Background The UK antibiotic guidelines for cystic fibrosis (CF) recommend that all infants should be prescribed a prophylactic narrow spectrum antibiotic, such as flucloxacillin, from diagnosis until 3 years of age. We wished to evaluate the prevalence of prophylactic antibiotic use in the UK and the effect this had on the microbiological outcome of children with CF.

Methods A registry search was conducted on the UK CF registry to include all children <3 years at the time of the 2009 dataset (UK CF registry. Cystic Fibrosis Trust, 2011). Information on antibiotic prophylaxis (“chronicoral antibiotic not prescribed to treat an exacerbation”) and bacterial status (no growth, intermittent or chronic) are entered at the time of annual assessment and refer to the previous year.

Results We identified 609 children who were born between August 2006 and December 2009, for whom data were available. Of these, 480 children (78.8%) were on prophylaxis and, 385 (80.2%) were on flucloxacillin alone. Prevalence of chronic/intermittent Staphylococcus aureus and Pseudomonas aeruginosa were similar between those not on antibiotics to those on flucloxacillin only. The use of “other” antibiotics was significantly associated with an increased prevalence of P aeruginosa (p=0.005, Bonferroni corrected threshold=0.0125).

Conclusions Despite current recommendations a sizeable minority of children with CF are not on anti-Staphylococcal prophylaxis. Of those who are, the majority receive flucloxacillin. Given the limited dataset, we did not detect any significant differences in microbiological outcome between those on regular Flucloxacillin to those on no antibiotics. Of note, the prevalence of S aureus in the under three group is around 7% compared with the overall UK prevalence of 15.2%. Prophylactic use of antibiotics other than Flucloxacillin (mostly cephalosporins; n=36 out of 95) appear associated with increased prevalence of P aeruginosa. This is consistent with findings from a previous US study implicating cephalosporin prophylaxis in acquisition of infection with P aeruginosa (J Pediatr 2002;140:299–305). Randomised controlled trials with long term follow-up, using clinically relevant outcomes, are warranted in order to better understand the effect antistaphylococcal prophylaxis has on the progression of CF lung disease.