173
Views
1
CrossRef citations to date
0
Altmetric
REVIEW

Diagnostic syndromic multiplex approaches for gastrointestinal infections

ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 743-757 | Received 07 Dec 2020, Accepted 04 Mar 2021, Published online: 19 Mar 2021

References

  • Dickinson B, Surawicz CM. Infectious diarrhea: an overview. Curr Gastroenterol Rep. 2014;16(8):399.
  • Diarrheal disease. https://www.who.int/en/news-room/fact-sheets/detail/diarrhoeal-disease. Accessed 2020 Nov 29. [Internet].
  • Graves NS. Acute gastroenteritis. Prim Care. 2013;40(3):727–741.
  • DuPont HL. Acute infectious diarrhea in immunocompetent adults. N Engl J Med. 2014;370(16):1532–1540.
  • DuPont HL. Persistent Diarrhea: a clinical review. JAMA. 2016;315(24):2712–2723.
  • Binnicker MJ. Multiplex molecular panels for diagnosis of gastrointestinal infection: performance, result interpretation, and cost-effectiveness. J Clin Microbiol. 2015;53(12):3723–3728.
  • Corinaldesi R, Stanghellini V, Barbara G, et al. Clinical approach to diarrhea. Intern Emerg Med. 2012;7(Suppl 3):S255–62.
  • Zollner-Schwetz I, Krause R. Therapy of acute gastroenteritis: role of antibiotics. Clin Microbiol Infect. 2015;21(8):744–749.
  • Kim S, Covington A, Pamer EG. The intestinal microbiota: antibiotics, colonization resistance, and enteric pathogens. Immunol Rev. 2017;279(1):90–105.
  • Riddle MS, DuPont HL, Connor BA. ACG clinical guideline: diagnosis, treatment, and prevention of acute diarrheal infections in adults. Am J Gastroenterol. 2016;111(5):602–622.
  • Alby K, Nachamkin I. Gastrointestinal Infections. Microbiol Spectr. 2016;4(3) :1-14.
  • Guh AY, Kutty PK. Clostridioides difficile Infection. Ann Intern Med. 2018;169(7):ITC49–ITC64.
  • Ramanan P, Bryson AL, Binnicker MJ, et al. Syndromic panel-based testing in clinical microbiology. Clin Microbiol Rev. 2018;31(1). doi: 10.1128/CMR.00024-17
  • Shane AL, Mody RK, Crump JA, et al., 2017 infectious diseases society of america clinical practice guidelines for the diagnosis and management of infectious Diarrhea. Clin Infect Dis. 65(12):1963–1973. 2017.
  • Liesman RM, Binnicker MJ. The role of multiplex molecular panels for the diagnosis of gastrointestinal infections in immunocompromised patients. Curr Opin Infect Dis. 2016;29(4):359–365.
  • Sell J, Dolan B. Common gastrointestinal Infections. Prim Care. 2018;45(3):519–532.
  • Schuetz AN. Emerging agents of gastroenteritis: aeromonas, Plesiomonas, and the diarrheagenic pathotypes of Escherichia coli. Semin Diagn Pathol. 2019;36(3):187–192.
  • Humphries RM, Linscott AJ. Practical Guidance for clinical microbiology laboratories: diagnosis of bacterial gastroenteritis. Clin Microbiol Rev. 2015;28(1):3–31.
  • Garcia LS, Arrowood M, Kokoskin E, et al. Practical guidance for clinical microbiology laboratories: laboratory diagnosis of parasites from the gastrointestinal tract. Clin Microbiol Rev. 2018;31(1). DOI:10.1128/CMR.00025-17.
  • Zhang H, Morrison S, Tang YW. Multiplex polymerase chain reaction tests for detection of pathogens associated with gastroenteritis. Clin Lab Med. 2015;35(2):461–486.
  • Amaral MS, Estevam GK, Penatti M, et al. The prevalence of norovirus, astrovirus and adenovirus infections among hospitalised children with acute gastroenteritis in Porto Velho, state of Rondonia, western Brazilian Amazon. Mem Inst Oswaldo Cruz. 2015;110(2):215–221.
