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Gastrointestinal pathogens detected by multiplex nucleic acid amplification testing in stools of pediatric patients and patients returning from the tropics

  • Clinical and Epidemiological Study
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Abstract

Background

Gastrointestinal infections are caused by a broad spectrum of pathogens. Conventional diagnostic procedures are resource and time consuming due to single pathogen testing, often in different laboratories.

Method

We analyzed 312 consecutive stool samples from pediatric patients (n = 127) with gastroenteritis or from adult travelers returning from the tropics with suspected parasite infestation (n = 185) using commercial multiplex nucleic acid amplification testing (NAT) (xTAG gastrointestinal pathogen panel, Luminex) covering 15 diarrhea-causing pathogens. The results of the positive samples and a representative number of negative samples were compared to standard methods, including NAT, direct antigen detection (DAD), bacterial culture and microscopy.

Results

Of the 185 samples from adult travelers, 21 (11 %) were multiplexNAT-positive, with enterotoxigenic Escherichia coli (4 %) being the predominant pathogen. Microscopic examination revealed Blastocystis hominis in 23 % not covered by the panel. MultiplexNAT scored positive in 66 pediatric samples (52 %), with rotavirus (27 %) being the most prevalent. All adenovirus-, rotavirus-, Clostridium difficile- and Cryptosporidium-positive samples were confirmed in external laboratories, but only 40 % of norovirus- and 29 % of Giardia-positive samples. Analysis of frozen specimens by bacterial culture showed the highest discrepancies with the multiplexNAT.

Conclusion

Our study demonstrates broad detection of relevant gastroenteritis pathogens by multiplexNAT with a short turnaround time. This is important for diagnosis, infection control and empiric management of gastroenteritis patients, but may be selectively complemented by bacterial culture and resistance testing.

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References

  1. Barbut F, Corthier G, Charpak Y, et al. Prevalence and pathogenicity of Clostridium difficile in hospitalized patients. A French multicenter study. Arch Intern Med. 1996;156:1449–54.

    Article  CAS  PubMed  Google Scholar 

  2. Barnes GL, Uren E, Stevens KB, et al. Etiology of acute gastroenteritis in hospitalized children in Melbourne, Australia, from April 1980 to March 1993. J Clin Microbiol. 1998;36:133–8.

    CAS  PubMed Central  PubMed  Google Scholar 

  3. Bernier C, Gounon P, Le Bouguenec C. Identification of an aggregative adhesion fimbria (AAF) type III-encoding operon in enteroaggregative Escherichia coli as a sensitive probe for detecting the AAF-encoding operon family. Infect Immun. 2002;70:4302–11.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  4. Black RE. Epidemiology of travelers’ diarrhea and relative importance of various pathogens. Rev Infect Dis. 1990;12:S73–9.

    Article  PubMed  Google Scholar 

  5. Boisen N, Scheutz F, Rasko DA, et al. Genomic characterization of enteroaggregative Escherichia coli from children in Mali. J Infect Dis. 2012;205:431–44.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  6. Bon F, Fascia P, Dauvergne M, et al. Prevalence of group A rotavirus, human calicivirus, astrovirus, and adenovirus type 40 and 41 infections among children with acute gastroenteritis in Dijon, France. J Clin Microbiol. 1999;37:3055–8.

    CAS  PubMed Central  PubMed  Google Scholar 

  7. Calderaro A, Gorrini C, Montecchini S, et al. Evaluation of a real-time polymerase chain reaction assay for the laboratory diagnosis of giardiasis. Diagn Microbiol Infect Dis. 2010;66:261–7.

    Article  CAS  PubMed  Google Scholar 

  8. Casemore DP, Jackson B. Sporadic cryptosporidiosis in children. Lancet. 1983;2:679.

    Article  CAS  PubMed  Google Scholar 

  9. Cohen SH, Gerding DN, Johnson S, et al. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the society for healthcare epidemiology of America (SHEA) and the infectious diseases society of America (IDSA). Infect Control Hosp Epidemiol. 2010;31:431–55.

    Article  PubMed  Google Scholar 

  10. Coste JF, Vuiblet V, Moustapha B, et al. Microbiological diagnosis of severe diarrhea in kidney transplant recipients by use of multiplex PCR assays. J Clin Microbiol. 2013;51:1841–9.

