CRE are an emerging threat to healthcare systems worldwide. Most guidelines recommend screening and isolation of carriers. But relying on conventional agar-based culture presents a dual threat of poor sensitivity (depending on which method is used) and slow turnaround time, with a minimum overnight incubation before a presumptive positive result. PCR solves both of these problems – but at a cost. I gave a talk today at a BD seminar considering whether it’s time to switch to PCR diagnostics for the detection of CRE. You can download my slides here. (The title of the talk “Time to throw away those agar plates” was inspired by a talk by Dr Dan Diekema at a recent SHEA conference.)

There are a number of options for CRE screening, summarized in the flow chart below:

Flow chart: Overview of laboratory methods for the diagnosis of CRE. (To be precise, throughout the blog I really mean CPE most of the time, but I’m using CRE for consistency with other blogs…)

I have recently started a study in London comparing the detection rate for CRE using PCR vs. a range of agar-based methods. We’re going to screen all admissions to Guy’s and St. Thomas’ for a few months to size the threat walking into our hospitals. Preliminary results are very interesting and show, as you’d expect, that PCR is more sensitive than conventional culture (I’m not going to give too much away in terms of actual data; just submitted an ECCMID late-breaker…).

But does that mean it’s time to throw away those agar plates? Molecular diagnostics offer greater sensitivity and shorter turnaround times but:

• turnaround time advantages may not be as great in the real world as on paper; you still need to get the specimen to the lab, batch process it and read the results;
• do not deal with changing epidemiology; struggle with target variability;
• are expensive;
• rely on validation of carriage sites;
• do not tell you about phenotypic susceptibility;
• have a limit of detection often around a couple of logs;
• need to manage shared resistance genes between species, especially for MDR-GNR;
• and is PCR+ culture- (as) clinically significant?

So we need to continue using PCR and culture in parallel, at least for now!