Detection of Shiga toxin-producing and other diarrheagenic Escherichia coli by the BioFire FilmArray® Gastrointestinal Panel in human fecal samples

Abstract

The purpose of this investigation was the evaluation of the performance of the BioFire FilmArray® Gastrointestinal (FA-GI) Panel, a multiplexed molecular stool screening assay, for the detection of diarrheagenic Escherichia coli (DEC), with emphasis on Shiga toxin-producing E. coli (STEC). A dilution series of 12 STEC reference strains was tested with the FA-GI Panel to assess the analytical sensitivity. A total of 389 patient samples were analyzed with the FA-GI Panel and confirmation of the detected DEC was attempted with an in-house culture-based polymerase chain reaction (PCR) method. All Shiga toxin genes, except the one encoding Stx2f, were detected in bacterial dilutions ranging from 10(4) to 10(2) colony-forming units (CFU)/ml. eae + stx2f + STEC was misclassified as enteropathogenic E. coli (EPEC). Different sensitivities for various gene targets present in one isolate led to differing identifications depending on the concentration. Using the in-house method as a reference, the FA-GI Panel had a sensitivity of 90.6 % [confidence interval (CI) 75.0 %-98.0 %] and a specificity of 97.2 % (CI 94.9 %-98.6 %) for STEC detection in feces. At least one DEC was reported in 35.5 % (171/389) of the patient specimens, with EPEC being the most prevalent (n = 71). Only 59.7 % of the detected DEC could be confirmed, presumably because the comparator method was not applied directly on feces. The FA-GI Panel could not detect the stx2f subtype, misclassified certain pathogens, and the high detection rate of EPEC needs further investigation. Nevertheless, we believe that this sensitive and convenient system will prove to be an invaluable tool for the rapid diagnosis of most DEC infections, but culturing of the detected microorganisms should always be attempted.

Twenty-seven years of screening for Shiga toxin-producing Escherichia coli in a university hospital. Brussels, Belgium, 1987-2014

“…The average positivity rate of stx -positive stool samples between 2008 and 2014 was 1.7%. Results of a recent study we conducted indicate that this number would probably even be higher if a culture-independent real-time molecular detection method was applied instead of our in-house stx PCR applied after culture [ 30 ]. Using this culture-based method implies that all STEC that cannot grow on SMAC(-CT) agar will not be detected.…”

“…All O63:H6 strains in this study were positive for the stx2f subtype, providing an explanation for its sudden occurrence. This Stx subtype is genetically and immunologically the most distant and is often not detected by commercial assays [ 30 ; 40 – 42 ]. Since 2008 12% of all our STEC isolates were stx2f positive which is comparable to the 13% that was seen in a study conducted in the Brussels-Capital region and the 16% that was noted in our neighboring country the Netherlands [ 13 ; 43 ].…”

Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: a systematic review and economic analysis

“…[45][46][47] These three studies consisted of a case-control study of Ghanaian children aged < 6 years using xTAG, 46 a study of 779 children aged < 18 years from the USA using FilmArray, 45 and a Belgian study of 386 mixed patients that assessed FilmArray for the detection of shiga toxin-producing E. coli compared with an in-house culture-based PCR method. 47 This final study is the only one of the three that would have contributed 2 × 2 data for the meta-analysis; however, the study considered only 1 out of 23 pathogens detectable with FilmArray. Full inclusion of the three studies would therefore not have influenced or changed the conclusions of this review.…”

Smartphone-based pathogen diagnosis in urinary sepsis patients

“…However, there is currently no direct specimen testing method approved for urine, principally due to the challenges of microbial contamination at the point of collection [ 14 , 18 ]. Thus, the gold standard of care entails a bacterial culture step, delaying identification for at least 16 h [ 18 , 59 , 60 ]. Once again, we demonstrated that smaRT-LAMP could match the performance of the more sophisticated and costly qPCR instrument, achieving a clinically-relevant LOD of 1–2 × 10 4 CFU/mL ( Fig.…”