Evaluation of a culture-independent gastrointestinal multiplex PCR panel for detection of gastrointestinal pathogens detection of gastrointestinal pathogens

Abstract

Objective: All across the world, gastrointestinal (GI) infections are an important cause of morbidity and mortality, especially in young children, patients in intensive care units, and patients with weakened immune systems. In this study we aimed to assess the Gastroenteritis RT-qPCR MX-24T Panel's utility as a standard technique for identifying gastrointestinal pathogens. Methods: In this study, 76 stool samples from intensive care patients were tested for bacterial, viral, and parasitic pathogens using the Bio-Speedy® Gastroenteritis RT-qPCR MX-24T Panel kit. Results: In this study, 31 out of 76 samples gave positive results. Eight bacterial (Salmonella spp., Campylobacter spp., Shigella/Enteroinvasive Escherichia coli (EIEC), Enteroaggregative E. coli (EAEC), Shiga toxin-producing E. coli (STEC), Enteropathogenic E. coli (EPEC), Enterotoxigenic E. coli (ETEC), and Clostridium difficile binary toxin A/B), three viral (Astrovirus, Norovirus (GI/GII and Rotavirus (A)) and two parasitic (Cryptosporidium spp., and Giardia lamblia) agents were detected from the stool samples of intensive care patients. While only a single agent was detected in the 22 samples, multiple agents were detected in 9 (30%). The most detected agent was EAEC (n=11), followed by Campylobacter spp. (n=7). EAEC and Campylobacter spp. were detected in 3 samples with multiple agents. Conclusion: The GI panel can minimize the need for additional diagnostic testing and unnecessary antibiotic use by rapidly identifying a wide range of infections detectable only by molecular methods, as well as agents detectable by traditional conventional diagnostic methods. In this way, it may lead to a shorter hospital stay. In addition, we think that further studies should be conducted to determine whether the simultaneous detection of multiple pathogens in a sample in our study is clinically important.

Keywords

• Gastrointestinal
• infection
• molecular panel
• multiplex polymerase chain reaction

References

1. 1. Gouveia MADC, Lins MTC, Silva GAPD. Acute diarrhea with blood: diagnosis and drug treatment. J Pediatr.2020;96:20-8.
2. 2.Gupta V, Singh M, Aditi RG. New insights intomolecular diagnostics for common gastrointestinalinfections. J Gastrointest Infect. 2021;11:16.
3. 3.Schiller LR. Chronic diarrhea evaluation in theelderly: IBS or something else? Curr Gastroenterol Rep. 2019;21:1-7.
4. 4.DuPont HL. Persistent diarrhea: a clinical review.JAMA. 2016;315(24):2712-23.
5. 5.Lucado J, Mohamoud S, Zhao L, et al. Infectiousenteritis and foodborne illness in the United States,2010: statistical brief# 150. 2013.
6. 6.Khamrin P, Okame M, Thongprachum A, et al. Asingle-tube multiplex PCR for rapid detection in fecesof 10 viruses causing diarrhea. J Virol Methods.2011;173(2):390-3.
7. 7.Akhter S, Turegun B, Kiyan M, et al. Investigation ofseven different RNA viruses associated withgastroenteritis in children under five years old.Mikrobiyol Bul. 2014;48(2):233-41.
8. 8.Eibach D, Krumkamp R, Hahn A, et al. Application ofa multiplex PCR assay for the detection ofgastrointestinal pathogens in a rural African setting.BMC Infect Dis. 2016;16:1-6.

9. 9.Semret M, Schiller I, Jardin BA, et al. Multiplexrespiratory virus testing for antimicrobialstewardship: a prospective assessment ofantimicrobial use and clinical outcomes amonghospitalized adults. J Infect Dis. 2017;216(8):936-44.
10. 10.Beal SG, Tremblay EE, Toffel S, et al. Agastrointestinal PCR panel improves clinicalmanagement and lowers health care costs. J ClinMicrobiol. 2018;56(1):10.1128/jcm. 01457-17.
11. 11.Marder EP. Incidence and trends of infections withpathogens transmitted commonly through food andthe effect of increasing use of culture-independentdiagnostic tests on surveillance—Foodborne DiseasesActive Surveillance Network, 10 US sites, 2013–2016.MMWR Morb Mortal Wkly Rep. 2017;66.
12. 12.Keske Ş, Zabun B, Aksoy K, et al. Rapid moleculardetection of gastrointestinal pathogens and its role inantimicrobial stewardship. J Clin Microbiol.2018;56(5): e00148-18
13. 13.Köffer J, Frontzek A, Eigner U. Development andvalidation of a bacterial gastrointestinal multiplex RT-PCR assay for use on a fully automated molecularsystem. J Microbiol Methods. 2023;210:106754.
14. 14.Zhang H, Morrison S, Tang Y-W. Multiplexpolymerase chain reaction tests for detection ofpathogens associated with gastroenteritis. Clin LabMed. 2015;35(2):461-486.
15. 15.Ozdamar M, Uzun B, Turkoglu S. Detection of viraland bacterial pathogens using multiplex real-timepolymerase chain reaction in acute gastroenteritis.Ann Med Res. 2020;27(3): 964-70.
16. 16.Yazici V, Gultekin B, Aydin N, et al. Akutgastroenteritli olgularin dişki örneklerinde bazibakteri ve virüslerin araştirilmasi. Ankem Derg.2009;23:59-65.
17. 17.Ozdemir S, Delialioğlu N, Emekdaş G. Investigationof rotavirus, adenovirus and astrovirus frequencies inchildren with acute gastroenteritis and evaluation ofepidemiological features. Mikrobiyol Bul.2010;44(4):571-578.
18. 18.Mohtar J, Mallah H, Mardirossian JM, et al.Enhancing enteric pathogen detection:implementation and impact of multiplex PCR forimproved diagnosis and surveillance. BMC Infect Dis.2024;24(1):171.
19. 19. Piralla A, Lunghi G, Ardissino G, et al. FilmArray™ GI panel performance for the diagnosis of acutegastroenteritis or hemorragic diarrhea. BMCMicrobiol. 2017;17:1-10.
20. 20.Khare R, Espy MJ, Cebelinski E, et al. Comparativeevaluation of two commercial multiplex panels fordetection of gastrointestinal pathogens by use ofclinical stool specimens. J Clin Microbiol.2014;52(10):3667-73.