The Infant Gut Resistome is Associated with E. coli and Early-life Exposures

Abstract

Background: Antibiotic resistance is an increasing threat to human health. The human gut microbiome harbors a collection of bacterial antimicrobial resistance genes (ARGs) known as the resistome. The factors associated with establishment of the resistome in early life are not well understood and clarifying these factors would inform strategies to decrease antibiotic resistance. We investigated the early-life exposures and taxonomic signatures associated with resistome development over the first year of life in a large, prospective cohort in the United States. Shotgun metagenomic sequencing was used to profile both microbial composition and ARGs in stool samples collected at 6 weeks and 1 year of age from infants enrolled in the New Hampshire Birth Cohort Study. Negative binomial regression and statistical modeling was used to examine infant factors such as sex, delivery mode, feeding method, gestational age, antibiotic exposure, and infant gut microbiome composition in relation to the diversity and relative abundance of ARGs.Results: Metagenomic sequencing was performed on paired samples from 195 full term (at least 37 weeks’ gestation) and 15 late preterm (33-36 weeks’ gestation) infants. 6-week samples compared to 1-year samples had 4.37 times (95% CI: 3.54-5.39) the rate of harboring ARGs. The majority of ARGs that were at a greater relative abundance at 6 weeks (chi-squared p < 0.01) worked through the mechanism of antibiotic efflux (i.e., by pumping antibiotics out of the cell). The overall relative abundance of the resistome was strongly correlated with Proteobacteria (Spearman correlation = 78.9%) and specifically E. coli (62.2%) relative abundance in the gut microbiome. Among infant characteristics, delivery mode was most strongly associated with the diversity and relative abundance of ARGs. Infants born via cesarean delivery had a higher risk of harboring unique ARGs [relative risk = 1.12 (95% CI: 0.97 – 1.29)] as well as a having an increased risk for overall ARG relative abundance [relative risk = 1.43 (95% CI: 1.12 – 1.84)] at 1 year compared to infants born vaginally. Additionally, 6 specific ARGs were at a greater relative abundance in infants delivered by cesarean section compared to vaginally delivered infants across both time points. Conclusions: Our findings suggest that the developing infant gut resistome may be alterable by early-life exposures. Establishing the extent to which infant characteristics and early-life exposures impact the resistome can ultimately lead to interventions that decrease the transmission of ARGs and thus the possibility of antibiotic resistant life threatening infections.

Impact of antibiotics to off-target infant gut microbiota and resistance genes in cohort studies

“…For CfxA2 , they found that it was also increased among infants given another antibiotic compared to no antibiotic exposure. Although they did not have resistome measurements taken before antibiotic exposures to establish baseline ARG abundances, the results of our study aligned with these results and those presented previously in our cohort 53 .…”

“…Among infants who attended day care by 1 year, we found that E. coli relative abundance increased in antibiotic exposed infants suggesting a synergistic interaction between antibiotic exposure and day care attendance. Although we were unable to identify other studies that assessed both antibiotic exposure and day care attendance, given E. coli ’s role in horizontal gene transfer 48,49 and previous studies in the NHBCS and others noting their association with harboring antibiotic resistance genes 21,50–53 , the corresponding changes to resistome composition aligned with changes to E. coli relative abundance.…”

“…While this study is one of the largest to consider the population-level impact of antibiotic exposures to the infant gut over a follow-up period, we note some important limitations. Our main limitation was the precise timing and dosage of antibiotic exposures in the NHBCS Antibiotic Exposure Cohort as well as limitations to generalizability among participants in New Hampshire and Vermont 53 . To mitigate this, we utilized stool samples from the DIABIMMUNE Study as a validation cohort since it obtained both precise timing and dose of antibiotic exposures [ Supplemental Notes (online)].…”

Metagenomic Analysis Reveals Associations between Salivary Microbiota and Body Composition in Early Childhood

“…This was directly examined in our prospective analyses by assessing child growth between 0 and 2 years of age. Based on the DAG, the potential confounders (i.e., related to our exposure and outcome directly or hypothesized to be based on previously identified indirect associations in separate studies) to adjust for in our analyses were age (measured by age in days of the saliva sample), sex (male or female) [37,60], delivery mode (vaginal or cesarean delivery) [3], gestational age (age in weeks) [27,61] and diet (age when child started to eat solid foods in months) [37]. Although previous studies have found associations between maternal BMI or weight gain and children's BMI [64], literature identifying associations between maternal BMI and the child's saliva microbiome have not found associations [37,65].…”

“…Negative control yields were too low to quantify at 2ul. Extracted DNA was amplified from all samples were prepared for sequencing on the NextSeq platform (shotgun metagenomics) using 150 nt paired end reads at the Marine Biological Laboratory (MBL) in Woods Hole, MA using established methods and as previously published [28,[59][60][61].…”