Viability tests have been introduced to improve understanding of positive molecular diagnostic test results, but routine use remains limited. Alongside this, antimicrobial resistance (AMR) continues to cause issues across the clinical landscape, complicating both diagnosis and patient care. In hopes of improving diagnostic outcomes, researchers at Harvard Medical School, Boston, explored the correlation of AMR markers and clinical outcomes in Neisseria gonorrhoeae. Tatum Mortimer presented this work at ESCMID Global 2025, and we connected after the event to discuss future outcomes.
What are the current challenges in detecting AMR in Neisseria gonorrhoeae and how do they impact clinical decision-making?
Culture is still the gold standard for testing gonococcal susceptibility, but it's not practical for routine use. Culturing takes several days, many labs lack the expertise to grow N. gonorrhoeae, and some samples that test positive can’t be cultured at all. Because of these limitations, doctors usually treat gonorrhea based on general resistance trends rather than individual test results. According to current guidelines, if more than 5 percent of tested gonorrhea samples are resistant to an antibiotic, that drug should no longer be used.
Some molecular tests, like the SpeeDx ResistancePlus GC, can detect gonorrhea and predict whether it will respond to ciprofloxacin. But modeling studies suggest that testing for just one antibiotic may actually contribute to the development of multi-drug resistance.
Ciprofloxacin resistance is relatively easy to predict, since it depends on changes at a single genetic site. But for other antibiotics, resistance is more complex. N. gonorrhoeae can resist treatment in several ways: by blocking drug entry, pumping drugs out, or mutating the drug’s target. These resistance mechanisms can involve many types of genetic changes, including single-letter mutations, insertions or deletions in DNA, missing or extra genes, and hybrid genes from other bacteria.
How is AMR in N. gonorrhoeae detected, and what are the limitations?
Traditional diagnostic tests for N. gonorrhoeae don’t detect AMR. Most infections are diagnosed using nucleic acid amplification tests (NAATs), which detect the bacteria’s genetic material in a patient sample. These tests can pick up DNA or RNA from dead bacteria, not just live ones. While this is known to happen in Chlamydia trachomatis, there hasn’t been much research yet on whether N. gonorrhoeae detected by NAATs is always from live bacteria.
Does viability testing help reduce false positives or false negatives in AMR detection, and if so, how significant is the reduction?
Viability testing could be especially helpful for test-of-cure situations.
Studies show that N. gonorrhoeae RNA usually clears from the body within 7 days for cervical, urethral, and rectal infections, and about 12 days for throat infections. DNA takes even longer – up to 14 days – to clear. This delay can be a problem when using tests of cure to check if treatment worked, because the tests may still detect leftover genetic material even after the infection is gone.
In a CDC study, 4.5 percent of patients tested positive during a test of cure, but about one-third of those were likely false positives.
Could the approach of measuring viability to enhance AMR marker correlation be expanded to other pathogens beyond N. gonorrhoeae?
These approaches are actually already farther along in other pathogens – like C. trachomatis – than in N. gonorrhoeae!
Are we fighting a losing battle considering how quickly diseases and AMR mutate/evolve?
Like many bacteria, N. gonorrhoeae quickly becomes resistant to antibiotics soon after they are introduced. I don’t think the situation is hopeless, but we do need several approaches to fight AMR. We should make the best use of current antibiotics and explore new treatments, like zoliflodacin and gepotidacin. Tools like at-home or point-of-care tests and vaccines could also help prevent infections.
Ongoing surveillance of AMR in N. gonorrhoeae is essential. Unfortunately, recent CDC budget cuts will make it harder to track resistance trends in the US. Much of my past research depended on public health agencies that collected and shared detailed data on gonorrhea infections and resistance.
What are the next steps in your research, and how close do you think we are to seeing viability-based diagnostics become a clinical standard?
We know a lot about the genetic basis of AMR in N. gonorrhoeae and can use whole genome sequencing (WGS) to predict how susceptible a strain is to treatment. Our team is working with the ESGEM-AMR Working Group to create standardized rules for interpreting resistance genes in gonorrhea. The group recently published a first set of rules for several bacterial species. Since it’s not practical to use WGS for every gonorrhea case, we’re also using genomic data to find targets for molecular tests that can predict resistance to multiple antibiotics.
As far as I know, there aren’t any molecular tests yet that measure N. gonorrhoeae viability. However, Petra Wolffs – who also presented at the ESCMID Global session – is developing one. She plans to share her findings at the STI & HIV 2025 World Congress, and I’m looking forward to seeing her results.
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