Abstract:
Infectious diarrhoea contributes to high morbidity and mortality in young children from
sub-Saharan Africa. The aim of this study was to assess the prevalence of single and multiple
diarrhoeal-causing pathogen combinations in children suffering from diarrhoea from rural and
peri-urban communities in South Africa. A total of 275 diarrhoea stool specimens were collected
between 2014 and 2016 from Hospitals and Primary Health Care clinics. The BioFire® FilmArray®
Gastrointestinal panel was used to simultaneously detect 22 diarrhoea pathogens (viruses, bacteria,
parasites) known to cause diarrhoea. A total of 82% (226/275) enteric pathogens were detected in the
stool specimens. The two most detected bacterial, viral and parasitic pathogens each included: EAEC
(42%), EPEC (32%), Adenovirus F40/41 (19%), Norovirus (15%), Giardia (8%) and Cryptosporidium
(6%), respectively. Single enteric pathogen infections were recorded in 24% (65/275) specimens
with EAEC, and Norovirus was found in 26% (17/65) and 14% (9/65) of the specimens, respectively.
Multiple enteric pathogen combinations were recorded in 59% (161/275) of the stool specimens with
53% (85/161) containing two pathogens, 22% (35/161) containing three pathogens and 25% (41/161)
containing four or more pathogens. The results from this study demonstrated the complex nature of
pathogen co-infections in diarrhoeal episodes which could have an impact on treatment effectiveness.
