Prevalence of pathogenic microorganisms and their correlation with the abundance of indicator organisms in riverbed sediments

The present study investigated the prevalence of pathogenic organisms (Salmonella spp, Vibrio cholerae, and Shigella spp) and their correlation to the abundance of faecal indicator organisms in water and riverbed sediments in the Apies River, South Africa. In all, 558 water and sediment samples were collected from 10 sites in the river (May 2013–February 2014) and analysed through culture and molecular (real-time PCR) techniques. Concentrations of faecal indicator organisms in sediments reached 1.39 × 10⁵ (±standard deviation) CFU/100 mL. All three pathogens were detected in water and sediments. Pathogens were mostly detected in sediments at sites influenced either by wastewater treatment works or by informal settlements. During the wet and dry seasons (water column), a strong positive correlation was observed between E. coli and all pathogens; C. perfringens only correlated with V. cholerae. Within sediments, strong positive correlations were only observed between E. coli and Salmonella spp, E. coli and V. cholerae (dry season); E. coli and V. cholerae and E. coli and Shigella spp (wet season). No correlation was observed between sediments C. perfringens counts and all the pathogens. Thus, sediments of the Apies River harbour pathogenic organisms. Correlation between E. coli and pathogenic organisms in the sediments suggests that E. coli could also be an indicator of pathogens’ presence. However, the lack of a correlation between E. coli and some pathogens in sediments and between C. perfringens and all the pathogens highlights the need to investigate for more indicators of pathogens’ presence in this complex matrix.