  • Oka T, Wang Q, Katayama K, et al. Comprehensive review of human sapoviruses. Clin Microbiol Rev. 2015;28(1):32–53.
  • Dien Bard J, McElvania E. Panels and syndromic testing in clinical microbiology. Clin Lab Med. 2020;40(4):393–420.
  • Machiels JD, Cremers AJH, Van Bergen-verkuyten M, et al. Impact of the bioFire filmArray gastrointestinal panel on patient care and infection control. PLoS One. 2020;15(2):e0228596.
  • Beal SG, Tremblay EE, Toffel S, et al. A gastrointestinal PCR panel improves clinical management and lowers health care costs. J Clin Microbiol. 2018;56(1):e01457-17.
  • Huang RS, Johnson CL, Pritchard L, et al. Performance of the Verigene(R) enteric pathogens test, Biofire FilmArray gastrointestinal panel and Luminex xTAG(R) gastrointestinal pathogen panel for detection of common enteric pathogens. Diagn Microbiol Infect Dis. 2016;86(4):336–339.
  • Axelrad JE, Freedberg DE, Whittier S, et al. Impact of gastrointestinal panel implementation on health care utilization and outcomes. J Clin Microbiol. 2019;57(3). DOI:10.1128/JCM.01775-18.
  • Hanson KE, Couturier MR. Multiplexed molecular diagnostics for respiratory, gastrointestinal, and central nervous system infections. Clin Infect Dis. 2016;63(10):1361–1367.
  • 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):915–925.
  • Rand KH, Tremblay EE, Hoidal M, et al. Multiplex gastrointestinal pathogen panels: implications for infection control. Diagn Microbiol Infect Dis. 2015;82(2):154–157.
  • Cybulski RJ Jr., Bateman AC, Bourassa L, et al. Clinical Impact of a multiplex gastrointestinal polymerase chain reaction panel in patients with acute gastroenteritis. Clin Infect Dis. 2018;67(11):1688–1696.
  • Torres-Miranda D, Akselrod H, Karsner R, et al. Use of BioFire FilmArray gastrointestinal PCR panel associated with reductions in antibiotic use, time to optimal antibiotics, and length of stay. BMC Gastroenterol. 2020;20(1):246.
  • Zhang J, Guan H, Zhao W, et al. Evaluation of the BioFire filmarray gastrointestinal panel and real-time polymerase chain reaction assays for the detection of major diarrheagenic pathogens by a multicenter diarrheal disease surveillance program in China. Foodborne Pathog Dis. 2019;16(11):788–798.
  • Zhan Z, Guo J, Xiao Y, et al. Comparison of BioFire FilmArray gastrointestinal panel versus luminex xTAG gastrointestinal pathogen panel (xTAG GPP) for diarrheal pathogen detection in China. Int J Infect Dis. 2020;99:414–420.
  • Gyawali P, Croucher D, Hewitt J. Preliminary evaluation of BioFire FilmArray((R)) gastrointestinal panel for the detection of noroviruses and other enteric viruses from wastewater and shellfish. Environ Sci Pollut Res Int. 2018;25(27):27657–27661.
  • Zboromyrska Y, Advanced VJ. PCR-based molecular diagnosis of gastrointestinal infections: challenges and opportunities. Expert Rev Mol Diagn. 2016;16(6):631–640.
  • Wang C, Zhou X, Zhu M, et al. The application research of xTAG GPP multiplex PCR in the diagnosis of persistent and chronic diarrhea in children. BMC Pediatr. 2020;20(1):309.
  • Perry MD, Corden SA, Howe RA. Evaluation of the Luminex xTAG gastrointestinal pathogen panel and the savyon diagnostics gastrointestinal infection panel for the detection of enteric pathogens in clinical samples. J Med Microbiol. 2014;63(Pt 11):1419–1426.
  • Yoo J, Park J, Lee HK, et al. Comparative evaluation of seegene Allplex Gastrointestinal, Luminex xTAG gastrointestinal pathogen panel, and BD MAX Enteric assays for detection of gastrointestinal pathogens in clinical stool specimens. Arch Pathol Lab Med. 2019;143(8):999–1005.
