Evaluation of the Vibrant DNA microarray for the high-throughput multiplex detection of enteric pathogens in clinical samples
Tóm tắt
Rapid detection of a wide range of etiologic agents is essential for appropriate treatment and control of gastrointestinal (GI) infections. A variety of microbial species including bacteria, viruses, parasites, and fungi have been recognized as diarrheagenic enteric pathogens. However, multiplex testing of various targets in a single reaction needs further improvement because of its limitation in species and throughput. This study aims at developing and evaluating a DNA microarray-based qualitative multiplexed polymerase chain reaction (PCR) assay, Vibrant GI pathogen panel (GPP), for simultaneous detection of 27 enteric GI pathogenic targets (16 bacteria, 5 viruses, 4 parasites, and 2 fungi) directly from stool specimens. Limits of detection ranged from 102 to 104 cells/mL for bacteria, 102 to 103 cells/mL for parasites, 102 to 103 RNA copies/mL for viruses, and 102 to 103 cells/mL for fungi. Performance characteristics were determined using 27 Quantitative Genomic DNAs, 212 spiked stool specimens, 1067 clinical and archived stool specimens. Overall sensitivity was 95.9% (95% CI 92.4–98.1) and specificity was 100% (95% CI 99.9–100). Polymicrobial detections contained either two or three organisms was 20.2% (35/173) of positive clinical specimens and 3.3% (35/1055) of all clinical specimens. The Vibrant GPP is a comprehensive, high-throughput, and rapid DNA microarray to provide etiologic diagnosis of GI infections in the laboratory setting.
Tài liệu tham khảo
Liu L, Johnson HL, Cousens S, et al. Child Health Epidemiology Reference Group of WHO and UNICEF. Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000. Lancet. 2012;379:2151–61.
Hatchette TF, Farina D. Infectious diarrhea: when to test and when to treat. CMAJ. 2011;183(3):339–44.
Hodges K, Gill R. Infectious diarrhea: cellular and molecular mechanisms. Gut Microbes. 2010;1(1):4–21.
Ternhag A, Törner A, Svensson A, Ekdahl K, Giesecke J. Short- and long-term effects of bacterial gastrointestinal infections. Emerg Infect Dis. 2008;14(1):143–8.
Guerrant RL, Van Gilder T, Steiner TS, et al. Practice guidelines for the management of infectious diarrhea. Clin Infect Dis. 2001;32(3):331–51.
Lagier JC, Edouard S, Pagnier I, et al. Current and past strategies for bacterial culture in clinical microbiology. Clin Microbiol Rev. 2015;28(1):208–36.
Haque R. Human intestinal parasites. J Health Popul Nutr. 2007;25(4):387–91.
Kirby A, Gurgel RQ, Dove W, et al. An evaluation of the RIDASCREEN and IDEIA enzyme immunoassays and the RIDAQUICK immunochromatographic test for the detection of norovirus in faecal specimens. J Clin Virol. 2010;49:254–7.
Freeman K, Tsertsvadze A, Taylor-Phillips S, et al. Agreement between gastrointestinal panel testing and standard microbiology methods for detecting pathogens in suspected infectious gastroenteritis: test evaluation and meta-analysis in the absence of a reference standard. PLoS ONE. 2017;12(3):e0173196.
Schreckenberger PC, McAdam AJ. Point-counterpoint: large multiplex PCR panels should be first-line tests for detection of respiratory and intestinal pathogens. J Clin Microbiol. 2015;53(10):3110–5.
Platts-Mills JA, Liu J, Houpt ER. New concepts in diagnostics for infectious diarrhea. Mucosal Immunol. 2013;6(5):876–85.
Buss SN, Leber A, Chapin K, et al. Multicenter evaluation of the BioFire FilmArray gastrointestinal panel for etiologic diagnosis of infectious gastroenteritis. J Clin Microbiol. 2015;53(3):915–25.
Binnicker MJ. Multiplex molecular panels for diagnosis of gastrointestinal infection: performance, result interpretation, and cost-effectiveness. J Clin Microbiol. 2015;53(12):3723–8.
Duong VT, Phat VV, Tuyen HT. Evaluation of Luminex xTAG gastrointestinal pathogen panel assay for detection of multiple diarrheal pathogens in fecal samples in Vietnam. J Clin Microbiol. 2016;54(4):1094.
Choung RS, Marietta EV, Van Dyke CT, et al. Determination of B-cell epitopes in patients with celiac disease: peptide microarrays. PLoS ONE. 2016;11(1):e0147777.
Choung RS, Jayaraman V, Marietta E, et al. Expanding immune reactivity against gliadin and TTG epitopes long precedes celiac disease diagnosis. Gastroenterology. 2018;154(6):119.
Ramakers C, Ruijter JM, Deprez RH, Moorman AF. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett. 2003;339(1):62–6.
Platts-Mills JA, Liu J, Houpt ER. New concepts in diagnostics for infectious diarrhea. Mucosal Immunol. 2013;6:876–85.
Beal SG, Tremblay EE, Toffel S, Velez L, Rand KH. A gastrointestinal PCR panel improves clinical management and lowers health care costs. J Clin Microbiol. 2017;56(1):e01457.
Bonkoungou IJ, Haukka K, Osterblad M, et al. Bacterial and viral etiology of childhood diarrhea in Ouagadougou, Burkina Faso. BMC Pediatr. 2013;13:36.