation time (urine 48 h, blood 120 h, others 48–72 h, all editable).
- Watch the worklist. Tabs show Incubating, Preliminary due, Final due and Finalised. A culture turns red when it runs 12 hours past its incubation time, so nothing sits forgotten in the incubator.
- Record growth. No growth after N hours, growth, mixed growth (three or more organisms, which suggests contamination) or contaminated and recollect, with an optional Gram stain line.
- Add isolates. Up to three organisms per culture, picked from your organism master, each with a colony count such as ≥ 10⁵ CFU/mL, Scanty, Moderate or Heavy.
- Enter the sensitivity panel. Pick the panel (for example Urine Enterobacterales); the antibiotics appear in your order. Type each zone in mm or MIC in µg/mL.
- Apply interpretation and cascade. Where your lab has entered a breakpoint, S/I/R fills in; staff can override it and the override is audited. Tier-2 agents are suppressed from the patient report when every tier-1 agent of the same group is sensitive.
- Submit and sign. The culture goes into the normal validation queue. On the pathologist's signature the final report is produced with its SHA-256 fingerprint and QR verification code, and the isolate starts counting in the antibiogram.
Preliminary report at 24 hours
From the culture screen, "Issue preliminary report" records the preliminary text and time and gives a printable report with a PRELIMINARY ribbon. If WhatsApp messaging is set up and the patient has opted in, the same text can be sent to the patient; the final report always follows through the normal signed route.
Final report with organism-wise sensitivity
The final report lists the specimen, incubation and growth, then each organism with its colony count and its own antibiotic table: antibiotic, zone or MIC, and the interpretation spelled out in words. If cascade rows were suppressed, the report adds "Additional antibiotics were tested; results available on request." The headings print in English with Hindi or Tamil alongside when the patient's report language is set to one of them.
Sample culture report and antibiogram
Below is what the two screens look like. The left card is a final urine culture report; the right card is a quarterly antibiogram. Both use fictional patients and numbers.
Revathi S · 45 F · Specimen: urine (midstream) · Incubation 48 h aerobic
Growth: Escherichia coli, ≥ 10⁵ CFU/mL
| Antibiotic | Zone (mm) | Interpretation |
|---|---|---|
| Nitrofurantoin | 21 | Sensitive |
| Fosfomycin | 24 | Sensitive |
| Amoxicillin-clavulanate | 19 | Sensitive |
| Gentamicin | 20 | Sensitive |
| Ciprofloxacin | 12 | Resistant |
| Ceftriaxone | 27 | suppressed (cascade) |
| Piperacillin-tazobactam | 23 | suppressed (cascade) |
| Meropenem | 28 | suppressed (cascade) |
Grey rows are visible to staff only. Footer: QR verification · "Interpretive criteria: as adopted by the laboratory".
| Organism (n) | AMC | CRO | CIP | NIT | FOS | GEN | AMK | MEM |
|---|---|---|---|---|---|---|---|---|
| E. coli (34) | 71 | 56 | 38 | 91 | 94 | 79 | 94 | 97 |
| K. pneumoniae (12)* | 50 | 42 | 42 | 42 | 67 | 67 | 83 | 83 |
Cells: ≥ 90 % · 70–89 % · < 70 %. * Fewer than 30 isolates: interpret with caution.
For a field-by-field guide to what a culture report should contain, see the culture and sensitivity report format guide, which has a complete sample report you can copy.
S, I, SDD and R: how interpretation works
A zone of inhibition or an MIC means nothing on its own; it becomes Sensitive, Intermediate, Susceptible-dose dependent or Resistant only when compared with a breakpoint for that organism group, antibiotic and method. Those breakpoints are published by CLSI (the M100 document) and EUCAST, they change every year, and CLSI's tables are copyrighted. That is why PathLab Software ships no breakpoint table at all.
- Your lab enters its breakpoints in the masters screen: organism group × antibiotic × method (disc or MIC), the S and R thresholds and a source label, for example "CLSI M100, edition adopted by the lab". Values in between are reported as Intermediate.