  • Amjad M. An overview of the molecular methods in the diagnosis of gastrointestinal infectious diseases. Int J Microbiol. 2020;2020:8135724.
  • Kosai K, Suzuki H, Tamai K, et al. Multicenter evaluation of verigene enteric pathogens nucleic acid test for detection of gastrointestinal pathogens. Sci Rep. 2021;11(1):3033.
  • Koziel M, Kiely R, Blake L, et al. Improved detection of bacterial pathogens in patients presenting with gastroenteritis by use of the entericBio real-time gastro panel i assay. J Clin Microbiol. 2013;51(8):2679–2685.
  • McAuliffe G, Bissessor L, Williamson D, et al. Use of the EntericBio gastro panel II in a diagnostic microbiology laboratory: challenges and opportunities. Pathology. 2017;49(4):419–422.
  • Koziel M, Corcoran D, O’Callaghan I, et al. Validation of the EntericBio panel II(R) multiplex polymerase chain reaction system for detection of Campylobacter spp., Salmonella spp., Shigella spp., and verotoxigenic E. coli for use in a clinical diagnostic setting. Diagn Microbiol Infect Dis. 2013;75(1):46–49.
  • Boers SA, Peters CJA, Wessels E, et al. Performance of the QIAstat-Dx Gastrointestinal panel for diagnosing infectious gastroenteritis. J Clin Microbiol. 2020;58(3). doi: 10.1128/JCM.01737-19.
  • Zimmermann S, Horner S, Altwegg M, et al. Workflow optimization for syndromic diarrhea diagnosis using the molecular Seegene Allplex GI-bacteria(I) assay. Eur J Clin Microbiol Infect Dis. 2020;39(7):1245–1250.
  • Amrud K, Slinger R, Sant N, et al. A comparison of the Allplex bacterial and viral assays to conventional methods for detection of gastroenteritis agents. BMC Res Notes. 2018;11(1):514.
  • Autier B, Gangneux JP, Robert-Gangneux F. Evaluation of the Allplex(TM) gastrointestinal panel-parasite assay for protozoa detection in stool samples: a retrospective and prospective study. Microorganisms. 2020;8(4):569.
  • Hyun J, Ko DH, Lee SK, et al. Evaluation of a new multiplex real-time PCR assay for detecting gastroenteritis-causing viruses in stool samples. Ann Lab Med. 2018;38(3):220–225.
  • Reddington K, Tuite N, Minogue E, et al., A current overview of commercially available nucleic acid diagnostics approaches to detect and identify human gastroenteritis pathogens. Biomol Detect Quantif. 1(1):3–7. 2014. .
  • Coupland LJ, McElarney I, Meader E, et al. Simultaneous detection of viral and bacterial enteric pathogens using the Seeplex(R) Diarrhea ACE detection system. Epidemiol Infect. 2013;141(10):2111–2121.
  • Higgins RR, Beniprashad M, Cardona M, et al. Evaluation and verification of the Seeplex Diarrhea-V ACE assay for simultaneous detection of adenovirus, rotavirus, and norovirus genogroups I and II in clinical stool specimens. J Clin Microbiol. 2011;49(9):3154–3162.
  • Lee JH, Kim YK, Lee CH. Clinical evaluation of Seeplex((R)) Diarrhea-V ACE detection (V2.0) kit for detection of rotavirus in stool specimens from children with acute gastroenteritis. Ann Clin Lab Sci. 2017;47(3):328–333.
  • Philip CO, Koech M, Kipkemoi N, et al. Evaluation of the performance of a multiplex reverse transcription polymerase chain reaction kit as a potential diagnostic and surveillance kit for rotavirus in Kenya. Trop Dis Travel Med Vaccines. 2019;5(1):12.
  • Biswas JS, Al-Ali A, Rajput P, et al. A parallel diagnostic accuracy study of three molecular panels for the detection of bacterial gastroenteritis. Eur J Clin Microbiol Infect Dis. 2014;33(11):2075–2081.
