University of Oulu

Weizhong Li, Terhi Tapiainen, Lauren Brinkac, Hernan A Lorenzi, Kelvin Moncera, Mysore V Tejesvi, Jarmo Salo, Karen E Nelson, Vertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth, The Journal of Infectious Diseases, Volume 224, Issue 7, 1 October 2021, Pages 1236–1246,

Vertical transmission of gut microbiome and antimicrobial resistance genes in infants exposed to antibiotics at birth

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Author: Li, Weizhong1; Tapiainen, Terhi2,3; Brinkac, Lauren4;
Organizations: 1J. Craig Venter Institute, La Jolla, California, USA
2Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
3PEDEGO Research Unit, Biocenter Oulu and Medical Research Center Oulu, University of Oulu, Oulu, Finland
4J. Craig Venter Institute, Rockville, Maryland, USA
5Ecology and Genetics, University of Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 8 MB)
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Language: English
Published: Oxford University Press, 2021
Publish Date: 2021-11-25


Vertical transmission of maternal microbes is a major route for establishing the gut microbiome in newborns. The impact of perinatal antibiotics on vertical transmission of microbes and antimicrobial resistance is not well understood. Using a metagenomic approach, we analyzed the fecal samples from mothers and vaginally delivered infants from a control group (10 pairs) and a treatment group (10 pairs) receiving perinatal antibiotics. Antibiotic-usage had a significant impact on the main source of inoculum in the gut microbiome of newborns. The control group had significantly more species transmitted from mothers to infants (P = 0.03) than the antibiotic-treated group. Approximately 72% of the gut microbial population of infants at 3–7 days after birth in the control group was transmitted from their mothers, versus only 25% in the antibiotic-treated group. In conclusion, perinatal antibiotics markedly disturbed vertical transmission and changed the source of gut colonization towards horizontal transfer from the environment to the infants.

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Series: Journal of infectious diseases
ISSN: 0022-1899
ISSN-E: 1537-6613
ISSN-L: 0022-1899
Volume: 224
Issue: 7
Pages: 1236 - 1246
DOI: 10.1093/infdis/jiaa155
Type of Publication: A1 Journal article – refereed
Field of Science: 3123 Gynaecology and paediatrics
Funding: The work performed in Finland was supported by the Academy of Finland and Pediatric Research Foundation, Finland. The work performed at the J. Craig Venter Institute, in the United States, was supported by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services (grant U19AI110819 to H. A. L. and K. E. N.).
Copyright information: © The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (, which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact