Effects of Therapeutic Antibiotic Exposure on the Oropharyngeal and Fecal Microbiota in Infants With Cystic Fibrosis

Abstract

Background: Systemic antibiotics can impact all microbes inhabiting patients, regardless of the intended target organism(s). We studied the simultaneous effects on respiratory and fecal microbiomes of β-lactam antibiotics administered for respiratory symptoms in infants with cystic fibrosis (IWCF).

Objective: To compare the magnitude and duration of intended (respiratory) and unintended (fecal) antimicrobial action by analyzing oropharyngeal (OP) and fecal microbiota in IWCF.

Design: Shotgun metagenomic sequencing and qPCR were performed on OP and fecal samples collected longitudinally from 14 IWCF (ages 1-17 months) during ("On Antibiotics") and after ("Off Antibiotics") β-lactam therapy, and from 5 IWCF (3-16 months) never treated with antibiotics.

Results: Total bacterial loads (TBL) for On Antibiotics samples were lower than for both Never (OP and fecal) and Off Antibiotics samples (fecal only). α-diversities (within-sample) for OP On Antibiotics samples were lower than for Never and Off Antibiotics samples but did not differ between fecal sample groups. β-diversity (between-sample) differed between all OP sample groups and between fecal On and Never Antibiotics and Off and Never antibiotics samples; however, fecal On and Off Antibiotics sample β-diversities did not differ. Patterns of change in antibiotic resistance gene abundances reflected shifts in microbial community composition.

Conclusions: β-lactam antibiotic exposure was followed by marked alterations in both OP and fecal microbiota. While microbiota appeared to rebound after treatment in both sample types, our results suggest that fecal microbiota recovered less than OP. The clinical consequences of these findings should be studied in IWCF and other populations frequently treated with antibiotics.

Keywords: antibiotic resistance; metagenome; respiratory symptoms.

Figure 1

Study schema. OP swab and stool samples were collected from IWCF never treated with antibiotics (n = 5) or IWCF who received β‐lactam antibiotics during the study period (n = 14). Eight of the IWCF who received β‐lactam antibiotics provided samples prior to receiving any antibiotics in their lifetime, and these samples were included in the Never Antibiotics category (here, marked with * for clarity). On Antibiotics samples from 11 of 14 IWCF were collected while infants were receiving β‐lactam therapy for pulmonary exacerbations, and Off Antibiotics samples from all 14 IWCF were collected after antibiotic exposure.

Figure 2

Total bacterial loads in (A) OP and (B) fecal samples for each study group. Box center lines indicate medians, with hinges at 25th and 75th percentiles; whiskers extend to the minimum and maximum values. Dots indicate individual sample values. p values of < 0.05 (linear mixed‐effects model) were considered significant. GE = genome equivalents. OP and fecal samples for individual infants displayed chronologically by age of collection are in Supporting Information S1: Figures 2 and 3. [Color figure can be viewed at wileyonlinelibrary.com]

Figure 3

Alpha (α)‐diversity using the Shannon Diversity Index for OP samples. (A) OP samples are grouped by antibiotic sample type. Box center lines indicate medians, with hinges at 25th and 75th percentiles; whiskers extend to the minimum and maximum values. Dots indicate individual sample values. p values of < 0.05 (linear mixed‐effects model) were considered significant. (B) OP samples for individual infants are displayed chronologically by age of collection. Samples are colored as in (A) with Never Antibiotics = purple, On Antibiotics = orange, and Off Antibiotics = green. Green points with a thick orange border were collected 7 days or less after cessation of antibiotic treatment. [Color figure can be viewed at wileyonlinelibrary.com]

Figure 4

Alpha (α)‐diversity using the Shannon Diversity Index for fecal samples. (A) Fecal samples grouped by antibiotic sample type. Box center lines indicate medians, with hinges at 25th and 75th percentiles; whiskers extend to the minimum and maximum values. Dots indicate individual sample values. P values of < 0.05 (linear mixed‐effects model) were considered significant. (B) Fecal samples for individual infants displayed chronologically by age of collection. Samples are colored as in (A) with Never Antibiotics = purple, On Antibiotics = orange, and Off Antibiotics = green. Green points with a thick orange border were collected 7 days or less after cessation of antibiotic treatment. [Color figure can be viewed at wileyonlinelibrary.com]

Figure 5

Beta (β)‐diversity of OP samples. (A) Principal coordinates analysis using the Aitchison dissimilarity metric of taxonomic relative abundances. Large dots represent the centroid of each group, with ellipses encircling 95% of individual samples. Colors indicate antibiotic sample type with Never Antibiotics = purple, On Antibiotics = orange, and Off Antibiotics = green. (B) Biplots demonstrating the taxa most responsible for the taxonomic difference among all sample types. Biplots were generated at species level; genus names are listed for illustration clarity. Length of vectors indicates the extent to which taxa contribute to inter‐sample dissimilarity. (C) Bar charts of family level relative abundances for each infant at each sample point are displayed chronologically by age. Only families that reach 25% abundance in at least one sample are shown. On = On Antibiotics, Off = Off Antibiotics, and NA = Never Antibiotics. [Color figure can be viewed at wileyonlinelibrary.com]

Figure 6

Beta (β)‐diversity of fecal samples. (A) Principal coordinates analysis using the Aitchison dissimilarity metric of taxonomic relative abundances. Large dots represent the centroid of each group, with ellipses encircling 95% of individual samples. Colors indicate antibiotic sample type with Never Antibiotics = purple, On Antibiotics = orange, and Off Antibiotics = green. (B) Biplots demonstrating the taxa most responsible for the taxonomic difference among all sample types. Biplots were generated at species level; genus names are listed for illustration clarity. Length of vectors indicates the extent to which taxa contribute to inter‐sample dissimilarity. (C) Bar charts of family level relative abundances for each infant at each sample point are displayed chronologically by age. Only families that reach 25% abundance in at least one sample are shown. On = On Antibiotics, Off = Off Antibiotics, and NA = Never Antibiotics. [Color figure can be viewed at wileyonlinelibrary.com]