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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).    Conclusion  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.

Application of a multiplex PCR assay for the detection of gastrointestinal pathogens in a rural African setting