  • Autier B, Belaz S, Razakandrainibe R, et al. Comparison of three commercial multiplex PCR assays for the diagnosis of intestinal protozoa. Parasite. 2018;25:48.
  • Kanwar N, Hassan F, Barclay L, et al. Evaluation of RIDA((R))GENE norovirus GI/GII real time RT-PCR using stool specimens collected from children and adults with acute gastroenteritis. J Clin Virol. 2018;104:1–4.
  • Redli PM, Wanzenried A, Huder JB, et al. Evaluation of the RIDA(R)GENE RT-PCR assays for detection of sapovirus, astrovirus, adenovirus, and rotavirus in stool samples of adults in Switzerland. Diagn Microbiol Infect Dis. 2020;96(2):114924.
  • Hirvonen JJ. Comparison of three multiplex real-time PCR assays for detection of enteric viruses in patients with diarrhea. Eur J Clin Microbiol Infect Dis. 2019;38(2):241–244.
  • Harrington SM, Buchan BW, Doern C, et al. Multicenter evaluation of the BD max enteric bacterial panel PCR assay for rapid detection of Salmonella spp., Shigella spp., Campylobacter spp. (C. jejuni and C. coli), and Shiga toxin 1 and 2 genes. J Clin Microbiol. 2015;53(5):1639–1647.
  • Anderson NW, Buchan BW, Ledeboer NA. Comparison of the BD MAX enteric bacterial panel to routine culture methods for detection of Campylobacter, enterohemorrhagic Escherichia coli (O157), Salmonella, and Shigella isolates in preserved stool specimens. J Clin Microbiol. 2014;52(4):1222–1224.
  • DeBurger B, Hanna S, Powell EA, et al. Utilizing BD MAX Enteric bacterial panel to detect stool pathogens from rectal swabs. BMC Clin Pathol. 2017;17(1):7.
  • Knabl L, Grutsch I, Orth-Holler D. Comparison of the BD MAX(R) enteric bacterial panel assay with conventional diagnostic procedures in diarrheal stool samples. Eur J Clin Microbiol Infect Dis. 2016;35(1):131–136.
  • Mortensen JE, Ventrola C, Hanna S, et al. Comparison of time-motion analysis of conventional stool culture and the BD MAX Enteric Bacterial Panel (EBP). BMC Clin Pathol. 2015;15(1):9.
  • Simner PJ, Oethinger M, Stellrecht KA, et al. Multisite evaluation of the bd max extended enteric bacterial panel for detection of Yersinia enterocolitica, Enterotoxigenic Escherichia coli, Vibrio, and Plesiomonas shigelloides from Stool Specimens. J Clin Microbiol. 2017;55(11):3258–3266.
  • Perry MD, Corden SA, Lewis White P. Evaluation of the BD MAX enteric parasite panel for the detection of Cryptosporidium parvum/hominis, Giardia duodenalis and Entamoeba histolytica. J Med Microbiol. 2017;66(8):1118–1123.
  • Batra R, Judd E, Eling J, et al. Molecular detection of common intestinal parasites: a performance evaluation of the BD Max Enteric Parasite Panel. Eur J Clin Microbiol Infect Dis. 2016;35(11):1753–1757.
  • Stokes W, Simner PJ, Mortensen J, et al. Multicenter clinical validation of the molecular BD max enteric viral panel for detection of enteric pathogens. J Clin Microbiol. 2019;57(9). DOI:10.1128/JCM.00306-19.
  • Buchan BW, Olson WJ, Pezewski M, et al. Clinical evaluation of a real-time PCR assay for identification of Salmonella, Shigella, Campylobacter (Campylobacter jejuni and C. coli), and shiga toxin-producing Escherichia coli isolates in stool specimens. J Clin Microbiol. 2013;51(12):4001–4007.
  • Kahlau P, Malecki M, Schildgen V, et al. Utility of two novel multiplexing assays for the detection of gastrointestinal pathogens - a first experience. Springerplus. 2013;2(1):106.
