Polymyxins Resistance

Resistance genes can be present in your stool when you feel well. Their medical significance depends on which gene is detected, which bacterium carries it, and whether that bacterium causes an infection.

Targeted resistance testing can support hospital and public health investigations. Using this stool marker to predict your future infection risk or guide routine preventive care remains exploratory. The studies described below do not establish that screening healthy adults before surgery, after travel, or every year improves health outcomes.

What This Stool Result Measures

This test uses qPCR to look for bacterial DNA associated with polymyxin resistance in stool. qPCR copies selected DNA sequences and tracks them as they accumulate. It can detect genetic material without recovering a living bacterium.

The catalog specifies stool and qPCR, but it does not name the individual genes or variants included. The mcr family contains well-studied examples of polymyxin resistance genes. Coverage of mcr-1, other mcr variants, or additional resistance mechanisms cannot be assumed from the test name.

The catalog also gives no reporting unit. Although qPCR can support quantitative measurements, that does not establish that this test reports gene abundance. A detected or not-detected result has no numerical level to trend.

How These Resistance Genes Work

Colistin and polymyxin B act against certain Gram-negative bacteria. These bacteria have an outer membrane in addition to their inner membrane. Polymyxins interact with molecules in these membranes and can disrupt them.

Many mcr genes direct bacteria to make a protein that modifies lipopolysaccharide. Lipopolysaccharide is a molecule found mainly in the outer membrane. Its modification can reduce the antibiotic's effect. Laboratory experiments in E. coli show that MCR-1 can protect the inner membrane even while colistin still damages the outer membrane, so resistance is more complicated than preventing the drug from sticking.

Other resistance mechanisms involve changes in the bacterium's main DNA. Commonly studied genes include mgrB, pmrAB, and phoPQ. Some bacterial species are naturally resistant to polymyxins. An assay targeting selected mcr genes would miss these other routes unless they were separately included.

What a Positive Result Means

A positive result means that a targeted DNA sequence was detected in the sample. It can be consistent with gut carriage, but it does not by itself establish that living resistant bacteria are present or that you have an infection. Stool DNA testing also cannot establish that a detected resistance gene caused diarrhea or another symptom.

A detected gene may not work. In a Dutch study, researchers recovered an E. coli strain that tested positive for mcr-1 but remained susceptible to colistin under the study's testing criteria. Sequencing showed that an inserted piece of DNA had interrupted the gene. Enough of the sequence survived for the PCR target to be found, but the gene itself was broken, which is a different situation from an intact gene that is simply not switched on.

Culture and susceptibility testing answer a different question: whether a recovered bacterium grows in the presence of an antibiotic. Broth microdilution is the reference laboratory method for assessing colistin susceptibility. The result still needs interpretation alongside the infection site, available treatments, and current susceptibility standards.

What a Negative Result Leaves Unanswered

A negative result means the assay did not detect its targets in that sample. Resistance may still be present through an untested gene, a mutation, a naturally resistant species, or an amount of DNA below the assay's detection limit.

A Brazilian hospital outbreak illustrates the distinction. Changes affecting mgrB were found in 87.5% of the cultured colistin-resistant Klebsiella pneumoniae isolates. These changes included several types of disruption, not only insertion sequences. All isolates tested negative for mcr-1. This was evidence about cultured bacteria and their chromosomes, not the performance of this stool assay.

How Resistance Spreads

Many mcr genes are carried on plasmids. Plasmids are separate pieces of DNA that some bacteria can pass to other bacteria. That provides a route for resistance to move between bacterial strains and species.

Bacteria with resistance caused by chromosomal changes can also spread between people. The Brazilian outbreak included closely related resistant strains in different hospital departments. Transferable genes and transmission of whole bacteria both matter.

A stool qPCR result alone cannot show which organism carries a gene, whether the gene is on a plasmid, or whether that plasmid can transfer. Finding several resistance genes in one sample also does not prove they occur in the same bacterium or on the same plasmid.

What Human Carriage Studies Found

Reported detection rates vary with location, the population studied, the sampling period, and the laboratory method. These studies measured selected mcr genes using their own assays, sometimes after growing bacteria. They are not validation studies of this catalog test, and their percentages are not estimates of your future infection risk.

The Singapore study shows that direct DNA testing and culture can yield different detection rates. It does not establish that PCR always outperforms culture, or that every additional DNA detection represents a living resistant organism. The Swiss and Czech findings depended on growing bacteria first, so neither is a directly comparable baseline for a result produced by testing stool DNA without any culture step.

What the Infection Studies Can Tell You

Polymyxin resistance can make an established bacterial infection harder to treat. In a hospital cohort of 246 people with cultured carbapenem-resistant Klebsiella pneumoniae, 13% had colistin-resistant isolates. Colistin resistance was associated with higher in-hospital mortality.

That cohort included people with infection and people with colonization. It assessed resistance in cultured organisms, so it cannot quantify the future risk from a positive stool resistance-gene result in someone who feels well.

Some bacteria carry both mcr genes and genes associated with resistance to other antibiotic classes. This combination can narrow treatment options, but mcr detection alone does not establish carbapenem resistance. In the Singapore stool study, none of the recovered mcr-1-positive isolates was carbapenem-resistant.

When Results Can Be Misleading

• Unconfirmed target coverage: the test name does not establish which genes or variants are included. Results apply only to the sequences the assay was designed and validated to detect.
• DNA without a living organism: qPCR can detect residual genetic material. Detection alone does not establish viable colonization, gene activity, or susceptibility to an antibiotic.
• A broken gene can still be detected: a PCR target can survive in a gene that has been interrupted and no longer produces a working protein.
• Low amounts and uneven sampling: a gene may be missed when little target DNA reaches the tested portion of stool. Changes between samples can reflect sampling variation.
• Extraction problems and PCR inhibition: substances in stool can interfere with DNA recovery or amplification. Laboratory controls help identify these problems.
• Recent antibiotics: treatment can change the bacterial community and the amount of target DNA. A result during or after treatment may differ from an earlier result without indicating that an infection has appeared or cleared.
• Differences between laboratories: target lists, sample preparation, detection limits, and reporting rules differ. Results from different assays are not automatically interchangeable, and a result from a culture-based or enrichment-based method is not directly comparable with one from direct stool qPCR.

What Serial Results Can Show

The bacterial genes detected in your stool can change over time. A change may reflect acquisition or loss of bacteria, shifts in their abundance, or the assay's detection limits. Repeated results have not been validated as a score for longevity or future infection risk, and a later negative sample does not necessarily establish lasting clearance.