Comparative Evaluation of Broad-Panel PCR Assays for the Detection of Gastrointestinal Pathogens in Pediatric Oncology Patients

Abstract

Broadly multiplexed molecular amplification assays offer an unprecedented ability to diagnose gastrointestinal infection in immunocompromised patients. However, little data are available to compare the performance of such systems in this population. A total of 436 stool samples were collected from 199 predominantly immunocompromised pediatric oncology patients. Remnant samples were tested in parallel with the use of the premarket (investigational use only) versions of two broadly multiplexed PCR assays (BioFire and Luminex), and the results of samples corresponding to the first episode per patient were compared with those from laboratory-developed molecular assays, culture, and antigen detection. Overall performance of the multiplexed systems was comparable, with BioFire and Luminex detecting 94 and 99 positives (P = 0.34), respectively. Stratifying by analyte, BioFire assay detected 51 samples positive for Clostridium difficile, whereas Luminex assay detected 60 (P = 0.01). Biofire and Luminex detected 28 and 38 norovirus-positive samples (P = 0.002), respectively. Astrovirus- and adenovirus-positive samples were detected in higher numbers by in-house PCR than by BioFire; the same was observed for adenovirus with Luminex. Differences observed with other analytes were minimal, did not reach statistical significance, or lacked the numbers needed to detect a difference between systems. Broadly multiplexed PCR offers an effective means of detecting a variety of gastrointestinal pathogens in pediatric oncology patients, with assay performance comparable among the tests examined.

Detection of gastrointestinal pathogens in oncology patients by highly multiplexed molecular panels

“…Our data show that the two assays had similar detection rates with an overall concordance of greater than 90% for targets common to both assays, similar to other studies performed in different patient populations [9, 14]. The most frequent GI pathogens in our oncology patient population were C. difficile , Norovirus, Campylobacter, and Salmonella species.…”

Modeling human enteric dysbiosis and rotavirus immunity in gnotobiotic pigs

“…was used for DNA samples. Norovirus I and II, sapovirus, adenovirus, and astrovirus real-time PCR primers, as well as, probes and conditions, were based on previous publications [43–46]. …”

Persistent Infections with Diverse Co-Circulating Astroviruses in Pediatric Oncology Patients, Memphis, Tennessee, USA

“…We showed that the singleplex rRT-PCR method ( 3 ) was unable to capture infections caused by noncanonical viruses and is, therefore, limited in its utility for accurate surveillance and diagnosis. Although our multiplex method was able to identify all canonical and 2 noncanonical viruses ( 4 ), it is possible that we missed infections with other strains. Given the limited knowledge about HAstV genotypes and clinical disease, particularly in immunocompromised persons, additional studies will be crucial to help develop better diagnostics to capture all known HAstV genotypes.…”

“…We screened samples from 2008 by using a singleplex real-time reverse transcription PCR (rRT-PCR) ( 3 ), an in-house multiplex PCR to identify canonical (HAstV1–8) and noncanonical (MLB1 and VA2) genotypes ( 4 ), and endpoint PCRs by using primers targeting open reading frame (ORF) 1( 5 ) and ORF2 ( 6 , 7 ). The singeplex method detected HAstV in 23/72 samples, compared with 61/67 (5 samples were not tested) by the multiplex method.…”