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The aim of this study was to determine the occurrence of renal cortical scarring and chronic kidney disease (CKD) in children with neurogenic bladder secondary to spina bifida (SB) managed at the Universiti Kebangsaan Malaysia Medical Centre. The secondary objective was to identify the clinical factors associated with these adverse outcomes.The medical records of 56 children managed from 1997 were available. Socio-demographic and clinical data for SB children managed for a minimum of 2 years (n = 45) were reviewed. This included age at referral, gender, ethnicity, duration of care, type of SB lesion, presence of vesico-ureteric reflux (VUR), symptomatic urinary tract infections, bladder trabeculation, catheterisations and renal function.Forty-nine per cent of SB lesions were open myelomeningocoele, 40% were closed lesions and 11% were occult. Majority (96%) were at lumbar L3 or below. Twenty-nine children (64.5%) were referred before 6 months of age (mean15.8 months; range newborn to 125 months). Thirty-five (77.8%) had neurogenic bladder and 31(69%) had neurogenic bowel. Sixteen developed renal scarring and six, CKD. Late referral (≥6 months of age), small kidneys at referral, dilating VUR and bladder trabeculation were significant independent factors associated with scarring. On multivariate analysis, late referral (odds ratio (OR) 17.4; 95% confidence interval (CI) 1.26–238.7) and dilating VUR (OR 137.0; CI 6.4–2921.1) remained significant.Prevention of renal scarring and CKD remains a challenge in Malaysia even with multidisciplinary proactive care of SB children. Early referrals and more stringent management strategies for dilating VUR are still required.