title: Genetic Diversity of Cryptosporidium in Children in an Urban Informal Settlement of Nairobi, Kenya.
abstract: BACKGROUND
  Globally Cryptosporidium and Giardia species are the most common non-bacterial causes of diarrhoea in children and HIV infected individuals, yet data on their role in paediatric diarrhoea in Kenya remains scant. This study investigated the occurrence of Cryptosporidium species, genotypes and subtypes in children, both hospitalized and living in an informal settlement in Nairobi.
  
  
  METHODS
  This was a prospective cross-sectional study in which faecal specimen positive for Cryptosporidium spp. by microscopy from HIV infected and uninfected children aged five years and below presenting with diarrhoea at selected outpatient clinics in Mukuru informal settlements, or admitted to the paediatric ward at the Mbagathi District Hospital were characterized. The analysis was done by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of the 18srRNA gene for species identification and PCR-sequencing of the 60 kDa glycoprotein (GP60) gene for subtyping.
  
  
  RESULTS
  C. hominis was the most common species of Cryptosporidium identified in125/151(82.8%) of the children. Other species identified were C. parvum 18/151(11.9%), while C. felis and C. meleagridis were identified in 4 and 2 children, respectively. Wide genetic variation was observed within C. hominis, with identification of 5 subtype families; Ia, Ib, Id, Ie and If and 21 subtypes. Only subtype family IIc was identified within C. parvum. There was no association between species and HIV status or patient type.
  
  
  CONCLUSIONS
  C. hominis is the most common species associated with diarrhoea in the study population. There was high genetic variability in the C. hominis isolates with 22 different subtypes identified, whereas genetic diversity was low within C. parvum with only one subtype family IIc identified.
authors.affiliation: Centre for Microbiological Research, Kenya Medical Research Institute, Nairobi, Kenya.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Mbae
authors.affiliation: Centre for Microbiological Research, Kenya Medical Research Institute, Nairobi, Kenya.
authors.forename: Erastus
authors.initials: E
authors.lastname: Mulinge
authors.affiliation: Kenya Medical Research Institute, Nairobi, Kenya.
authors.forename: Anthony
authors.initials: A
authors.lastname: Waruru
authors.affiliation: Centre for Microbiological Research, Kenya Medical Research Institute, Nairobi, Kenya.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Ngugi
authors.affiliation: Bioscience eastern and central Africa, International Livestock Research Institute, Nairobi, Kenya.
authors.forename: James
authors.initials: J
authors.lastname: Wainaina
authors.affiliation: Centre for Microbiological Research, Kenya Medical Research Institute, Nairobi, Kenya.
authors.forename: Samuel
authors.initials: S
authors.lastname: Kariuki
mesh_terms: D000818:Animals; D001483:Base Sequence; D002675:Child, Preschool; D003457:Cryptosporidiosis / Q000453:epidemiology / Q000235:genetics*; D003458:Cryptosporidium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D015658:HIV Infections / Q000453:epidemiology / Q000382:microbiology; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007630:Kenya / Q000453:epidemiology; D008297:Male; D008969:Molecular Sequence Data; D012150:Polymorphism, Restriction Fragment Length; D015800:Protozoan Proteins / Q000235:genetics*; D016053:RNA, Protozoan / Q000235:genetics*; D012337:RNA, Ribosomal, 18S / Q000235:genetics*; D014505:Urban Population
chemical_list: D015800:Protozoan Proteins; D016053:RNA, Protozoan; D012337:RNA, Ribosomal, 18S