Appraising the options for detecting carbapenemase-producing organisms

CPE agar

Carbapenemase-producing organisms (including CPE) present important clinical challenges: the “triple threat” of high levels of antibiotic resistance, virulence, and potential for rapid spread (locally, regionally, nationally, and globally)! However, these organisms somewhat ironically also present challenges to detection in the clinical laboratory. You’d expect that since these organisms are so important clinically they’d be dead easy to detect in the clinical lab – but this isn’t the case.

A comprehensive review published in Clinical Microbiology Reviews provides an overview of the diagnostic approaches to detect carbapenemase producers in the clinical lab. Figures 6 and 7 of the review provide a useful overview of the two broad approaches you could take: culturing organisms on agar plates, or using nucleic acid amplification techniques (NAAT – most commonly PCR) directly from a rectal swab.

In terms of culture based approaches, there is now a large array of media available for detecting carbapenemase producers. It is clear that ‘traditional’ approaches such as sticking an ertapenem disc on MacConkey agar lack sensitivity so chromogenic media is the way to go. One carbapenemase, most commonly found in CPE, OXA-48 is particularly difficult to detect using agar, and may require the use of media separately formulated for OXA-48 to be successful. The two key points that came out for me were that SUPERCARBA and chromID CARBA seem to come out on top in most diagnostic evaluations of agar, and that there is a startling range in the limit of detection of the various media for some carbapenemase-producing bacteria. The limit of detection ranges from 1 cfu right up to 107 cfu. Yep – you read that right – 107 cfu. So you’d need 10,000,000 bacteria to be present in the sample for it to grow!

The other broad approach is the use of NAAT (most commonly PCR). There are now a range of commercial multiplex PCRs available that detect the key carbapenemases in Enterobacteriaceae (although none of the available systems are able to detect all of the “big 5” carbapenemases – NDM, KPC, IMP, VIM and OXA-48). I have some hands-on experience of using one of the PCR systems for detecting carbapenemase producers directly from rectal swabs – and you can read more about the findings here. The sensitivity of PCR for detecting CPE seems satisfactory, and it does offer considerably faster turnaround time. But PCR is not without its limitations (not least higher per-test cost, and the need to culture the organism to determine its antibiotic sensitivity). Still, I do see a bright future for NAAT methods as part of the clinical lab algorithm for detecting CPE.

You can download a recent talk that I gave on diagnostic approaches to detecting carbapenemase-producers here. The best clinical lab approach to detect carbapenemase-producing organisms will depend on local prevalence. In high prevalence settings, the faster turnaround time of PCR may be warranted to alter the patient pathway in some areas of the hospital. But in low prevalence settings, the slower turnaround time of culture based approaches is probably ok. The use of PCR (or other NAAT) to confirm whether a carbapenem-resistant organism is a carbapenemase-producer and, if so, which carbapenemase is present (rather than waiting for confirmation from a reference laboratory) does seems like a necessary local facility in this era of emerging CPE.

Image: Nathan Reading.

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