  • Yalamanchili H, Dandachi D, Okhuysen PC. Use and Interpretation of Enteropathogen multiplex nucleic acid amplification tests in patients with suspected infectious Diarrhea. Gastroenterol Hepatol. 2018;14(11):646–652.
  • Weiner LM, Fridkin SK, Aponte-Torres Z, et al. Vital signs: preventing antibiotic-resistant infections in hospitals - United States, 2014. MMWR Morb Mortal Wkly Rep. 2016;65(9):235–241.
  • Wallace MJ, Fishbein SRS, Dantas G. Antimicrobial resistance in enteric bacteria: current state and next-generation solutions. Gut Microbes. 2020;12(1):1799654.
  • Pickering LK. Antimicrobial resistance among enteric pathogens. Semin Pediatr Infect Dis. 2004;15(2):71–77.
  • Macfarlane-Smith LR, Ahmed S, Wilcox MH. Molecular versus culture-based testing for gastrointestinal infection. Curr Opin Gastroenterol. 2018;34(1):19–24.
  • Flores-Trevino S, Mendoza-Olazaran S, Bocanegra-Ibarias P, et al. Helicobacter pylori drug resistance: therapy changes and challenges. Expert Rev Gastroenterol Hepatol. 2018;12(8):819–827.
  • Pohl D, Keller PM, Bordier V, et al. Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing. World J Gastroenterol. 2019;25(32):4629–4660.
  • Leonardi M, La Marca G, Pajola B, et al. Assessment of real-time PCR for Helicobacter pylori DNA detection in stool with co-infection of intestinal parasites: a comparative study of DNA extraction methods. BMC Microbiol. 2020;20(1):131.
  • Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020;20(5):533–534.
  • Ravi N, Cortade DL, Ng E, et al. Diagnostics for SARS-CoV-2 detection: a comprehensive review of the FDA-EUA COVID-19 testing landscape. Biosens Bioelectron. 2020;165:112454.
  • D’Amico F, Baumgart DC, Danese S, et al. Diarrhea during COVID-19 Infection: pathogenesis, epidemiology, prevention, and management. Clin Gastroenterol Hepatol. 2020;18(8):1663–1672.
  • Hajifathalian K, Mahadev S, Schwartz RE, et al. SARS-COV-2 infection (coronavirus disease 2019) for the gastrointestinal consultant. World J Gastroenterol. 2020;26(14):1546–1553.
  • Wong SH, Lui RN, Sung JJ. Covid-19 and the digestive system. J Gastroenterol Hepatol. 2020;35(5):744–748.
  • Chen L, Lou J, Bai Y, et al. COVID-19 disease with positive fecal and negative pharyngeal and sputum viral tests. Am J Gastroenterol. 2020;115(5):790.
  • Wong MC, Huang J, Lai C, et al. Detection of SARS-CoV-2 RNA in fecal specimens of patients with confirmed COVID-19: a meta-analysis. J Infect. 2020;81(2):e31–e8.
  • Creager HM, Cabrera B, Schnaubelt A, et al. Clinical evaluation of the BioFire(R) respiratory panel 2.1 and detection of SARS-CoV-2. J Clin Virol. 2020;129:104538.
  • Szymczak WA, Goldstein DY, Orner EP, et al. Utility of stool PCR for the diagnosis of COVID-19: comparison of two commercial platforms. J Clin Microbiol. 2020;58(9). DOI:10.1128/JCM.01369-20.
  • Genetic Analysis AS. GA-map® COVID-19 Fecal Test. http://www.genetic-analysis.com/wp-content/uploads/2020/06/GA-map-Covid-19-Fecal-Test-Technical-performance-1.pdf2020. cited 2020 Nov 29. [Internet].
  • Hitchcock MM, Gomez CA, Banaei N. Low yield of filmarray GI panel in hospitalized patients with diarrhea: an opportunity for diagnostic stewardship intervention. J Clin Microbiol. 2018;56(3). DOI:10.1128/JCM.01558-17
  • Miller MB. Opinion on syndromic panel-based testing in clinical microbiology. Clin Chem. 2020;66(1):42–44.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.