Infection

, Volume 42, Issue 6, pp 961–970 | Cite as

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

  • C. Beckmann
  • U. Heininger
  • H. Marti
  • H. H. Hirsch
Clinical and Epidemiological Study

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.

Keywords

Gastrointestinal infection Multiplex PCR NAT Stool Diarrhea Parasites Bacteria Virus 

References

  1. 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.PubMedCrossRefGoogle Scholar
  2. 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.PubMedCentralPubMedGoogle Scholar
  3. 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.PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Black RE. Epidemiology of travelers’ diarrhea and relative importance of various pathogens. Rev Infect Dis. 1990;12:S73–9.PubMedCrossRefGoogle Scholar
  5. 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.PubMedCentralPubMedCrossRefGoogle Scholar
  6. 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.PubMedCentralPubMedGoogle Scholar
  7. 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.PubMedCrossRefGoogle Scholar
  8. 8.
    Casemore DP, Jackson B. Sporadic cryptosporidiosis in children. Lancet. 1983;2:679.PubMedCrossRefGoogle Scholar
  9. 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.PubMedCrossRefGoogle Scholar
  10. 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.PubMedCentralPubMedCrossRefGoogle Scholar
  11. 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.PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Dupont HL. Acute infectious diarrhea in immunocompetent adults. N Engl J Med. 2014;370:1532–40.PubMedCrossRefGoogle Scholar
  13. 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.PubMedCrossRefGoogle Scholar
  14. 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.PubMedCentralPubMedCrossRefGoogle Scholar
  15. 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.PubMedCrossRefGoogle Scholar
  16. 16.
    Henriksen SA, Pohlenz JF. Staining of cryptosporidia by a modified Ziehl-Neelsen technique. Acta Vet Scand. 1981;22:594–6.PubMedGoogle Scholar
  17. 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.PubMedCrossRefGoogle Scholar
  18. 18.
    Johnson S, Gerding DN. Clostridium difficile—associated diarrhea. Clin Infect Dis. 1998;26:1027–34 (quiz 1035–1026).PubMedCrossRefGoogle Scholar
  19. 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.PubMedCentralPubMedCrossRefGoogle Scholar
  20. 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.PubMedCrossRefGoogle Scholar
  21. 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.PubMedCentralPubMedCrossRefGoogle Scholar
  22. 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.PubMedCrossRefGoogle Scholar
  23. 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.PubMedCrossRefGoogle Scholar
  24. 24.
    Marti H, Escher E. SAF—an alternative fixation solution for parasitological stool specimens. Schweiz Med Wochenschr. 1990;120:1473–6.PubMedGoogle Scholar
  25. 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.PubMedCrossRefGoogle Scholar
  26. 26.
    Meinhardt PL, Casemore DP, Miller KB. Epidemiologic aspects of human cryptosporidiosis and the role of waterborne transmission. Epidemiol Rev. 1996;18:118–36.PubMedCrossRefGoogle Scholar
  27. 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.PubMedCrossRefGoogle Scholar
  28. 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. 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.PubMedGoogle Scholar
  30. 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. 31.
    Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev. 1998;11:142–201.PubMedCentralPubMedGoogle Scholar
  32. 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.PubMedCrossRefGoogle Scholar
  33. 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.PubMedCentralPubMedCrossRefGoogle Scholar
  34. 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.PubMedCrossRefGoogle Scholar
  35. 35.
    Scheier E, Aviner S. Septicemia following rotavirus gastroenteritis. Isr Med Assoc J. 2013;15:166–9.PubMedGoogle Scholar
  36. 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.PubMedCentralPubMedGoogle Scholar
  37. 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.PubMedCrossRefGoogle Scholar
  38. 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.PubMedCrossRefGoogle Scholar
  39. 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.PubMedCentralPubMedCrossRefGoogle Scholar
  40. 40.
    Thielman NM, Guerrant RL. Clinical practice. Acute infectious diarrhea. N Engl J Med. 2004;350:38–47.PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • C. Beckmann
    • 1
  • U. Heininger
    • 2
  • H. Marti
    • 3
  • H. H. Hirsch
    • 1
    • 4
    • 5
  1. 1.Division of Infection Diagnostics, Department of Biomedicine (Haus Petersplatz)University of BaselBaselSwitzerland
  2. 2.Division of Pediatric Infectious DiseasesUniversity Children’s Hospital BaselBaselSwitzerland
  3. 3.Swiss Tropical and Public Health InstituteUniversity of BaselBaselSwitzerland
  4. 4.Transplantation and Clinical Virology, Department Biomedicine (Haus Petersplatz)University of BaselBaselSwitzerland
  5. 5.Infectious Disease and Hospital EpidemiologyUniversity Hospital BaselBaselSwitzerland

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