Effect of intra-partum azithromycin on the development of the infant nasopharyngeal microbiota: A post hoc analysis of a double-blind randomized trial

Abstract

Background: Sepsis is a leading cause of neonatal death. Intrapartum azithromycin reduces neonatal nasopharyngeal carriage of potentially pathogenic bacteria, a prerequisite for sepsis. Early antibiotic exposure has been associated with microbiota perturbations with varying effects. This study aims to understand the effect of intrapartum azithromycin intervention on the developing nasopharyngeal microbiota of the child.

Methods: Using 16S rRNA gene sequencing, we analysed the microbiota of 343 nasopharyngeal samples collected from birth to 12 months from 109 healthy infants selected from a double-blind randomized placebo-controlled clinical trial conducted in the Gambia (PregnAnZI-1). In the trial, 829 women were given 2g oral azithromycin or placebo (1:1) during labour with the objective of reducing bacterial carriage in mother and child during the neonatal period. The post-hoc analysis presented here assessed the effect of the intervention on the child nasopharyngeal microbiota development.

Findings: 55 children were from mothers given azithromycin and 54 from mothers given placebo. Comparing arms, we found an increase in alpha-diversity at day-6 (p = 0·018), and a significant effect on overall microbiota composition at days 6 and 28 (R² = 4.4%, q = 0·007 and R² = 2.3%, q = 0·018 respectively). At genus level, we found lower representation of Staphylococcus at day-6 (q = 0·0303) and higher representation of Moraxella at 12 months (q = 0·0443). Unsupervised clustering of samples by microbial community similarity showed different community dynamics between the intervention and placebo arms during the neonatal period.

Interpretation: These results indicate that intrapartum azithromycin caused short-term alterations in the nasopharyngeal microbiota with modest overall effect at 12 months of age. Further exploration of the effects of these variations on microbiome function will give more insight on the potential risks and benefits, for the child, associated with this intervention.

Funding: This work was jointly funded by the Medical Research Council (UK) (MC_EX_MR/J010391/1/MRC), Bill & Melinda Gates Foundation (OPP1196513), and MRCG@LSHTM Doctoral Training Program.

Keywords: Azithromycin; Infant; Intrapartum; Nasopharyngeal microbiota; West Africa.

Figure 1

Selection of samples for microbiome study.

Figure 2

Box and whisker plot showing distribution of alpha-diversity scores between the trial arms at each time-point (day 0 p = 0.785, day 6 p = 0.031, day 28 p = 0.231, 12 months p = 0.234). The box shows the median and lower and upper quartiles (middle 50% of the scores) while the upper and lower whiskers show the upper and lower 25% scores respectively excluding outliers.

Figure 3

A non-metric multidimensional scaling (NMDS) plot showing bacterial community structure measured by Bray-Curtis dissimilarity index, compared by age in either trial arm and between trial arms at each age time-point using multivariate analysis.

Figure 4

(a) Distribution of partitions generated by Dirichlet Multinomial Mixtures (dmm), clustering samples into community types (partitions) based on similarities of their community profiles. (b) A heatmap showing relative abundances of the top 20 OTUs in the dataset across the five partitions in “a”. A detailed list of main OTUs driving the individual partitions and their taxonomic annotations can be found in supplementary Table 4. d0 = day 0, d6 = day 6, d28 = day 28, 12m = 12 months, A = Azithromycin, P = Placebo, P_1 = Partition_1, P_2 = Partition_2, P_3 = Partition_3, P_4 = Partition_4, P_5 = Partition_5

Figure 5

Genus profiles of trial arms grouped by time-point. The plot shows the mean relative abundance of the top 20 genera in either arm of the trial. The profiles show a dynamic trend from birth (day 0) to age 12 months, with some differences in taxa representation between arms.

Figure 6

Genera that had significantly different representation between the trial arms grouped by time point. Horizontal axis shows fold change in abundance in the azithromycin arm compared to the placebo arm. Blue colour indicates reduction and yellow indicates increase. The magnitude of increase or decrease is indicated by the length and direction of the bar. Details on relative abundance of these genera in the trial arms and statistical significance of differences are listed in table supplementary Table 5.