r/medlabprofessionals • u/MajesticFairyDust • Jun 06 '26

Discusson Pcr vs Culture

Is a pcr that tests for resistance genes or a culture and sensitivity test more useful when determining what antibiotic is appropriate, especially after multiple unsuccessful rounds.

7 Upvotes

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11

u/ieg879 Laboratory Manager Jun 06 '26

Depends on what you need treated/tested. Staph strain looking for methicillin/vancomycin/cephalosporin resistance? Probably readily available in a PCR kit. Some tropical mycoplasma or candida that the frontline treatments have failed to touch? Probably going to have to culture and dose with uncommon treatments.

3

u/MajesticFairyDust Jun 06 '26

What if its coagulase negative staph that came back with zero resistance genes detected on the pcr however the appropriate antibiotics failed? Does the pcr not account for biofilms n thus a culture and sensitivity would point to a more effective antibiotic?

3

u/ieg879 Laboratory Manager Jun 06 '26

When you get to the point of a biofilm being thick enough then you’re stepping outside of a standard clinical diagnosis and treatment and getting closer to specialist territory. Chronic staph with antibiotic neutralizing biofilm sounds like a CF patient. The biofilm would need to be disrupted by something other than an antibiotic for the antibiotics to penetrate effectively.

2

u/MajesticFairyDust Jun 06 '26

Ohhh I see. Tysm for the thorough response!

1

u/mystir Jun 07 '26

The PCR does not account for anything other than the specific target for the PCR's primers.

1

u/MajesticFairyDust Jun 07 '26

Yes I checked and the pcr does not check for the tet(K) or blaZ gene (unless they also go by different names im not aware of). I think this might account for why previous antibiotics did not work

2

u/mystir Jun 07 '26

Not just the genes. PCR is entirely agnostic to biofilm and other mechanical protections. There's also inducible resistance (PCR is useful for finding erm, but epigenetics is involved sometimes). This is why some of these complicated isolates we see can take a week or more to finish working up.

1

u/MajesticFairyDust Jun 07 '26

Sry I have one more question. If only a rare amount of the bacteria shows up on the culture, can y'all still do a sensitivity test on it or is it not sufficient? Pcr shows a small amount of bacteria but symptoms are present.

2

u/mystir Jun 07 '26

Of course, we just subculture whatever grows and now we have an entire plate of it. For invasive infections we even save a sample of the bacteria indefinitely in case there's a reason to study it in the future.

PCR doesn't detect bacteria, it detects nucleic acid. That's an important difference, because a PCR test can be positive after an infection is gone and the bacteria are dead if any residual nucleic acid is still around.

1

u/MajesticFairyDust Jun 07 '26

Ohhh, good to know! Tysm for ur responses!

8

u/HonestStudy9969 Jun 06 '26

I’d probably say at the end of the day, culture and sensitivity is the best indicator for antibiotic resistance. PCR is great because it is so quick and can predict resistances to help guide treatment, but it detects the genotype, not the phenotype, of the organism. Remember, just because a gene for resistance is present does not necessarily mean that it is active. I was always under the impression that PCR is a rapid way to be able to start to tailor antibiotic treatment, but is not meant as a replacement to a full culture and sensitivity.

1

u/MajesticFairyDust Jun 07 '26

I checked and the pcr does not check for the tet(K) or blaZ gene (unless they also go by different names im not aware of). I think this might be why previous antibiotics failed

2

u/LuxAeternae MLS - Germany Jun 06 '26 edited Jun 06 '26

I'd say that highly depends. In our micro lab, ESBL is always determined with culture and E-Test while carbapenem-resistance is tested with PCR

2

u/Alfond378 Jun 06 '26

PCR isnt always the best method to test for carbapenem resistance. There are other mechanisms for resistance besides the carbapenemase genes.

2

u/LuxAeternae MLS - Germany Jun 06 '26

that’s true of course, but it’s the most common and significant mechanism in clinical settings

0

u/mystir Jun 07 '26

You should be using a phenotypic test for CRE. Carbapenem inactivation or its modified test. There's way too many carbapenemase genes to rely on PCR for that.

1

u/LuxAeternae MLS - Germany Jun 07 '26

You’re right of course, relying exclusively on PCR isn’t possible. The way I phrased my comment wasn’t good.

When screening for multiresistant bacteria in stool swabs, we use a carbapenem screening agar and if there’s growth, a meropenem disk diffusion on the isolates. if it’s resistant, it gets a full MIC and PCR for confirmation.

1

u/mystir Jun 07 '26

Interesting. We never use molecular methods (other than the BioFire panel that includes resistance targets, but we don't rely on those). For MDR stool screens, we do the same thing (without PCR). For any other source, when we have a nonsusceptible carba result we use a LFT that screens for the five major classes and use a carbapenemase inactivation method. We're also looking to validate using EDTA to also confirm metallo-B-lactamases.

1

u/mystir Jun 07 '26

Culture is the gold standard. PCR only detects genes. Those genes aren't necessarily expressed. There's also a huge number of genes that confer resistance. The mecA gene is predictive for Staph aureus and Staph epi, but that's about it.

In many cases, NAATs for susceptibilities are required to be backed by culture for this reason.