Background: Selection for resistance to azithromycin (AZM) and other antibiotics such as tetracyclines and lincosamides remains a concern with long-term AZM use for treatment of chronic lung diseases (CLD). We investigated the impact of 48 weeks of AZM on the carriage and antibiotic resistance of common respiratory bacteria among children with HIV-associated CLD.

Methods: Nasopharyngeal (NP) swabs and sputa were collected at baseline, 48 and 72 weeks from participants with HIV-associated CLD randomised to receive weekly AZM or placebo for 48 weeks and followed post-intervention until 72 weeks. The primary outcomes were prevalence and antibiotic resistance of Streptococcus pneumoniae (SP), Staphylococcus aureus (SA), Haemophilus influenzae (HI), and Moraxella catarrhalis (MC) at these timepoints. Mixed-effects logistic regression and Fisher's exact test were used to compare carriage and resistance respectively.

Results: Of 347 (174 AZM, 173 placebo) participants (median age 15 years [IQR =13–18], females 49%),NP carriage was significantly lower in the AZM (n=159) compared to placebo (n=153) arm for SP (18% vs 41%, p<0.001), HI (7% vs 16%, p=0.01), and MC (4% vs 11%, p=0.02); SP resistance to AZM (62% [18/29] vs 13%[8/63], p<0.0001) or tetracycline (60%[18/29] vs 21%[13/63], p<0.0001) were higher in the AZM arm. Carriage of SA resistant to AZM (91% [31/34] vs 3% [1/31], p<0.0001), tetracycline (35% [12/34] vs 13% [4/31], p= 0.05) and clindamycin (79% [27/34] vs 3% [1/31], p<0.0001) was also significantly higher in the AZM arm and persisted at 72 weeks. Similar findings were observed for sputa.

Conclusions: The persistence of antibiotic resistance and its clinical relevance for future infectious episodes requiring treatment needs further investigation.

This is a sub-study of the BREATHE trial (ClinicalTrials.gov Identifier: NCT02426112).  Approval for the main trial was obtained from local regulatory bodies at the study sites and the research ethics committees of the London School of Hygiene and Tropical Medicine, the University of Cape Town, and the Medical and Health Research in Norway. This sub-study was approved by the Human Research Ethics Committee of the University of Cape Town (HREC/REF: 092/2019). Written informed consent and age-appropriate assent were provided by guardians and participants under 18 years, respectively. Older participants (≥18 years) consented independently. BREATHE (Bronchopulmonary function in response to azithromycin treatment for chronic lung disease in HIV- infected children) is a two-site, double-blind, placebo- controlled, individually randomised trial that enrolled 346 perinatally HIV-infected children and adolescents aged 6–19 years with HIV-associated chronic lung disease (CLD) who have been receiving ART for a minimum of 6 months. Participants were enrolled from the outpatient HIV clinics in Harare, Zimbabwe, and Blantyre, Malawi. CLD was defined as forced expiratory volume in 1 second (FEV₁) z-score less than -1.0 with no reversibility [<12% improvement in FEV₁ after 200 µg of salbutamol inhaled using a spacer]. Participants were individually randomised to receive weight-based dosing of AZM (10 to 19.9 kg, 250 mg; 20 to 29.9 kg, 500 mg; 30 to 39.9 kg, 750 mg; and 40 kg or more, 1250 mg) or placebo once-weekly up to 48 weeks, with follow-up for a further 24 weeks post-intervention. Adherence to trial medication was defined as not missing, on average, more than two of the 12 dispensed doses, as assessed by pill count, splitting time in the study into four 12-week periods, according to visit and study medication dispensing schedule. Socio-demographic and clinical data were obtained through questionnaire administered by a study nurse. Nasopharyngeal (NP) swabs and sputa were collected from participants at baseline, 48- and 72-week visits. Samples were immediately stored in 1 ml of skim milk, tryptone, glucose, and glycerine (STGG) medium, placed on ice for a maximum of 1 h and then frozen down to at -80 °C. Streptococcus pneumoniae (SP), Staphylococcus aureus (SA), Haemophilus influenzae (HI) and Moraxella catarrhalis (MC) were recovered from the samples and identified using conventional microbiological culture and biochemical techniques. Gram negative bacilli were identified using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility testing (AST) to AZM, tetracycline and cotrimoxazole was conducted for all four bacterial species using the Kirby-Bauer disk diffusion method. Additionally, AST was done for SP to oxacillin, SA to clindamycin, cefoxitin, and penicillin, HI to amoxicillin-clavulanate, cefuroxime, and ampicillin, and MC to amoxicillin-clavulanate. Inducible clindamycin resistance was assessed as previously reported. SA susceptibility to cefoxitin was tested as a surrogate for methicillin resistance. Beta lactamase production by HI and MC was assessed using nitrocefin disc. AST was conducted in accordance with the 2018 Clinical and Laboratory Standards Institute guidelines and breakpoints.

The meaning of each variable in the dataset is detailed in the file labelled "data_dictionary_for_variables".