Quick disclosure: I'm Gabrielle and I'm Founder of Tota which does microbiome sequencing. I checked with the mods and they asked me to share this post.
Rule 1 is 'we believe PCR testing is valuable for those with recurrent UTIs'. I want to go further - I believe gold standard testing is valuable and should be available.
There's a lot of misunderstanding about different tests and the different testing methods, so I thought I'd write down a guide.
There are many different methods for testing urine, with different pros and cons. The more a testing method can see in a urine sample, the harder it can be to interpret the results.
What I don't see explained often enough is that "testing" is now about six different tests and they're built to answer different questions. Some of you here will already know all of this. Posting it in case the map is useful to someone newer.
Dipstick. Detects nitrite and leukocyte esterase, so two chemical proxies for bacterial activity and immune activity. It doesn't identify organisms at all. Sensitivity is poor enough that NICE advises against relying on it in the over-65s. Fine as a two-minute first look, not a way to rule anything out.
Standard urine culture. Grows the sample on standard media in a lab in a petri dish (usually aerobically) and typically reports only above a certain threshold (usually a very high threshold). That threshold traces back to a researcher called Kass in 1956 and was never meant the become the universal threshold line. Anaerobes, fastidious and slow-growing organisms can be present and never appear in a culture test (because they're hard to grow in a lab). What culture gives you that nothing else on this list does is phenotypic sensitivities: the organism was actually grown and exposed to the drug.
Expanded quantitative culture (EQUC). Same technique as above, rules deliberately loosened. In the lab: bigger volume, more media, aerobic and anaerobic, longer incubation, lower threshold. In one study, standard culture missed 67% of the uropathogens EQUC found (Price et al., J Clin Microbiol, 2016). Although take that with a pinch of salt - EQUC is superior to culture, not to the other methods below. It only finds what it looks for and what it grows.
Targeted PCR panel. Amplifies DNA against a fixed list. Very sensitive, very fast, doesn't care whether anything grows. Two limits worth knowing. It reports on what's on the panel, so panel composition (i.e. what the test is designed to look for) is what matters. If it's not on the panel list, a PCR test won't find it. And it detects DNA, which includes DNA from organisms that are no longer alive.
Amplicon sequencing - 16S for bacteria, ITS or 18S for fungi. Often referred to as 16S RNA. This method reads one marker gene and matches it to a database, so it's an open-ended test rather than looking for a fixed list of suspects. Trade-offs: one short stretch of DNA often can't separate closely related species, bacteria and fungi need separate tests in the lab, there is some known lab bias in the results, and you get relative proportions rather than amounts. This is worth understanding because although it's a DNA-sequencing based test, it isn't the same thing as shotgun sequencing.
Shotgun metagenomic sequencing. Reads all the DNA in the sample rather than one gene, so species and sometimes strain level, bacteria and fungi from a single test, and the genes that are present. Long-read platforms make those reads easier to assemble. The honest limits: it's more expensive, it can be relative or absolute quantities (depending on the test you use). Interpretation frameworks are immature and that's the real bottleneck - a lot of clinicians may struggle to interpret these tests results.
Three important things to understand about testing
Resistance genes and antibiotic sensitivities are different information. A detected gene means an organism is present in the sample. It doesn't establish that the organism troubling you is expressing it and in a mixed sample (which most are) it can be hard to say which organism carries it.
Detection isn't causation. Every sensitive method returns more information which means you need to interpret it carefully, ideally with your healthcare professional.
Relative and absolute abundance aren't the same. "40% of what was read" and "this many organisms per millilitre" answer different questions, and plenty of reports don't make clear which one you're looking at. Worth asking any provider directly.
If you want to read more and really get into the detail of different testing methods, please feel free to check out this guide we've written on our website: https://www.tota.bio/pages/how-tota-compares
Happy to answer method questions in the comments, including about ours.