On the whole, rapid microbiological diagnostics are a good thing, as they can cut the diagnosis time from days (often 36-48 hours) down to a few hours. Depending on the organism and the test, they are often either be a glorified PCR test that looks for a specific gene or an immunoassay designed to find a particular protein like an enterotoxin that causes disease. The advantage of rapid diagnostics, regardless of the actual mechanism underlying the test, is that you don’t have to spend 24 hours (or longer) growing up the bacterium in isolation (hence, the term rapid diagnostics).
The problem with rapid diagnostics is that you don’t spend 24 hours (or longer) growing up the bacterium in isolation. No, that’s not a typo. Here’s what I mean (boldface mine):
CDC, several states, the U.S. Food and Drug Administration, and the U.S. Department of Agriculture’s Food Safety and Inspection Service are investigating a multistate outbreak of Shiga toxin-producing E. coli O157:H7 infections…
Public health investigators are using the PulseNet system to identify illnesses that may be part of this outbreak. PulseNet is the national subtyping network of public health and food regulatory agency laboratories coordinated by CDC. DNA fingerprinting is performed on E. coli bacteria isolated from ill people using techniques called pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). CDC PulseNet manages a national database of these DNA fingerprints to identify possible outbreaks. WGS gives a more detailed DNA fingerprint than PFGE.
Illnesses reported by investigators in New Jersey also included ill people who had a diagnostic test showing they were infected with E. coli bacteria. Laboratory testing is ongoing to link their illnesses to the outbreak using DNA fingerprinting. Some people may not be included in CDC’s case count because no bacterial isolates are available for the DNA fingerprinting needed to link them to the outbreak.
In other words, there are patients who test positive for having Shiga toxin in their feces (here’s an example of one such test), but no E. coli isolate was ever cultured. This means when we want to do molecular epidemiology to determine if these particular O157:H7 E. coli are related to other O157:H7 E. coli, we can’t. This is a problem: what is helping the individual patient and doctor is hurting the epidemiologist (and could lead to others getting sick.
While rapid diagnostics aren’t going away, we are either going to need large sentinel culture isolation programs or more funding so that both rapid diagnostics and traditional culture can be performed*. The massive fragmentation of the U.S. healthcare system doesn’t help matters (and is why I regularly complain about the difference between healthcare insurance and actual healthcare).
*At some point, metagenomic sequencing might be able to help here, but, so far, it’s not close to being a routine diagnostic assay (and there are still many kinks to work out in terms of resolution).