    Article  PubMed Central  PubMed  Google Scholar 

  11. Denno DM, Shaikh N, Stapp JR, et al. Diarrhea etiology in a pediatric emergency department: a case control study. Clin Infect Dis. 2012;55:897–904.

    Article  PubMed Central  PubMed  Google Scholar 

  12. Dupont HL. Acute infectious diarrhea in immunocompetent adults. N Engl J Med. 2014;370:1532–40.

    Article  CAS  PubMed  Google Scholar 

  13. Farkas T, Jiang X, Guerrero ML, et al. Prevalence and genetic diversity of human caliciviruses (HuCVs) in Mexican children. J Med Virol. 2000;62:217–23.

    Article  CAS  PubMed  Google Scholar 

  14. Fasel D, Mellmann A, Cernela N, et al. Hemolytic uremic syndrome in a 65 year-old male linked to a very unusual type of stx2e and eae harboring O51:H49 Shiga-toxin producing Escherichia coli. J Clin Microbiol. 2014;52:1301–3.

    Article  PubMed Central  PubMed  Google Scholar 

  15. Flem ET, Latipov R, Nurmatov ZS, et al. Costs of diarrheal disease and the cost-effectiveness of a rotavirus vaccination program in kyrgyzstan. J Infect Dis. 2009;200:S195–202.

    Article  PubMed  Google Scholar 

  16. Henriksen SA, Pohlenz JF. Staining of cryptosporidia by a modified Ziehl-Neelsen technique. Acta Vet Scand. 1981;22:594–6.

    CAS  PubMed  Google Scholar 

  17. Jiang ZD, Lowe B, Verenkar MP, et al. Prevalence of enteric pathogens among international travelers with diarrhea acquired in Kenya (Mombasa), India (Goa), or Jamaica (Montego Bay). J Infect Dis. 2002;185:497–502.

    Article  PubMed  Google Scholar 

  18. Johnson S, Gerding DN. Clostridium difficile—associated diarrhea. Clin Infect Dis. 1998;26:1027–34 (quiz 1035–1026).

    Article  CAS  PubMed  Google Scholar 

  19. Kirkwood CD, Bishop RF. Molecular detection of human calicivirus in young children hospitalized with acute gastroenteritis in Melbourne, Australia, during 1999. J Clin Microbiol. 2001;39:2722–4.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Laubach HE, Bentley CZ, Ginter EL, et al. A study of risk factors associated with the prevalence of Cryptosporidium in villages around Lake Atitlan, Guatemala. Braz J Infect Dis. 2004;8:319–23.

    Article  CAS  PubMed  Google Scholar 

  21. Lindell AT, Grillner L, Svensson L, et al. Molecular epidemiology of norovirus infections in Stockholm, Sweden, during the years 2000 to 2003: association of the GGIIb genetic cluster with infection in children. J Clin Microbiol. 2005;43:1086–92.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Liu L, Johnson HL, Cousens S, et al. Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000. Lancet. 2012;379:2151–61.

    Article  PubMed  Google Scholar 

  23. Marie-Cardine A, Gourlain K, Mouterde O, et al. Epidemiology of acute viral gastroenteritis in children hospitalized in Rouen, France. Clin Infect Dis. 2002;34:1170–8.

    Article  PubMed  Google Scholar 

  24. Marti H, Escher E. SAF—an alternative fixation solution for parasitological stool specimens. Schweiz Med Wochenschr. 1990;120:1473–6.

    CAS  PubMed  Google Scholar 

  25. Martin-Ampudia M, Mariscal A, Lopez-Gigosos RM, et al. Under-notification of cryptosporidiosis by routine clinical and laboratory practices among non-hospitalised children with acute diarrhoea in Southern Spain. Infection. 2012;40:113–9.

    Article  CAS  PubMed  Google Scholar 

  26. Meinhardt PL, Casemore DP, Miller KB. Epidemiologic aspects of human cryptosporidiosis and the role of waterborne transmission. Epidemiol Rev. 1996;18:118–36.

    Article  CAS  PubMed  Google Scholar 

  27. Mengelle C, Mansuy JM, Prere MF, et al. Simultaneous detection of gastrointestinal pathogens with a multiplex Luminex-based molecular assay in stool samples from diarrhoeic patients. Clin Microbiol Infect. 2013;19:E458–65.

