Comparative evaluation of BD MAX™ Enteric Panels and Luminex NxTAG® GPP for the detection of gastrointestinal pathogens in clinical stool samples.

PurposeAccurate and rapid diagnosis of gastrointestinal infections is essential for effective patient management. This study compared the diagnostic performance of two multiplex PCR panels— the Seegene Allplex™ Gastrointestinal Panels (Seegene, Seoul, Korea) and the Luminex NxTAG®Gastrointestinal Pathogen Panel (Luminex Corporation, Austin, Texas, a Diasorin Company)—in detecting gastrointestinal pathogens from clinical stool samples.MethodsA total of 196 stool samples, collected from patients at a Spanish hospital during 2023, were analyzed using both assays through prospective and retrospective approaches. The performance of each test was assessed based on Positive Percentage Agreement (PPA), Negative Percentage Agreement (NPA), and overall agreement. Discrepancies between methods were resolved with a third confirmatory technique when available.ResultsBoth assays demonstrated high overall concordance, with NPA values consistently above 95% and overall Kappa values exceeding 0.8 for most pathogens. The average PPA was greater than 89% for nearly all targets; however, lower agreement was observed for Cryptosporidium spp. (86.6%). Notably, discrepancies were primarily observed for certain pathogens, such as Salmonella spp. and Cryptosporidium spp., highlighting the diagnostic challenges associated with these targets.ConclusionTo our knowledge, this is the first study to compare the novel Luminex NxTAG® panels from Diasorin with the Seegene Allplex™. Both multiplex assays provide rapid and reliable detection of gastrointestinal pathogens, making them valuable tools in clinical diagnostics. Future research should focus on improving detection accuracy for challenging pathogens and expanding target panels to further enhance patient management and reduce disease burden.

Detection of Norovirus by BD MAX™, Xpert® Norovirus, and xTAG® Gastrointestinal Pathogen Panel in stool and vomit samples

Detection of Clostridioides difficile toxins in patients with gastroenteritis has increasingly been accomplished through the use of enteric multiplex syndromic panels. Comparisons of the performance of these panels to both direct-from-stool (DFS) and culture-enriched stools followed by polymerase chain reaction (PCR) methods in pediatric populations are limited. Here, we compare the performance of the Luminex xTAG® Gastrointestinal Pathogen Panel (GPP) to our DFS in-house real-time PCR (DFS RT-PCR) assay for the detection of C. difficile toxin gene, tcdB, using 2641 stool specimens collected from children enrolled in the Alberta Provincial Pediatric EnTeric Infection Team (APPETITE) study in Alberta, Canada. We used culture enrichment followed by in-house RT-PCR to resolve discordant results between the two assays. We found excellent agreement (k = 0.89) between the GPP and our DFS RT-PCR assay: the positive percent agreement between the two assays was 97%, and the negative percent agreement was 99%. GPP, a multi-analyte platform can easily be implemented into a routine diagnostic laboratory for detecting enteric pathogens including C. difficile.

Comparative analysis of three multiplex platforms for the detection of respiratory viral pathogens.

Imaging Methods for Differentiating Pediatric Papilledema from Pseudopapilledema: A Report by the American Academy of Ophthalmology

The standard for detecting vector-borne pathogens is real-time PCR (rtPCR). However, this requires many individual tests to obtain an accurate diagnosis. The purpose of this study was to develop and validate a targeted next-generation sequencing (NGS) assay for vector-borne pathogens. Pathogen target regions were amplified via PCR using two primer pools that were developed in conjunction with ThermoFisher Scientific, and barcoded DNA libraries were prepared and sequenced with the Ion Torrent S5 system. Data were assembled using SPAdes and mapped to a reference file containing sequences from the pathogens. The raw reads were analyzed to confirm the results. Test feasibility and analytical specificity were evaluated with type strains or validated positive clinical samples from dogs. The analytical sensitivity of the method was compared to Ct values obtained by rtPCR testing. Diagnostic sensitivity and specificity were assessed with a set of known positive and negative clinical samples based on rtPCR testing. Positive and negative percent agreements and Cohen’s kappa were calculated. The primer sets were specific for the intended targets, based on sequence analysis of the amplified products, and the method detected 17 different pathogens. Analytical sensitivity was equivalent to an rtPCR Ct value of approximately 35–36. The positive percent agreement was 92%, and the negative percent agreement was 88%. Cohen’s kappa was 0.804, which indicates almost perfect agreement between the rtPCR assays and the targeted NGS assay. Using a targeted method reduces the costs associated with NGS sequencing and allows for a 2–3 day turn-around time, making this a viable method for detection of vector-borne pathogens in canine whole blood samples.

