The distribution of and factors associated with intestinal parasitic infections are poorly defined in high risk vulnerable populations such as urban slums in tropical sub-Saharan Africa. In a cross sectional study, children aged 5 years and below who presented with diarrhoea were recruited from selected outpatient clinics in Mukuru informal settlement, and from Mbagathi District hospital, Nairobi, over a period of two years (2010–2011). Stool samples were examined for the presence of parasites using direct, formal-ether concentration method and the Modified Ziehl Neelsen staining technique. Overall, 541/2112 (25.6%) were positive for at least one intestinal parasite, with the common parasites being; Entamoeba histolytica, 225 (36.7%),Cryptosporidium spp. 187, (30.5%), Giardia lamblia, 98 (16%).The prevalence of intestinal parasites infection was higher among children from outpatient clinics 432/1577(27.4%) than among those admitted in hospital 109/535 (20.1%) p < 0.001. Infections with E. histolytica, and G. lamblia were higher among outpatients than inpatients (13.8% vs 1.3% p < 0.001 and 5.8% vs 1.3% p < 0.049) respectively, while infection with Cryptosporidium spp. was higher among inpatients than outpatients (15.3% vs 6.7%) respectively p < 0.001. Other parasites isolated among outpatients included Isospora belli, 19 (1.2%), Ascaris lumbricoides, 26 (1.6%), and Hymenolepis nana 12 (0.8%), with the remainder detected in less than ten samples each. HIV-infected participants were more likely to be infected with any parasite than uninfected participants, Adjusted Odds Ratio (AOR), 2.04, 95% CI, 1.55-2.67, p < 0.001), and with Cryptosporidium spp. (AOR, 2.96, 95% CI 2.07-4.21, p < 0.001).The inpatients were less likely to be infected with E. histolytica than outpatients (AOR, 0.11, 95% CI, 0.51- 0.24, p < 0.001), but more likely for inpatients to be infected with Cryptosporidium spp. than outpatients (AOR, 1.91, 95% CI, 1.33-2.73, p < 0.001). Mixed parasitic infections were seen in 65 (12.0%) of the 541 infected stool samples. Intestinal parasitic infections are common in urban informal settlements’ environment. Routine examinations of stool samples and treatment could benefit both the HIV infected and uninfected children in outpatient and inpatient settings.

Giardia duodenalis is an important intestinal protozoan in humans worldwide with high infection rates occurring in densely populated and low resource settings. The parasite has been recorded to cause diarrhea in children. This study was carried out to identify G. duodenalis assemblages and sub-assemblages in children presenting with diarrhea in Kenya. A total of 2112 faecal samples were collected from children aged ≤5 years and screened for the presence of Giardia cysts using microscopy. A total of 96 (4.5 %) samples were identified as Giardia positive samples and were genotyped using glutamate dehydrogenase (gdh), triose phosphate isomerase (tpi) and β-giardin loci. The three markers successfully genotyped 72 isolates and grouped 2 (1.4) isolates as Assemblage A, 64 (88.9) as Assemblage B and 7 (9.7 %) consisted of mixed infections with assemblage A and B. A further analysis of 50 isolates using GDH Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) categorized 2 assemblage A isolates as sub-assemblage AII while 6 and 14 assemblage B isolates were categorized into sub-assemblage BIII and BIV respectively. A mixed infection with sub-assemblage BIII and BIV was recorded in 28 isolates. Over half (55.6 %) of Giardia infections were recorded among the children between 13 to 48 months old. This paper reports the first data on the assemblages and sub-assemblages of Giardia duodenalis in children representing with diarrhea in Kenya.