Prophylactic azithromycin in preterm infants reduced microbial diversity and health-associated Bifidobacterium while increasing pathobionts and macrolide-resistant genes including erm(C), effects not fully mitigated by probiotic use.
Key Findings
Results
Azithromycin treatment reduced microbial diversity in the preterm gut microbiome.
Study enrolled 693 preterm infants across 28 centers in the AZTEC double-blind, randomized, placebo-controlled trial.
Infants were born at less than 30 weeks of gestation and treated from birth for 10 days with intravenous azithromycin or placebo.
Gut microbiome was assessed using 16S rRNA gene sequencing with longitudinal sampling for 21 days or until discharge.
Alpha diversity was reduced in the azithromycin-treated group compared to placebo.
Results
Azithromycin reduced the relative abundance of health-associated Bifidobacterium in the preterm gut.
Bifidobacterium is considered a health-associated genus in the preterm gut microbiome.
Reduction in Bifidobacterium relative abundance was observed in the azithromycin group compared to placebo.
Sampling was conducted longitudinally across the 21-day study period or until discharge.
The effect was assessed via 16S rRNA gene sequencing.
Results
Azithromycin increased the relative abundances of pathobionts Staphylococcus and Enterobacter/Klebsiella.
Both Staphylococcus and Enterobacter/Klebsiella are described as pathobionts in the context of preterm gut microbiome health.
Enrichment of these taxa was observed in azithromycin-treated infants relative to placebo recipients.
These genera are clinically relevant as potential sources of neonatal infection in preterm populations.
The study used 16S rRNA gene sequencing to identify and quantify microbial taxa.
Results
Azithromycin treatment increased the number of macrolide-resistant genes, including erm(C), which persisted for the duration of the study.
Antibiotic resistance genes (ARGs) were assessed using antibiotic susceptibility testing and quantitative PCR.
The macrolide resistance gene erm(C) was specifically identified as emerging and persisting in azithromycin-treated infants.
Resistance gene enrichment persisted for the full duration of the 21-day study period.
Both the number and presence of macrolide-resistant genes were increased in the azithromycin group.
Results
Probiotic use increased alpha diversity and Bifidobacterium relative abundance but did not fully mitigate the effects of azithromycin.
Probiotic use was at individual unit discretion rather than randomized, representing an observational comparison within the trial.
Probiotics were associated with increased alpha diversity in the preterm gut microbiome.
Probiotics increased the relative abundance of Bifidobacterium.
Despite these beneficial effects, probiotics could not fully counteract the microbiome disruption caused by azithromycin.
Results
Combined azithromycin and probiotic use further increased the enrichment of Enterobacter/Klebsiella and total ARGs, including erm(C).
The combination of azithromycin and probiotics was associated with greater enrichment of Enterobacter/Klebsiella than either intervention alone.
Total antibiotic resistance genes, including erm(C), were further increased in infants receiving both azithromycin and probiotics.
This finding suggests potential unintended consequences of concurrent probiotic and antibiotic use in preterm infants.
The authors describe these findings as highlighting 'the impacts of antibiotic and probiotic use, both important in balancing infection control issues and microbiome disruption and antimicrobial resistance.'
Methods
The AZTEC study was a large multi-center, double-blind, randomized, placebo-controlled trial examining 693 preterm infants across 28 centers.
Infants were born at less than 30 weeks of gestation.
Treatment was administered as intravenous azithromycin or placebo for 10 days starting from birth.
Longitudinal stool sampling was conducted for 21 days or until hospital discharge.
The study used 16S rRNA gene sequencing, antibiotic susceptibility testing, and quantitative PCR as analytical methods.
The full trial name was AZithromycin ThErapy for Chronic Lung Disease of Prematurity (AZTEC).
What This Means
This research examined what happens to the gut bacteria of very premature babies (born before 30 weeks of pregnancy) when they are given azithromycin, an antibiotic, as a preventive treatment. The study was large and carefully designed, involving 693 premature babies across 28 hospitals, where babies were randomly assigned to receive either azithromycin or a placebo (inactive treatment) through an IV for the first 10 days of life. Researchers analyzed the babies' stool samples over three weeks to track changes in gut bacteria and antibiotic resistance genes.
The study found that azithromycin disrupted the gut microbiome in several important ways: it reduced bacterial diversity, decreased beneficial bacteria called Bifidobacterium (which are normally important for healthy development), and increased the presence of potentially harmful bacteria including Staphylococcus and Enterobacter/Klebsiella. It also promoted the growth of bacteria carrying antibiotic resistance genes—particularly a gene called erm(C) that makes bacteria resistant to macrolide antibiotics like azithromycin—and these resistance genes persisted throughout the study period. Some babies also received probiotics (live beneficial bacteria), which helped restore some of the lost diversity and beneficial bacteria, but could not fully undo the damage from azithromycin. Interestingly, babies who received both azithromycin and probiotics had even higher levels of potentially harmful bacteria and antibiotic resistance genes than those who received azithromycin alone.
This research suggests that giving azithromycin prophylactically to very premature babies comes with significant costs to the developing gut microbiome and contributes to the broader problem of antibiotic resistance. The finding that probiotics did not fully compensate for these effects—and may have worsened some outcomes when combined with azithromycin—highlights the complexity of managing infection risk and microbiome health in premature infants. These findings are important for clinicians and researchers weighing the potential benefits of preventive antibiotics against their unintended consequences for long-term microbiome development and antimicrobial resistance.
Check Your Own Numbers
Upload your bloodwork. We'll cross-reference your results against this study and 4,700 others.
Ahearn-Ford S, Aboklaish A, Young G, Lowe J, Masi A, Gallacher D, et al.. (2026). The impact of prophylactic azithromycin on the developing preterm gut microbiome and resistome.. Gut microbes. https://doi.org/10.1080/19490976.2026.2748147