- Auto-fill, never auto-sign. When a breakpoint exists, the interpretation fills in as you type the zone. When none exists, staff choose S, I, SDD or R by hand. Either way, the microbiologist or pathologist who signs the report is responsible for it.
- Overrides are audited. Changing an auto-filled S to R (or the reverse) is allowed, shows a small "edited" badge and writes the old and new value, user and time to the audit trail.
- Intrinsic resistance. Pairs on your lab's intrinsic-resistance list, for example Klebsiella with ampicillin, show "Intrinsic R, not reported", are left off the patient report and are excluded from the antibiogram.
PathLab Software supports the microbiologist's judgement; it does not replace it. Starter organism, antibiotic and panel lists are provided for you to review with your microbiologist before use.
What is cascade reporting and should your lab use it?
Cascade (selective) reporting means the lab tests a full panel but shows broader-spectrum or reserve antibiotics on the patient report only when the first-line ones fail. If an E. coli from urine is sensitive to every tier-1 agent of a group, reporting meropenem as well invites its use when it is not needed. Many antimicrobial-stewardship programmes ask labs to report this way.
In PathLab Software each antibiotic in a panel is tier 1 or tier 2, and each antibiotic belongs to a group in the antibiotic master (for example beta-lactam or aminoglycoside). When every tier-1 agent of a group is S, the tier-2 agents of that group are suppressed: greyed for staff, hidden on the patient report, still counted in the antibiogram. A pathologist can un-suppress any row, for example for a patient with a penicillin allergy, and the change is logged. Cascade reporting can be switched off for the whole lab in settings.
Cumulative antibiogram from your own isolates
An antibiogram summarises, for each organism, the percentage of isolates that tested susceptible to each antibiotic over a period. Referring doctors use it to choose empirical treatment before a patient's own culture is back. PathLab Software builds it from finalised cultures only, using simplified conventions in the style of CLSI M39:
First isolate per patient
A patient with three positive urine cultures in one quarter counts once per organism, so repeat testing does not skew the percentages. The toggle is on by default.
At least 30 isolates
Organisms with fewer than 30 isolates in the period are greyed and footnoted "interpret with caution". The minimum is editable.
Filters and exports
Period (default: last full quarter), specimen, branch and referrer type (OPD vs hospitals and clinics). CSV export and a print view with the lab header and method note.
Percentages exclude intrinsic-resistance pairs and untested agents and include cascade-suppressed results, so the table reflects what was actually tested. It is a local summary for your referrers, not a surveillance system, and it exports as CSV rather than WHONET format.
Where microbiology fits with QC, NABL records and WhatsApp delivery
Cultures use the same order, barcode, validation, signature and delivery path as every other test, so the rest of the lab's records stay in one place. Sample rejections for microbiology (for example a non-sterile container or a contaminated sample) go into the sample rejection register with a recollection. The incubator's twice-daily temperature readings sit in the equipment and temperature log. Internal QC for your analyzers stays on the QC page, the audit trail covers every override, and the signed final report goes out with QR verification on WhatsApp like any other report. The clause-by-clause view of these records is on the NABL software page, and the culture indicators sit beside the others in the quality indicators dashboard.
How does it compare with other ways of reporting cultures?
| Task | Handwritten register | Word / Excel templates | Typical small-lab LIS (India) | PathLab Software |
|---|---|---|---|---|
| Preliminary and final report on one order | Two separate papers | Two files, manual | Usually one free-text result | Built in, with timestamps |
| Organisms with colony counts | Handwritten | Typed each time | Free text or fixed format | Up to 3 isolates from your master |
| AST panel filled from your list | No | Copy-paste | Varies | Lab-defined panels with tiers |
| S/I/R from your breakpoints, overrides audited | No | No | Varies | Yes; no tables shipped |
| Cascade reporting | No | Manual deletion | Not shown publicly* | Automatic, un-suppress logged |
| Cumulative antibiogram | Hours of counting | Pivot tables | Not shown publicly* | First isolate, n ≥ 30, CSV |
| Signed report with QR verification | No | No | Some | SHA-256 fingerprint and QR |
* As of November 2026, in the public material of the 20 Indian and global LIS vendors we reviewed, we could not find a cumulative antibiogram or cascade reporting; check with each vendor, as features change.
