Multiplex PCR for bacterial, viral and protozoal pathogens in persistent diarrhoea or persistent abdominal pain in Côte d'Ivoire, Mali and Nepal.

In contrast to acute diarrhoea, the aetiology of persistent digestive disorders (≥ 14 days) is poorly understood in low-resource settings and conventional diagnostic approaches lack accuracy. In this multi-country study, we compared multiplex real-time PCR for enteric bacterial, parasitic and viral pathogens in stool samples from symptomatic patients and matched asymptomatic controls in Côte d'Ivoire, Mali and Nepal. Among 1826 stool samples, the prevalence of most pathogens was highest in Mali, being up to threefold higher than in Côte d'Ivoire and up to tenfold higher than in Nepal. In all settings, the most prevalent bacteria were EAEC (13.0-39.9%) and Campylobacter spp. (3.9-35.3%). Giardia intestinalis was the predominant intestinal protozoon (2.9-20.5%), and adenovirus 40/41 was the most frequently observed viral pathogen (6.3-25.1%). Significantly different prevalences between symptomatic and asymptomatic individuals were observed for Campylobacter, EIEC and ETEC in the two African sites, and for norovirus in Nepal. Multiple species pathogen infection was common in Côte d'Ivoire and Mali, but rarely found in Nepal. We observed that molecular testing detected multiple enteric pathogens and showed low discriminatory accuracy to distinguish between symptomatic and asymptomatic individuals. Yet, multiplex PCR allowed for direct comparison between different countries and revealed considerable setting-specificity.

Molecular and culture-based diagnosis of Clostridium difficile isolates from Côte d'Ivoire after prolonged storage at disrupted cold chain conditions.

BACKGROUND: Although Clostridium difficile is a major cause of diarrhoea, its epidemiology in tropical settings is poorly understood. Strain characterisation requires work-up in specialised laboratories, often after prolonged storage without properly maintained cold chain. METHODS: We screened 298 human faecal samples from Côte d'Ivoire using a rapid test for C. difficile glutamate dehydrogenase (GDH). GDH-positive samples were aerobically stored at disrupted cold chain conditions (mean duration: 11 days) before transfer to a reference laboratory for anaerobic culture, susceptibility testing, PCR assays and ribotyping. RESULTS: Sixteen samples (5.4%) had a positive GDH screening test. C. difficile infection was confirmed in six specimens by culture and PCR, while no nucleic acids of C. difficile were detected in the culture-negative samples. Further analysis of stool samples harbouring toxigenic C. difficile strains confirmed that both GDH and toxins remained detectable for at least 28 days, regardless of storage conditions (aerobic storage at 4°C or 20°C). CONCLUSIONS: Storage conditions only minimally affect recovery of C. difficile and its toxins in stool culture. A rapid GDH screening test and subsequent transfer of GDH-positive stool samples to reference laboratories for in-depth characterisation may improve our understanding of the epidemiology of C. difficile in the tropics.