Rapid molecular syndromic testing for aetiological diagnosis of gastrointestinal infections and targeted antimicrobial prescription: experience from a reference paediatric hospital in Spain

Abstract

Aetiological diagnosis of gastrointestinal infections is challenging since a wide range of bacteria, parasites and viruses can be causal agents and derived clinical manifestations appear quite similar. Our aim was to evaluate contribution of the novel QIAstat-DxGastrointestinal Panel (GIP) to aetiological diagnosis of gastrointestinal infections and rational antimicrobial prescription in a reference paediatric hospital. Evaluation included comparison of diagnostic yield and agreement of results of QIAstat-Dx GIP and conventional microbiological methods. Parallel testing was performed on stool samples collected prospectively from children admitted to Sant Joan de Deu Barcelona Hospital (Spain) during the period February–March 2019. Influence of the panel test use on antimicrobial prescription was assessed using a pre–post study design. Eighty-six (68.8%) out of 125 specimens were positive by QIAstat-Dx GIP versus 44 (35.2%) positive by a composite of conventional methods (p<0.001). Global agreement of panel test results with rotavirus-adenovirus antigen detection (92.8%) and a two-step antigen/toxin and PCR-based algorithm for toxigenic Clostridioides difficile detection (87.5%) was greater than that with bacterial culture (76.0%) and parasite microscopic identification (64.3%). Panel test results orientated antimicrobial prescription changes in 18 (14.4%) patients, including antimicrobial start in 11 cases initially untreated, targeted antimicrobial prescription in 5 and discontinuation in 2 cases empirically treated. Results showed that QIAstat-Dx GIP significantly expanded aetiological diagnosis of gastrointestinal infections compared to conventional microbiological methods while orientating a more judicious use of antimicrobial drugs in hospitalised children.

Epidemiology of gastrointestinal infections: lessons learned from syndromic testing, Region Zealand, Denmark

“…no. 691411) (QIAGEN, Hilden, Germany) that can detect 24 gastrointestinal pathogens: 14 bacteria, 6 viruses, and 4 protozoa in a single run [ 6 , 7 ].…”

Clinical progress note: Multiplex panels for identifying infection in children

“…This allows for quicker TAT (from 31–72 h for cultures to 2–8 h), increased sensitivity to identify some organisms, and decreased personnel technical expertise required for stool testing (e.g., parasite detection) 12 . Multiplex PCR stool testing may be useful in patients pretreated with bismuth or antibiotic therapy, both of which may cause falsely negative culture results, or in patients with suspected hemolytic uremic syndrome, where rapid identification of Shiga‐toxin producing infections is critical to avoid antibiotics, which may exacerbate illness 13,14 . PCR panels can improve infection control practices by reducing costs due to unnecessary use of isolation rooms and decreasing the time to appropriate isolation, which limits time windows for spread of pathogens.…”

“…This is especially true for Clostridium difficile testing as most panels detect toxin A and B genes, which do not distinguish between colonization and active disease; thus, confirmatory testing with enzyme immunoassay for toxin production or stool culture cytotoxicity assays are recommended. One currently available platform begins to address this by reporting quantitative cycle threshold values for detection; however, there is not yet literature to suggest appropriate cutoffs to indicate a true infection 13,15 . Additionally, commonly used open collection and testing environments introduce the risk of contamination in sample handling.…”

“…12 Multiplex PCR stool testing may be useful in patients pretreated with bismuth or antibiotic therapy, both of which may cause falsely negative culture results, or in patients with suspected hemolytic uremic syndrome, where rapid identification of Shiga-toxin producing infections is critical to avoid antibiotics, which may exacerbate illness. 13,14 PCR panels can improve infection control practices by reducing costs due to unnecessary use of isolation rooms and decreasing the time to appropriate isolation, which limits time windows for spread of pathogens. GI PCR panels also decreased rates of imaging and endoscopy in some studies.…”

“…One currently available platform begins to address this by reporting quantitative cycle threshold values for detection; however, there is not yet literature to suggest appropriate cutoffs to indicate a true infection. 13,15 Additionally, commonly used open collection and testing environments introduce the risk of contamination in sample handling.…”