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Plus, an in-house PCR test for HSV in CSF

For infection control, PCR and culture compared
Plus, an in-house PCR test for HSV in CSF

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William Check, PhD

January 2016—There is a reason why rigorous studies are done to prove even the seemingly apparent benefits of advanced techniques. Sometimes comparisons turn up unexpected findings, as demonstrated by two selected infectious disease abstracts about real-time PCR presented at the Nov. 5–7, 2015 meeting of the Association for Molecular Pathology. Even so, both abstracts show the value of PCR testing.

In one report, Barbara L. Voss, BS, of the Department of Pathology and Laboratory Medicine at NorthShore University HealthSystem, Evanston, Ill., described a comparison of real-time PCR with culture for identification of multidrug-resistant organisms in screening ICU patients. Patients infected with pathogens carrying dangerous resistance genes—specifically enterobacteria carrying the Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM-1), and the extended-spectrum β-lactamase (ESBL) CTX-M—require isolation. Earlier isolation is possible with real-time PCR—which returns a result in 24 hours, even doing overnight growth in broth before the assay—whereas culture takes 72 hours (Mangold KA, et al. J Clin Microbiol. 2011;49:3338–3339).

In the comparison study, 1,168 patients were screened over 14 months with both PCR and culture, using axillary, respiratory, and perianal swabs. Culture found 97 positive specimens, while PCR detected 96 (it missed one CTX-M). Five specimens were positive by PCR and negative by culture (two KPC and three CTX-M). Thus, PCR was 98.9 percent sensitive and 99.5 percent specific.

“The molecular approach excelled in speed of results necessary for rapid patient isolation,” Voss concluded. “Culture detected a broader spectrum of MDROs [multidrug-resistant organisms], but its turnaround time is longer.”

In an interview with CAP TODAY, Becky Smith, MD, chief hospital epidemiologist at NorthShore and clinical assistant professor at the University of Chicago Pritzker School of Medicine, notes two important points. First, “PCR is highly sensitive when you are searching for specific targets, and it is easy to perform.” However, “PCR has a downside when you don’t have a primer for a specific target. If there was a new target, you would miss it. And adding more primers is expensive and more difficult to do.”

Asked about the five specimens that were PCR-positive and culture-negative, Dr. Smith says, “Culture is always considered the gold standard, but we know from studies that culture is less sensitive than PCR.” In this study, the discrepancies were not adjudicated. “We are still trying to work out the best way to do all this,” Dr. Smith says. PCR is being used now with culture as backup. “Ultimately, we may say let’s do culture periodically just to make sure we’re not missing anything.”

Kathy Mangold, PhD, of the Department of Pathology and Laboratory Medicine at NorthShore, who designed and directed this study, noted that an additional 23 of the 1,168 specimens were found positive by supplementary PCR testing for the untargeted resistance genes SHV, TEM, and OXA. “We’re already thinking of replacing the current CTX-M target with an OXA target, since it appears to be more relevant in current infection control practice,” Dr. Mangold tells CAP TODAY. “Substituting one target for the other, once the new assay has been validated, would mean no increase in per-test cost. Even if we just added that target to the existing assay, it would only increase the cost per test by less than a dollar—to cover the cost of additional custom synthesized oligonucleotides—in a validated assay.”

In the second abstract, presented by fourth-year pathology resident Salwa Khedr, MD, of Baystate Medical Center/Tufts University, Springfield, Mass., clinical and financial outcomes were determined before and after an in-house PCR test was implemented for herpes simplex virus in cerebrospinal fluid in patients suspected of herpes meningoencephalitis. Doing the test in the hospital laboratory, as compared with sending the testing out, reduced turnaround time from three to five days to less than 24 hours.

Dr. Khedr compared pre- and post-implementation periods using a retrospective review of hospital records for 526 patients. The data showed a significant initial decrease in admission-to-test-result time, duration of acyclovir treatment, patient length of hospital stay, and total hospitalization charges. However, Dr. Khedr said, “This was followed by a perplexing rebound of the parameters over the ensuing year.

“Our hypothesis is that the rebound is likely related to a change in clinician test ordering behavior after the in-house test became available,” Dr. Khedr tells CAP TODAY. “Our data suggest that after bringing the test in-house, there is less stringency in the testing criteria used by clinicians and a greater tendency to order the test more often later during the patient’s hospitalization.” A drop in positivity from 3.3 percent to 0.8 percent suggested this lower stringency. “The result of these changed practices would be decreased applicability of test results to the patient’s hospital course and thus decreased clinical impact, leading to the observed rebound effect.”

Dr. Khedr and her colleagues have communicated this to the hospital infectious disease team and are working to gain more evidence to support it.

“One possible post-study intervention that we believe may impact patient care,” she says, “is to communicate any negative test results to the pharmacy to help expedite the cessation of acyclovir.”
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William Check is a writer in Ft. Lauderdale, Fla.

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