Diarrhoeagenic Escherichia coli strains are pathogens of great public health importance, affecting both adults and children worldwide, but are infrequently sought because molecular or tissue culture methods are required to delineate them from commensals [6, 13]. While rotavirus often takes center stage as a leading cause of childhood diarrhoea, particularly in Africa, diarrheagenic Escherichia coli (DEC) strains, especially ETEC, EAEC, and EPEC, can contribute significantly to the overall burden [5, 13–14]. The epidemiological significance of each DEC pathotypes in childhood diarrhoea varies from one geographical area to another [5]. Also, there are important regional differences in the prevalence of the different categories of DEC over time and seasons [5, 14–18]. The prevalence of three DEC categories (ETEC, EAEC, and EPEC), was significantly higher in cases than in the controls (p˂0 001). Similar outcomes have also been reported in western (Ghana and Nigeria) [19–21] and south-eastern Africa (Mozambique) [22]. The fact that DEC was recovered from 23.7% of the controls in this study area shows that healthy children, who might act as reservoirs for transmission and/or suffer long term consequences of colonization [23], also harbour these pathogens. In this study, the five common pathotypes of E. coli—ETEC, EIEC, EPEC, EAEC, and STEC were identified; where ETEC, EPEC and STEC were significantly recovered more in diarrhoea cases than controls. This is consistent with the findings of other researchers from other developing countries, where the frequencies of recovery of ETEC, EPEC, and STEC were significantly higher in the cases than in the controls [22, 24–26]. Enterotoxigenic Escherichia coli (ETEC)-associated diarrhoea has been reported by many studies as the most common bacterial diarrhoea affecting children under 5 years old living in developing countries, as well as travelers to these countries [27]. In this study, ETEC was the most prevalent DEC pathotype, among both cases and controls, and was significantly associated with diarrhoea. This figure was comparable to findings from many [28–30], but not all [31–32] other resource-limited countries. In addition, in a study on DEC among children with and without diarrhoea in Burkina Faso by Bonkoungou et. al., ETEC was highly significantly associated with diarrhoea [33]. Altogether, reviews on DEC in sub-Saharan Africa stated that ETEC is associated with infantile diarrhoea in African countries and also the most common cause of acute diarrhoea [5, 34].
As in other studies, DEC were most predominantly recovered from children under one year of age [13, 16, 35–37]. This age group represents a particularly vulnerable population to DEC infections due to factors such as immature immune systems and increased susceptibility to environmental pathogens. Additionally, our study highlighted the significance of inadequate breastfeeding (less than 6 months) as another notable risk factor for DEC infection. This is comparable to what Ali et al. [38] and Akinlabi et al. [39] observed in northern and southwestern Nigeria. Breastfeeding provides infants with essential nutrients and antibodies that bolster their immune defences against infections, including DEC-related ones [13, 38]. Therefore, the absence or early cessation of breastfeeding may leave infants more susceptible to diarrheal illnesses, including those caused by DEC. Our finding and similar reports from elsewhere emphasize the importance of promoting exclusive breastfeeding for the first six months of life as an infectious diarrhoea prevention measure [39–40].
Our study revealed a significant association between caregivers with a limited educational background and DEC infection. This finding underscores the multifactorial nature of diarrheal illnesses in children, highlighting the impact of socioeconomic factors on disease transmission [40–41]. Caregivers with lower levels of education may have limited access to health education and resources, leading to suboptimal hygiene practices and increased susceptibility to DEC contamination in the household environment [40–42]. Our study also identified caregivers who are siblings as being associated with DEC infection among children. This suggests the potential contribution of intra-familial transmission routes in DEC spread. Siblings may facilitate close contact and shared exposure to contaminated environments, thereby increasing the risk of transmission within households [43].
This study revealed a seasonal variation in the prevalence of DEC infection in the environment. When compared to the dry season, the overall prevalence of DEC was shown to be significantly higher in the rainy season (p < 0.001). The peak prevalence of DEC (ETEC and EPEC) was observed in August, which is regarded as one of the months with the most rainfall in the study area, and is characterized by the contamination of surface waterways by sewage spills, feces spills, and other waste spills. This finding is consistent with earlier research on the seasonal variation of DEC infection, including those by Tumwine and colleagues [44–45]
Antimicrobial drug resistance in bacteria that cause diarrhoeal disease is a serious and growing problem [46]. Antimicrobials are not indicated for the treatment of most childhood diarrheas but should be administered to children with invasive or protracted infections. Moreover, resistance in enteric isolates provides a picture of the gut reservoir of resistance genes, which can be transmitted to enteric organisms causing infections in other niches.
This study revealed high rates of antibiotic resistance among different DEC categories, in particular, resistance to sulphonamide, trimethoprim, amoxicillin clavulanic-acid, streptomycin and ampicillin, probably as a result of its increased availability of multiple generic formulations in the markets [16, 47] but also because mobile genes encoding resistance to these antimicrobials are often linked and transmitted together. Substandard oral drugs, common in our setting [13] that are insufficiently absorbed could leave sufficient drug behind in the intestine to select resistant enterics [48–49]. Notably, the DEC isolates in this study remained susceptible to quinolones and carbapenems, highlighting the importance of preserving these critically-important antibiotics for severe infections [50]
Salmonella spp were not recovered in this study in spite of enrichment and have been found uncommon in childhood diarrhoea studies performed in or close to our study area [51–52]. As with those studies, we additionally did not identify any Shigella or many EIEC.
This study has several limitations. Controls were not time-matched with cases, possibly introducing temporal confounding. Only 1–2 isolates per specimen were screened for DEC by PCR. Typically screening 3–5 colonies can increase the yield of DEC, particularly from children without diarrhoea, who often carry multiple E. coli lineages. Akinlabi et al [51] recently reported that the Aranda et al multiplex PCR protocol, which they compared with whole genome sequencing, had suboptimal sensitivity and specificity for certain DEC lineages that are common elsewhere in south western Nigeria. As we did not also identify DEC by whole genome sequencing, the degree to which this might affect our results is unclear. These limitations notwithstanding, the data point to a high incidence of DEC infections, strong association with diarrhoea for multiple pathotypes and the need for more in-depth investigations with more predictive tools in this study area, as well as further study of the isolates we obtained.