A cohort study in family triads: impact of gut microbiota composition and early life exposures on intestinal resistome during the first two years of life

Roosa Jokela, Katariina M.M. Pärnänen, Alise J. Ponsero, Leo Lahti, Kaija-Leena Kolho, Willem M. de Vos, Anne Salonen

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Abstract

Antibiotic resistance genes (ARGs) are prevalent in the infant gut microbiota and make up the intestinal resistome, representing a community ARG reservoir. This study focuses on the dynamics and persistence of ARGs in the early gut microbiota, and the effect of early exposures therein. We leveraged 2,328 stool metagenomes from 475 children in the HELMi cohort and the available parental samples to study the diversity, dynamics, and intra-familial sharing of the resistome during the first two years of life. We found higher within-family similarity of the gut resistome composition and ARG load in infant-mother pairs, and between spouses, but not in father-infant pairs. Early gut microbiota composition and development correlated with the ARG load; Bacteroides correlated positively and Bifidobacterium negatively with the load, reflecting the typical resistance levels in these taxa. Caesarean delivered infants harbored lower ARG loads, partly reflecting the scarcity of Bacteroides compared to vaginally delivered. Exposure to intrapartum or post-natal antibiotics showed only modest associations with the ARG load and composition, mainly before 12 months. Our results indicate that the resistome is strongly driven by the normal development of the microbiota in early life, and suggest importance of longer evolution of ARGs over effects of recent antibiotic exposure.

Original languageEnglish
Article number2383746
JournalGUT MICROBES
Volume16
Issue number1
DOIs
Publication statusPublished - 2024
Publication typeA1 Journal article-refereed

Keywords

  • antibiotic resistance
  • early resistome
  • infant microbiome
  • Infant resistome

Publication forum classification

  • Publication forum level 1

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)
  • Gastroenterology
  • Infectious Diseases

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