title: Application of a multiplex PCR assay for the detection of gastrointestinal pathogens in a rural African setting.
abstract: BACKGROUND
  Despite high morbidity and mortality, the laboratory diagnosis of gastrointestinal infections is largely neglected in tropical African settings. This study aims to apply the Luminex multiplex PCR assay for the diagnosis of gastrointestinal pathogens in rural Ghana to evaluate its usefulness as a routine method.
  
  
  METHODS
  A case-control study was conducted at the Agogo Presbyterian Hospital in Ghana. Stool samples were collected from children below 6 years of age with (cases) and without (controls) diarrhoea. Samples were screened for 15 different diarrhoeal pathogens by the Luminex xTAG GPP assay and associations between diarrhoea and gastrointestinal infections and fractions attributable to diarrhea (AF) were determined.
  
  
  RESULTS
  The Luminex PCR assay identified organisms in 96.6% (n = 428) of 443 cases and in 92.5% (n = 221) of 239 selected controls. A mean of 2.5 (standard deviation [SD]: ± 1.3) and 2.3 (SD: ± 1.3) organisms per sample were detected in cases and controls respectively. An association with diarrhoea was found for rotavirus (adjusted odds ratio [aOR] = 7.2; 95% confidence interval [CI]: 2.9-18.1), norovirus (aOR = 2.7; 95% CI: 1.4-5.3) and Shigella spp. (aOR = 1.7; 95% CI: 1.2-2.4) with respective AFs of 12.5% (95% CI: 9.6-15.3), 7.9% (95% CI: 3.8-11.7) and 16.9% (95% CI: 6.9-25.9).
  
  
  CONCLUSIONS
  The high proportion of pathogen-positive stool samples with a high number of co-infections in cases and controls suggests a substantial amount of transient or colonizing microorganisms for which treatment is not necessarily implicated. The use of sequential diagnostic algorithms with pathogen specific or quantitative PCRs might be most appropriate for diagnosing gastrointestinal infections.
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany. eibach@bnitm.de.
authors.forename: Daniel
authors.initials: D
authors.lastname: Eibach
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.|German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck, Hamburg, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Krumkamp
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.|German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck, Hamburg, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Hahn
authors.affiliation: Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana.
authors.forename: Nimako
authors.initials: N
authors.lastname: Sarpong
authors.affiliation: Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.
authors.forename: Yaw
authors.initials: Y
authors.lastname: Adu-Sarkodie
authors.affiliation: Institute for Virology, University Medical Center, Freiburg, Germany.
authors.forename: Amelie
authors.initials: A
authors.lastname: Leva
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Käsmaier
authors.affiliation: Institute for Virology, University Medical Center, Freiburg, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Panning
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.|German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck, Hamburg, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: May
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany.|German Center for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck, Hamburg, Germany.
authors.forename: Egbert
authors.initials: E
authors.lastname: Tannich
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D016022:Case-Control Studies; D002675:Child, Preschool; D004269:DNA, Bacterial / Q000032:analysis / Q000378:metabolism; D003967:Diarrhea; D005243:Feces / Q000382:microbiology / Q000821:virology; D005260:Female; D005767:Gastrointestinal Diseases / Q000175:diagnosis / Q000382:microbiology* / Q000821:virology; D005869:Ghana; D006801:Humans; D007223:Infant; D008297:Male; D060885:Multiplex Polymerase Chain Reaction; D029322:Norovirus / Q000235:genetics / Q000302:isolation & purification; D016017:Odds Ratio; D012367:RNA, Viral / Q000032:analysis / Q000378:metabolism; D012401:Rotavirus / Q000235:genetics / Q000302:isolation & purification; D012760:Shigella / Q000235:genetics / Q000302:isolation & purification
chemical_list: D004269:DNA, Bacterial; D012367:RNA, Viral
keywords: Gastrointestinal infections; Ghana; Multiplex Polymerase Chain Reaction; West Africa