The diagnosis of acute gastroenteritis is an ongoing clinical challenge in terms of identification of the etiologic agent, time to results, and appropriate treatment. Rapid detection of gastrointestinal pathogens is needed to improve patient care. This study evaluates the performance of the QIAstat-Dx gastrointestinal panel (Q-GP; Investigational Use Only) compared to the Luminex xTAG gastrointestinal pathogen panel (L-GPP; US-IVD). Using 245 stool specimens, we evaluated 10 different targets including rotavirus, norovirus, Salmonella, Shigella, Campylobacter, Giardia, Cryptosporidium, Escherichia coli O157, enterotoxigenic E. coli (ETEC), and Shiga toxin-producing E. coli (STEC). For the viral targets, the percent positive agreement (PPA) for rotavirus was 100% (n = 19) and that for norovirus was 91% (20/22). For the parasitic targets, the PPA was 100% for Giardia and Cryptosporidium (n = 18 and n = 23, respectively). The PPA was 96% for Salmonella (22/23) and Campylobacter (22/23), and the PPA for Shigella was 100% (n = 23). For the E. coli targets, a PPA of 94% was achieved for STEC (32/34) and 96% for ETEC (24/25). We did not assess PPA for the E. coli O157 target as the Q-GP O157 call is stx dependent. The negative percent agreement across all targets was 99.1%. Our study suggests that QIAstat-Dx GP provides comparable results to Luminex GPP based on the analysis of targets found on both panels.

Which trial do we need? Plasma metagenomic next-generation sequencing to diagnose infections in patients with haematological malignancies and febrile neutropenia: proposal for a randomized-controlled trial

The presence of mismatch repair deficiency is frequently assessed in gastrointestinal and gynecologic neoplasms by surgical pathologists using immunohistochemical methods. Targeted next-generation sequencing (NGS) covering some genes in the mismatch repair complex is used with increasing frequency, however, the percent positive and negative agreement of immunohistochemical methods and NGS of mismatch repair genes is not well-described in the literature. We sought to compare performance of immunohistochemistry (IHC) and NGS of mismatch repair genes on our institutional targeted panel. We evaluated the concordance of immunohistochemical and panel-based gene sequencing methods in a retrospective cohort study of patients evaluated at our center with both immunohistochemical and panel-based sequencing. Our NGS panel covers only MLH1 and MSH2, whereas our immunohistochemical panel assesses for expression of MLH1, PMS2, MSH2, and MSH6. We identified 68 unique patients with both immunohistochemical evaluation of mismatch repair protein expression and NGS panel sequencing, of which 67 were suitable for analysis given the patterns of immunohistochemical loss of expression observed. The percent positive agreement for NGS with IHC was 50%, albeit with very rare positive cases (n=2/4). Percent negative agreement was also high at 100% (n=63/63). One case with loss of MLH1, PMS2, and MSH6 expression by IHC and no pathogenic variants by NGS exhibited MLH1 promoter hypermethylation. Percent negative agreement between immunohistochemical and NGS gene sequencing is high, although firm conclusions regarding percent positive agreement between NGS and IHC are limited by low numbers of positive cases in our cohort. In general, we consider the findings to support continued use of immunohistochemical methods to screen for the presence of mismatch repair deficiency and consider additional testing by NGS likely to add little diagnostic value in the context of intact immunohistochemical expression of mismatch repair proteins.

The COVID-19 pandemic underscored the critical need to enhance screening capabilities and streamline diagnosis. Point-of-care (POC) tests offer a promising solution by decentralizing testing. We aimed to validate the PLUM device (LSK Technologies Inc.), a portable optical reader, to detect SARS-CoV-2 RNA using direct RT-LAMP targeting the ORF1a and E1 genes and patient antibodies by ELISA. The direct RT-LAMP assays employ nasopharyngeal swabs and bypass RNA extraction protocols through a brief chemical and physical lysis step. Test sensitivity and specificity were assessed against gold-standard detection methods in laboratory and field conditions. For samples with Ct values below 25, direct RT-LAMP showed 83% sensitivity and 90% specificity under laboratory conditions and 91% sensitivity and 92% specificity under field conditions. The nucleocapsid antigen antibody assay had 99% positive percent agreement (PPA) and 97% negative percent agreement (NPA), outperforming spike-RBD antigen (98% PPA, 92% NPA) and seroprevalence (98% PPA, 88% NPA) under laboratory conditions. Under field conditions, similar results were found for antibody detection for the nucleocapsid antigen (93% PPA; 100% NPA), spike-RBD (100% PPA; 94% NPA), and seroprevalence (90% PPA; 94% NPA). This study validated the PLUM device as a dual POC tool for direct RT-LAMP-based SARS-CoV-2 and ELISA-based COVID-19 antibody detection.

