Metagenomics analysis of the neonatal intestinal resistome
IntroductionThe intestinal microbiome forms a major reservoir for antibiotic resistance genes (ARGs). Little is known about the neonatal intestinal resistome.ObjectiveThe objective of this study was to investigate the intestinal resistome and factors that influence the abundance of ARGs in a large c...
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| Format: | Article |
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Frontiers Media S.A.
2023-06-01
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| Series: | Frontiers in Pediatrics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fped.2023.1169651/full |
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| author | Stefano Leo Stefano Leo Omer F. Cetiner Laure F. Pittet Laure F. Pittet Laure F. Pittet Nicole L. Messina Nicole L. Messina William Jakob Laurent Falquet Nigel Curtis Nigel Curtis Nigel Curtis Petra Zimmermann Petra Zimmermann Petra Zimmermann Petra Zimmermann |
| author_facet | Stefano Leo Stefano Leo Omer F. Cetiner Laure F. Pittet Laure F. Pittet Laure F. Pittet Nicole L. Messina Nicole L. Messina William Jakob Laurent Falquet Nigel Curtis Nigel Curtis Nigel Curtis Petra Zimmermann Petra Zimmermann Petra Zimmermann Petra Zimmermann |
| author_sort | Stefano Leo |
| collection | DOAJ |
| description | IntroductionThe intestinal microbiome forms a major reservoir for antibiotic resistance genes (ARGs). Little is known about the neonatal intestinal resistome.ObjectiveThe objective of this study was to investigate the intestinal resistome and factors that influence the abundance of ARGs in a large cohort of neonates.MethodsShotgun 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.ResultsOverall, 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.ConclusionEven in the absence of direct antibiotic exposure, the neonatal intestine harbours a high abundance and a variety of ARGs. |
| first_indexed | 2024-03-13T05:07:03Z |
| format | Article |
| id | doaj.art-a704e0e937b947fcac702429c88d10bc |
| institution | Directory Open Access Journal |
| issn | 2296-2360 |
| language | English |
| last_indexed | 2024-03-13T05:07:03Z |
| publishDate | 2023-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Pediatrics |
| spelling | doaj.art-a704e0e937b947fcac702429c88d10bc2023-06-16T08:30:29ZengFrontiers Media S.A.Frontiers in Pediatrics2296-23602023-06-011110.3389/fped.2023.11696511169651Metagenomics analysis of the neonatal intestinal resistomeStefano Leo0Stefano Leo1Omer F. Cetiner2Laure F. Pittet3Laure F. Pittet4Laure F. Pittet5Nicole L. Messina6Nicole L. Messina7William Jakob8Laurent Falquet9Nigel Curtis10Nigel Curtis11Nigel Curtis12Petra Zimmermann13Petra Zimmermann14Petra Zimmermann15Petra Zimmermann16Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, SwitzerlandDepartment of Paediatrics, Fribourg Hospital, Fribourg, SwitzerlandIstanbul Faculty of Medicine, Istanbul University, Istanbul, TürkiyeDepartment of Paediatrics, The University of Melbourne, Parkville, VIC, AustraliaInfectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, AustraliaPediatric Infectious Diseases Unit, Geneva University Hospitals and Faculty of Medicine, Geneva, SwitzerlandDepartment of Paediatrics, The University of Melbourne, Parkville, VIC, AustraliaInfectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, AustraliaMicrobiology Laboratory, Fribourg Hospital, Fribourg, SwitzerlandDepartment of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, SwitzerlandDepartment of Paediatrics, The University of Melbourne, Parkville, VIC, AustraliaInfectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, AustraliaInfectious Diseases Unit, The Royal Children’s Hospital Melbourne, Parkville, VIC, AustraliaDepartment for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, SwitzerlandDepartment of Paediatrics, Fribourg Hospital, Fribourg, SwitzerlandDepartment of Paediatrics, The University of Melbourne, Parkville, VIC, AustraliaInfectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, AustraliaIntroductionThe intestinal microbiome forms a major reservoir for antibiotic resistance genes (ARGs). Little is known about the neonatal intestinal resistome.ObjectiveThe objective of this study was to investigate the intestinal resistome and factors that influence the abundance of ARGs in a large cohort of neonates.MethodsShotgun 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.ResultsOverall, 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.ConclusionEven in the absence of direct antibiotic exposure, the neonatal intestine harbours a high abundance and a variety of ARGs.https://www.frontiersin.org/articles/10.3389/fped.2023.1169651/fullantibiotic resistancemobilomestoolmicrobiomemicrobiotagut |
| spellingShingle | Stefano Leo Stefano Leo Omer F. Cetiner Laure F. Pittet Laure F. Pittet Laure F. Pittet Nicole L. Messina Nicole L. Messina William Jakob Laurent Falquet Nigel Curtis Nigel Curtis Nigel Curtis Petra Zimmermann Petra Zimmermann Petra Zimmermann Petra Zimmermann Metagenomics analysis of the neonatal intestinal resistome Frontiers in Pediatrics antibiotic resistance mobilome stool microbiome microbiota gut |
| title | Metagenomics analysis of the neonatal intestinal resistome |
| title_full | Metagenomics analysis of the neonatal intestinal resistome |
| title_fullStr | Metagenomics analysis of the neonatal intestinal resistome |
| title_full_unstemmed | Metagenomics analysis of the neonatal intestinal resistome |
| title_short | Metagenomics analysis of the neonatal intestinal resistome |
| title_sort | metagenomics analysis of the neonatal intestinal resistome |
| topic | antibiotic resistance mobilome stool microbiome microbiota gut |
| url | https://www.frontiersin.org/articles/10.3389/fped.2023.1169651/full |
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