A fecal PCR panel looks for DNA from 4 organisms at once: Giardia, Cryptosporidium, Tritrichomonas foetus and Salmonella. Results come back in 24 to 72 hours, which is fast enough to change a plan. The trap is that a positive result means DNA is present, not that the organism is causing the diarrhea.
Three things make a positive PCR unreliable: DNA left behind after treatment, an asymptomatic carrier passing organisms through, and a low-level signal that is really contamination. All 3 are common, and all 3 are visible on the report if you know where to look.
The 4 targets, and what each one needs
Giardia cysts run 10 to 15 µm and are shed in waves. Cryptosporidium oocysts are smaller, 4 to 6 µm, and need a special stain to be seen under a microscope. Tritrichomonas foetus is a flagellated protozoan that lives in the colon and dies quickly outside the body. Salmonella is a bacterium, and for that one PCR is only half a result, because a PCR cannot tell you which drug works.
Giardia: 3 samples beat 1
Shedding is intermittent, so 1 negative sample means little. Collecting 3 samples over 5 to 7 days raises the yield substantially, and PCR holds up better than a microscope exam on a sample that spent the night in a fridge. A positive in a cat with no diarrhea is common in catteries, where cats share trays.
Tritrichomonas: fresh, or not at all
The organism is fragile. A sample kept at room temperature for 12 hours may still be PCR positive and completely non-viable; a sample refrigerated overnight may be negative because the DNA degraded unevenly. Best practice is a fresh sample, under 24 hours old, or a colonic wash collected at the clinic. A wet mount sees the organism maybe half the time; PCR does better, which is why a cat with chronic large-bowel diarrhea and a negative wet mount still gets the panel.
Cryptosporidium: the size that hides
At 4 to 6 µm the oocyst is smaller than a red cell and easy to miss on a routine fecal float. A negative float therefore does not rule it out. PCR gives the species, and the species matters: the cat-associated type is not the same public health story as the cattle type. A positive result in a cat with watery diarrhea and weight loss is worth acting on; the same result in a healthy kitten in a multi-cat house is often carriage.
Salmonella: why culture still matters
PCR tells you the genus is present. It cannot tell you the serovar, and it cannot give a minimum inhibitory concentration for any drug. If the cat is systemically ill, the sample goes for culture as well, and the susceptibility panel decides what is possible. Salmonella also has a human health dimension: litter trays, hand washing, and a household with a toddler or an immunocompromised adult change how urgent the result is.
False positive 1: DNA after treatment
Dead organisms still carry DNA. After an effective course, PCR can stay positive for 1 to 3 weeks while the cat is clinically normal and shedding nothing infectious. Retesting 48 hours after the last dose is the classic way to get a misleading positive and a second unnecessary course. Wait 2 to 4 weeks, or judge by the cat, not by the swab.
False positive 2: carriage without disease
Giardia and Cryptosporidium both turn up in healthy cats, especially where many cats share space. A positive result plus a normal fecal score plus a normal weight is carriage, not disease. The panel reports presence; the clinical picture decides whether presence matters. That is also why a positive result in a cat whose diarrhea started 3 days ago is weaker evidence than the same result in a cat that has had diarrhea for 3 weeks.
False positive 3: contamination and low signal
PCR amplifies. A few copies of DNA from a contaminated tube, a reused scoop, or a lab bench can produce a positive curve. The defence is the cycle threshold: a signal at 35 cycles or beyond is weak, and many labs will call it equivocal and ask for a repeat. Environmental DNA from litter, from a shared water bowl, or from a previous sample on the same day does the same thing.
The 4 rows and the numbers to ask for
| Target | Sample | Strong signal (Ct) | Result time |
|---|---|---|---|
| Giardia | fresh feces, 1 to 2 g | under 30 | 24 to 48 hours |
| Cryptosporidium | fresh feces, 1 to 2 g | under 30 | 24 to 48 hours |
| Tritrichomonas foetus | fresh feces or colonic wash | under 32 | 24 to 72 hours |
| Salmonella | feces plus culture swab | under 30 | 48 to 72 hours |
| Repeat after treatment | fresh feces | 2 to 4 weeks later | 24 to 48 hours |
Five rows, and 1 of them is about timing rather than a target. Ask for the Ct value for every positive, because 35 and 22 are not the same result even when both are printed as positive.
A positive panel is not a prescription
Four things decide what happens next: whether the cat has diarrhea, how long it has lasted, whether the weight is falling, and whether anyone in the house is at risk. A positive Giardia result in a cat with soft stool for 2 days and a normal weight may need nothing more than a repeat in 2 weeks. The same result in a kitten losing weight for 3 weeks needs a plan built by the veterinarian, with the drug and the dose chosen there.
Bring the numbers: fecal score from 1 to 7, weekly weight change in grams, and each collection date. Those 3 turn a positive PCR into a decision.
When to call the clinic the same day
Blood in the stool, more than 4 episodes of diarrhea in 12 hours, vomiting with no water kept down for 12 hours, a kitten under 12 weeks with any diarrhea, or a cat that stops eating for 24 hours. Those are the signs where dehydration moves faster than any PCR result.
5 steps before you send the sample
- Collect fresh feces into a clean container, 1 to 2 g is enough, and deliver within 24 hours.
- Do not freeze the sample and do not scoop it out of the tray with a used scoop.
- Ask for the 4 targets by name, plus the Ct value on any positive.
- If the cat has had treatment in the last 2 weeks, say so on the form, and expect a repeat in 2 to 4 weeks instead.
- Write the fecal score and the weight on the form; they are what turns a result into a plan.
Diarrhea workups often start with a blood count, and the ranges plus what a stress response looks like are in the WBC guide; breed tendencies for sensitive guts are collected in the breed quiz.
Frequently asked
Does a positive PCR mean the cat needs treatment?
No. A positive means DNA from that organism is present. Treatment depends on diarrhea, its duration, weight trend and the risk to people in the house. A healthy cat with a positive Giardia result and a normal fecal score is usually a carrier, and the plan is a repeat in 2 to 4 weeks rather than a course of drugs.
Why retest 2 to 4 weeks later instead of right after treatment?
Because dead organisms still release DNA, so a test at 48 hours can read positive on a cat that is cured. Waiting 2 to 4 weeks lets the DNA clear. Judge the cat in the meantime by fecal score and weight, and report any relapse to the clinic rather than repeating the test early.
What does the Ct value add?
It estimates how much DNA was in the sample. A low cycle threshold, around 22 to 28, means a strong signal. A value at 35 or beyond is weak and often called equivocal, because contamination can produce the same curve. Ask for the Ct on every positive and compare it with the lab's own cutoff.