Performance of a new molecular assay for the detection of gastrointestinal pathogens

Performance validation of the BD MAX Enteric Parasite Panel using simulated samples in low endemic regions

Molecular diagnostics are essential for detecting intestinal parasites, but evaluating clinical samples from low endemic areas, including Korea, is challenging. We tested the performance of the BD MAX Enteric Parasite Panel in simulated samples for clinical use. Simulated samples were prepared with residual stool samples to confirm the diagnostic performance of the kits. Standard materials for Cryptosporidium parvum, Giardia lamblia, and Entamoeba histolytica were obtained for assessment. Limit of detection was determined by diluting standard materials into multiple concentrations and testing each in duplicate. Repeatability was assessed by retesting all samples twice. Accuracy was evaluated by comparing BD MAX System results with intended results. The limit of detection values obtained using standard materials were 781 cysts/ml, 6,250 oocysts/ml, and 125 DNA copies/ml for G. lamblia, C. parvum, and E. histolytica, respectively. Simulated G. lamblia-positive stool samples with concentrations above 6,250 cysts/ml consistently yielded positive results (100% concordance). However, C. parvum-positive stool samples at 6,250 oocysts/ml showed 50% concordance initially and 75% after retesting. At 62,500 oocysts/ml, the concordance rates were 89% initially and 100% after retesting. Overall agreement was 95.2%, but that for C. parvum was relatively low (82.4%). The diagnostic performances were 87.8% of sensitivity and 100% of specificity. Despite the limited clinical samples, BD MAX Enteric Parasite Panel showed good performance for clinical use, and spiked samples proved useful for evaluating protozoan PCR in low-incidence regions.

Multiple cross displacement amplification-based lateral flow biosensor for rapid and sensitive detection of Helicobacter pylori

Helicobacter pylori (H. pylori, HP), recognized globally as one of the most widespread bacteria, serves as primary etiological agent for numerous gastroduodenal diseases, highlighting the urgent need to develop rapid and sensitive diagnostic method for H. pylori infection. Here, we devised a new diagnostic test that merged multiple cross displacement amplification (MCDA) with nanoparticle-based lateral flow biosensor (LFB), termed HP-MCDA-LFB, to facilitate the rapid and sensitive detection of H. pylori. The whole detection workflow, which includes stages such as DNA template extraction (~15 min), MCDA pre-amplification (~40 min), and result readout (~2 min), was efficiently completed within 1 h. After optimization, the HP-MCDA-LFB assay demonstrated remarkable sensitivity in detecting H. pylori, with a detection threshold as low as 60 fg of genomic DNA (~56 copies) per microliter. Furthermore, the HP-MCDA-LFB assay also achieved a perfect specificity rate of 100%, exhibiting no cross-reactivity with non-Helicobacter isolates. Particularly, the clinical feasibility of HP-MCDA-LFB assay was validated using 40 antral mucosa samples, among which 17 tested positive for H. pylori, which was in complete agreement with the results obtained from the rapid urease test. In conclusion, the HP-MCDA-LFB method developed in this study is a rapid, sensitive, and specific method for diagnosing H. pylori infection, indicating great potential for H. pylori eradication therapy.

Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance

Despite the recent decrease in overall prevalence of Helicobacter pylori infection, morbidity and mortality rates associated with gastric cancer remain high. The antimicrobial resistance developments and treatment failure are fueling the global burden of H. pylori-associated gastric complications. Accurate diagnosis remains the opening move for treatment and eradication of infections caused by microorganisms. Although several reports have been published on diagnostic approaches for H. pylori infection, most lack the data regarding diagnosis from a clinical perspective. Therefore, we provide an intensive, comprehensive, and updated description of the currently available diagnostic methods that can help clinicians, infection diagnosis professionals, and H. pylori researchers working on infection epidemiology to broaden their understanding and to select appropriate diagnostic methods. We also emphasize appropriate diagnostic approaches based on clinical settings (either clinical diagnosis or mass screening), patient factors (either age or other predisposing factors), and clinical factors (either upper gastrointestinal bleeding or partial gastrectomy) and appropriate methods to be considered for evaluating eradication efficacy. Furthermore, to cope with the increasing trend of antimicrobial resistance, a better understanding of its emergence and current diagnostic approaches for resistance detection remain inevitable.

Future potential of metagenomics in clinical laboratories

INTRODUCTION

Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents.

AREAS COVERED

High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories.

EXPERT OPINION

The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.