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Weaning is complex for children with phenylketonuria (PKU). Breastmilk/infant formula and phenylalanine (Phe)-free infant protein-substitute (PS) are gradually replaced with equivalent amounts of Phe-containing food, a semi-solid/spoonable weaning PS and special low-protein foods. In PKU, feeding patterns/practices during weaning in PKU have not been formally evaluated. In this longitudinal, prospective, case-control study (<i>n</i> = 20) infants with PKU transitioning to a second-stage PS, were recruited at weaning (4&#8315;6 months) for a comparison of feeding practices and development with non-PKU infants. Subjects were monitored monthly to 12 months and at age 15 months, 18 months and 24 months for: feeding progression; food textures; motor skill development and self-feeding; feeding environment; gastrointestinal symptoms; and negative feeding behaviours. Children with PKU had comparable weaning progression to non-PKU infants including texture acceptance, infant formula volume and self-feeding skills. However, children with PKU had more prolonged Phe-free infant formula bottle-feeding and parental spoon feeding than controls; fewer meals/snacks per day; and experienced more flatulence (<i>p</i> = 0.0005), burping (<i>p</i> = 0.001), retching (<i>p</i> = 0.03); and less regurgitation (<i>p</i> = 0.003). Negative behaviours associated with PS at age 10&#8315;18 months, coincided with the age of teething. Use of semi-solid PS in PKU supports normal weaning development/progression but parents require support to manage the complexity of feeding and to normalise the social inclusivity of their child&#8217;s family food environment. Further study regarding parental anxiety associated with mealtimes is required.