161P MammaPrint and BluePrint diagnostic tests can be robustly assessed on Whole-Transcriptome NGS platform

Evaluation of the rapid antigen test Panbio COVID-19 in saliva and nasal swabs in a population-based point-of-care study

Validation and Characterization of FGFR2 Rearrangements in Cholangiocarcinoma with Comprehensive Genomic Profiling

BackgroundRapid and accurate diagnosis of chronic obstructive pulmonary disease (COPD) is problematic in acute care settings, particularly in the presence of infective comorbidities.ObjectiveThe aim of this study was to develop a rapid smartphone-based algorithm for the detection of COPD in the presence or absence of acute respiratory infection and evaluate diagnostic accuracy on an independent validation set.MethodsParticipants aged 40 to 75 years with or without symptoms of respiratory disease who had no chronic respiratory condition apart from COPD, chronic bronchitis, or emphysema were recruited into the study. The algorithm analyzed 5 cough sounds and 4 patient-reported clinical symptoms, providing a diagnosis in less than 1 minute. Clinical diagnoses were determined by a specialist physician using all available case notes, including spirometry where available.ResultsThe algorithm demonstrated high positive percent agreement (PPA) and negative percent agreement (NPA) with clinical diagnosis for COPD in the total cohort (N=252; PPA=93.8%, NPA=77.0%, area under the curve [AUC]=0.95), in participants with pneumonia or infective exacerbations of COPD (n=117; PPA=86.7%, NPA=80.5%, AUC=0.93), and in participants without an infective comorbidity (n=135; PPA=100.0%, NPA=74.0%, AUC=0.97). In those who had their COPD confirmed by spirometry (n=229), PPA was 100.0% and NPA was 77.0%, with an AUC of 0.97.ConclusionsThe algorithm demonstrated high agreement with clinical diagnosis and rapidly detected COPD in participants presenting with or without other infective lung illnesses. The algorithm can be installed on a smartphone to provide bedside diagnosis of COPD in acute care settings, inform treatment regimens, and identify those at increased risk of mortality due to seasonal or other respiratory ailments.Trial RegistrationAustralian New Zealand Clinical Trials Registry ACTRN12618001521213; http://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=375939

BackgroundThe BD MAX™ Enteric Bacterial Panel (BDM-EBP) is designed and FDA-cleared to detect Salmonella, Shigella, Campylobacter, and Shiga toxin genes stx1/2 from stool samples. However, rectal swabs, which are not FDA-cleared for clinical testing with the BDM-EBP, are common specimens received from pediatric patients for enteric pathogen testing. The purpose of this study was to evaluate the ability of the BDM-EBP to detect stool pathogens from rectal swabs.MethodsRoutine cultures, Shiga toxin testing, and molecular testing with BDM-EBP were performed on 272 sequential rectal swabs collected from August 2015 to December 2015. Discrepant test results were resolved using Verigene® Enteric Pathogens Nucleic Acid Test (EP). 36 challenge samples (13 Salmonella spp., 3 Shigella spp., 10 Campylobacter spp., and 10 Shiga toxin positive Escherichia coli) were tested using reference strains (American Type Culture Collection) and previous patient isolates diluted to103-104 cfu/ml in saline then added to Sample Buffer Tube (SBT) with negative stool matrix delivered via a swab. Limit of detection testing was performed by serial 10 fold dilutions in saline then added to SBT with negative stool matrix provided via a swab.ResultsA total of 272 rectal swab specimens were evaluated and 89 were positive by culture and/or MAX EBP. All discrepant results were BDM-EBP positive and culture negative. 21 of 31 (68%) of the apparent false positive BDM-EBP discrepant results resolved as positive with Nanosphere’s Verigene® EP. After resolution of the discordant results, the Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) are as follows for each target: Salmonella (n = 4) 100%, PPA and 100%, NPA; Shigella (n = 79) 100%, PPA and 95.3%, NPA; Campylobacter (n = 4) 100%, PPA and 99.6%, NPA; and Shiga toxin producing organisms (n = 2) 100%, PPA and 100%, NPA. 8.8% of the patient samples did not initially yield a result on the BDM-System. Upon repeat, half of the problematic samples resolved, and 4.4% of the total specimen tested did not yield a result. All organisms in the challenge samples were detected. Limits of detection for BDM-EBP testing of rectal swabs were as follows (in cfu/ml in SBT): Salmonella-1.44 × 102; Shigella-5.10 × 100; Campylobacter-1.51 × 101; and Shiga Toxin-1.13 ×103.ConclusionRectal swabs are acceptable samples for detecting Salmonella, Shigella, Campylobacter, and Shiga toxin using BDM-EBP.