    Article  CAS  PubMed  Google Scholar 

  28. Moore JE, Madden RH. Survival of Campylobacter coli in porcine liver. Food microbiology. New York: Academic Press; 2001. p. 1–10.

    Google Scholar 

  29. Morin N, Tirling C, Ivison SM, et al. Autoactivation of the AggR regulator of enteroaggregative Escherichia coli in vitro and in vivo. FEMS Immunol Med Microbiol. 2010;58:344–55.

    CAS  PubMed  Google Scholar 

  30. Murray PR, Boron EJ, Jorgensen JH, Landry ML, Pfaller MA. Manual of clinical microbiology. Washington: American Society of Microbiology Press; 2007.

    Google Scholar 

  31. Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev. 1998;11:142–201.

    CAS  PubMed Central  PubMed  Google Scholar 

  32. Owen RJ, On SL, Costas M. The effect of cooling rate, freeze-drying suspending fluid and culture age on the preservation of Campylobacter pylori. J Appl Bacteriol. 1989;66:331–7.

    Article  CAS  PubMed  Google Scholar 

  33. Rheingans R, Kukla M, Adegbola RA, et al. Exploring household economic impacts of childhood diarrheal illnesses in three African settings. Clin Infect Dis. 2012;55:S317–26.

    Article  PubMed Central  PubMed  Google Scholar 

  34. Roman E, Wilhelmi I, Colomina J, et al. Acute viral gastroenteritis: proportion and clinical relevance of multiple infections in Spanish children. J Med Microbiol. 2003;52:435–40.

    Article  PubMed  Google Scholar 

  35. Scheier E, Aviner S. Septicemia following rotavirus gastroenteritis. Isr Med Assoc J. 2013;15:166–9.

    PubMed  Google Scholar 

  36. Schmidt H, Knop C, Franke S, et al. Development of PCR for screening of enteroaggregative Escherichia coli. J Clin Microbiol. 1995;33:701–5.

    CAS  PubMed Central  PubMed  Google Scholar 

  37. Shkalim V, Amir A, Samra Z, et al. Characteristics of non-typhi Salmonella gastroenteritis associated with bacteremia in infants and young children. Infection. 2012;40:285–9.

    Article  CAS  PubMed  Google Scholar 

  38. Simpson R, Aliyu S, Iturriza-Gomara M, et al. Infantile viral gastroenteritis: on the way to closing the diagnostic gap. J Med Virol. 2003;70:258–62.

    Article  CAS  PubMed  Google Scholar 

  39. Stark D, Al-Qassab SE, Barratt JL, et al. Evaluation of multiplex tandem real-time PCR for detection of Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis in clinical stool samples. J Clin Microbiol. 2011;49:257–62.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  40. Thielman NM, Guerrant RL. Clinical practice. Acute infectious diarrhea. N Engl J Med. 2004;350:38–47.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We thank Sibylle Stauffer, Hülya Atici, Rita Reuter, Michelle Dobler, Grethe Sägesser, and Nicole Cernela for excellent technical assistance, as well as Roger Stephan, and Herbert Hächler from the National Centre for Enteropathogenic Bacteria and Listeria (NENT) for testing and for helpful advice.

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Division of Infection Diagnostics, Department of Biomedicine (Haus Petersplatz), University of Basel, Petersplatz 10, 4003, Basel, Switzerland

    C. Beckmann & H. H. Hirsch

  2. Division of Pediatric Infectious Diseases, University Children’s Hospital Basel, Basel, Switzerland

    U. Heininger

  3. Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland

    H. Marti

  4. Transplantation and Clinical Virology, Department Biomedicine (Haus Petersplatz), University of Basel, Basel, Switzerland

    H. H. Hirsch

  5. Infectious Disease and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland

    H. H. Hirsch

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  1. C. Beckmann
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  2. U. Heininger
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  4. H. H. Hirsch
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Correspondence to H. H. Hirsch.

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Beckmann, C., Heininger, U., Marti, H. et al. Gastrointestinal pathogens detected by multiplex nucleic acid amplification testing in stools of pediatric patients and patients returning from the tropics. Infection 42, 961–970 (2014). https://doi.org/10.1007/s15010-014-0656-7

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  • DOI: https://doi.org/10.1007/s15010-014-0656-7

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