Metagenomics analysis of the neonatal intestinal resistome

Abstract

Introduction: The intestinal microbiome forms a major reservoir for antibiotic resistance genes (ARGs). Little is known about the neonatal intestinal resistome.

Objective: The objective of this study was to investigate the intestinal resistome and factors that influence the abundance of ARGs in a large cohort of neonates.

Methods: Shotgun metagenomics was used to analyse the resistome in stool samples collected at 1 week of age from 390 healthy, term-born neonates who did not receive antibiotics.

Results: Overall, 913 ARGs belonging to 27 classes were identified. The most abundant ARGs were those conferring resistance to tetracyclines, quaternary ammonium compounds, and macrolide-lincosamide-streptogramin-B. Phylogenetic composition was strongly associated with the resistome composition. Other factors that were associated with the abundance of ARGs were delivery mode, gestational age, birth weight, feeding method, and antibiotics in the last trimester of pregnancy. Sex, ethnicity, probiotic use during pregnancy, and intrapartum antibiotics had little effect on the abundance of ARGs.

Conclusion: Even in the absence of direct antibiotic exposure, the neonatal intestine harbours a high abundance and a variety of ARGs.

Keywords: antibiotic resistance; gut; infant; microbiome; microbiota; mobilome; stool.

Figure 1

Principal coordinate analyses of resistome profiles done on the normalised read counts of 913 ARGs detected in 390 infants. Axes indicate the percentage of total variance. Colours indicate delivery mode (A), formula milk during the first 7 days of life (B), probiotics use during pregnancy (any trimester) (C), antibiotics use during pregnancy (last trimester) (D), and intrapartum antibiotic use (E). The centroids indicate average resistome composition. Lines connect centroids to corresponding data points. ARGs, antibiotic resistance genes; CS, Caesarean section.

Figure 2

Differentially abundant antibiotic resistance genes. Dots depict genes associated with an FDR-corrected p-value of less than 0.05 and linear fold-change of at least 1.5 in the DESeq2 analyses. Colours of the dots represent the log₂FC and size of the dots the number of neonates in whom ARGs were detected. Red colour and positive values of log₂FC indicate the gene is more abundant in neonates born by Caesarean section, who received formula milk in the first 7 days of life, or whose mothers took probiotics (any trimester) or antibiotics during pregnancy (last trimester) or received intrapartum antibiotics. Blue colour and negative value of log₂FC indicate that the gene is more abundant in neonates born vaginally, who were exclusively breastfed in the first 7 days of life or whose mothers did not take probiotics (any trimester) or antibiotics during pregnancy (last trimester) or did not receive intrapartum antibiotics. Wilcoxon rank sum test: *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001. log₂FC, log₂-transformed fold-change; StAB, steroid antibacterial; QAC, quaternary ammonium compounds; MLSb, macrolide, lincosamide, streptogramin-B; MacSb, macrolide, streptogramin-B; MacrAmgTQAmRi, macrolide, aminoglycoside, tetracycline, quinolone, amphenicol, rifamycin; LSaP, lincosamide, streptogramin-A, pleuromutilin; LinSa, lincosamide, streptogramin-A; FPA, folate pathway antagonist; AmQQACFLA, amphenicol, quinolone, quaternary ammonium compounds, folate pathway antagonist.