What it does not do
- It does not ship CLSI or EUCAST breakpoint tables; your lab enters and maintains its own.
- It does not interface AST instruments such as VITEK, Phoenix or MicroScan yet; zones and MICs are typed in.
- It does not export to WHONET; the antibiogram exports as CSV.
- It does not replace the microbiologist: every final culture report is authorised by the lab's pathologist or microbiologist.
Pricing
Microbiology culture and sensitivity with preliminary and final reports, panels, cascade reporting and the antibiogram is included in the Complete plan at ₹3,290 a month and in Network at ₹6,490 a month, plus 18% GST, billed monthly with no setup fee. It is not part of the Essential plan.
| Plan | Price a month | Microbiology module |
|---|---|---|
| Essential | ₹1,290 | — |
| Complete | ₹3,290 | Included |
| Network | ₹6,490 | Included, all branches |
See every plan on the pricing page and the other new modules on the features page.
Frequently asked questions
What is microbiology lab software?
Microbiology lab software records cultures the way the bench works: specimen, incubation, growth, each organism with its colony count and an antibiotic sensitivity (AST) table, then a preliminary and a signed final report. PathLab Software adds lab-defined AST panels, cascade reporting and a cumulative antibiogram built from the lab's own finalised isolates.
How do you report a culture and sensitivity test?
Report the specimen and incubation, the growth result, each organism with its colony count, and for each organism the antibiotics tested with zone size or MIC and the interpretation (Sensitive, Intermediate, Susceptible-dose dependent or Resistant). PathLab Software lays this out automatically and adds the interpretive-criteria line your lab sets.
What does S, I and R mean in a culture report?
S (sensitive or susceptible) means the organism is likely to respond to a standard dose, R (resistant) means it is unlikely to respond, and I (intermediate) means the result is uncertain or needs a higher dose or a site where the drug concentrates. SDD means susceptible-dose dependent. The cut-offs come from the breakpoints your lab adopts.
What is a cumulative antibiogram and how is it calculated?
A cumulative antibiogram is a table of the percentage of isolates of each organism that tested susceptible to each antibiotic over a period, usually a quarter or a year. PathLab Software counts the first isolate per patient per organism, excludes intrinsic resistance, includes cascade-suppressed results and greys organisms with fewer than 30 isolates.
How long does a urine culture report take?
A no-growth urine culture is commonly reported after 24 to 48 hours of incubation, and a positive culture with sensitivity usually takes 48 to 72 hours; your lab's SOP sets the times. In PathLab Software each specimen has a default incubation time, and the worklist flags cultures that run 12 hours past it.
Can the software interpret zone sizes automatically?
Yes, from breakpoints your laboratory enters. PathLab Software does not ship CLSI or EUCAST breakpoint tables, because they are revised every year and are the lab's responsibility. When your lab has entered a breakpoint for that organism group, antibiotic and method, the S/I/R fills in; any manual change is recorded in the audit trail.
Can I send a preliminary culture report on WhatsApp?
Yes, optionally. When you issue a preliminary report, for example "Gram-negative bacilli isolated; sensitivity to follow", PathLab Software can send that text on WhatsApp if messaging is set up and the patient opted in, and the preliminary report can be printed. The signed final report then goes through the normal QR-verified delivery.
Which PathLab Software plan includes microbiology?
Microbiology culture and sensitivity with the antibiogram is included in the Complete plan at ₹3,290 a month and in Network at ₹6,490, plus 18% GST, with monthly billing and no per-module fee. It is not part of the Essential plan. Every plan starts with a 21-day free trial.
Report your next culture in PathLab Software
Start the 21-day free trial, load the starter organism and panel lists, add your lab's breakpoints, and issue a preliminary and final report the same week. Want help? Book a free setup call on the contact page.