Approaches to Detect Antimicrobial Susceptibility

Romney Humphries, PhD, D(ABMM), section chief of Clinical Microbiology at the University of California, Los Angeles, discusses the two approaches used to detect antimicrobial susceptibility: genotypic and phenotypic.

Interview Transcript (slightly modified for readability)

“To date, new technology to detect antimicrobial susceptibility has really taken one of two approaches: we can look for a gene in an organism that’s thought to predict its resistance to a given antimicrobial, so that’s the genotypic approach, or we can do a phenotypic method which answers the question, 'If I incubate [these] bacteria with this drug, does it prevent it from growing or is the organism resistant and can grow even in the presence of the drug?'

Both have advantages and disadvantages. To date, most technologies have really focused on genotypic approaches, and so there are some challenges with that, particular[ly] for some organisms that we have real problems with today, like the gram-negative bacteria. By looking for just a single gene, you don’t get the entire story of what’s happening in that bacterium. We know in gram-negative infections resistance is usually multi-factorial [with] a combination of [the] presence of a gene, its expression, as well as other factors, like porins or efflux; and so, by asking 'is that gene there?' you don’t really know what else is going on. When you detect a gene you must assume resistance, but we know that often the gene will be present and there will be no resistance; and so, this is one big challenge. You’re not really able to detect susceptibility using a genetic approach, you’re only able to assume resistance.

The other challenge with it is there’s a disconnect between what we use, called a clinical breakpoint, versus a genotypic method. When you’re [using] a genotypic method, you’re looking to see if the organism is wild-type, natural state, or if it's acquired a resistance mechanism. [However], that doesn’t necessarily mean that it will have an MIC that’s above the clinical breakpoint and so you still may be able to treat some of these infections even though they have a resistance gene. We’ve seen that numerous times in our lab. When we started to do things like whole genome sequencing of bacteria, [we found] a lot of resistance genes but either they’re not being expressed or on their own do not contribute to a resistance phenotype.

For these reasons, I really think that having a phenotypic approach is a lot more desirable. However, you need an awful lot of bacteria to [test using] a phenotypic approach. It also needs more time than we really want to spend waiting for a result, because you need to give the organisms time to respond to the antimicrobial. So, those two things combined make it very difficult to make a very rapid, direct-from-patient specimen phenotypic test. Nonetheless, [with] a phenotypic test [it] does not matter which mechanism is causing the resistance phenotype; as we have new antimicrobials come to market, and we don’t know what those resistance mechanisms will be, a phenotypic approach should be able to detect resistance or susceptibility in those cases.”