Old Folks, Bad Boon: Antimicrobial Resistance in the Infant Gut Microbiome

The development of the intestinal microbiome in the neonate starts, mainly, at birth, when the infant receives its founding microbial inoculum from the mother. This microbiome contains genes conferring resistance to antibiotics since these are found in some of the microorganisms present in the intestine. Similarly to microbiota composition, the possession of antibiotic resistance genes is affected by different perinatal factors. Moreover, antibiotics are the most used drugs in early life, and the use of antibiotics in pediatrics covers a wide variety of possibilities and treatment options. The disruption in the early microbiota caused by antibiotics may be of great relevance, not just because it may limit colonization by beneficial microorganisms and increase that of potential pathogens, but also because it may increase the levels of antibiotic resistance genes. The increase in antibiotic-resistant microorganisms is one of the major public health threats that humanity has to face and, therefore, understanding the factors that determine the development of the resistome in early life is of relevance. Recent advancements in sequencing technologies have enabled the study of the microbiota and the resistome at unprecedent levels. These aspects are discussed in this review as well as some potential interventions aimed at reducing the possession of resistance genes.

This research was funded by MCIN/AEI/10.13039/501100011033/ and FEDER “Una forma de hacer Europa”, grant number PID2021-125337OB-I00, and Generalitat Valenciana (GVA) through the PROMETEO grant, “NeoHealth project PROMETEO 2020/012”. S.A. was the recipient of a postdoctoral contract; S.S. was a recipient of a predoctoral contract awarded by the Biosanitary Research Foundation in Asturias (FINBA, Spain); and A.S. was a recipient of a predoctoral Generalitat Valenciana–European Social Fund (ACIF/2021) grant. The authors also acknowledge the support of the Institute of Agrochemistry and Food Technology (IATA-CSIC) and the Centre of Excellence Severo Ochoa (CEX2021-001189-S MCIN/AEI/10.13039/501100011033).

With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2021-001189-S).

Peer reviewed