Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life

BackgroundAlongside microbiota development, the evolution of the resistome is crucial in understanding the early-life acquisition and persistence of Antibiotic Resistance Genes (ARGs). Therefore, the aim of this study is to provide a comprehensive view of the evolution and dynamics of the neonatal r...

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Autores: Samarra, A, Cabrera-Rubio, R, Martínez-Costa, C, Collado, MC
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:INCLIVA
Repositorio:r-INCLIVA. Repositorio Institucional de Producción Científica de INCLIVA
OAI Identifier:oai:incliva.fundanetsuite.com:p18470
Acceso en línea:https://incliva.portalinvestigacion.com/publicaciones/18470
Access Level:acceso abierto
Palabra clave:Antibiotic resistance
Infant
Gut
Breastfeeding
Microbiota
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spelling Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of lifeSamarra, ACabrera-Rubio, RMartínez-Costa, CCollado, MCAntibiotic resistanceInfantGutBreastfeedingMicrobiotaBackgroundAlongside microbiota development, the evolution of the resistome is crucial in understanding the early-life acquisition and persistence of Antibiotic Resistance Genes (ARGs). Therefore, the aim of this study is to provide a comprehensive view of the evolution and dynamics of the neonatal resistome from 7 days to 4 months of age using a high-throughput qPCR platform.MethodsIn the initial phase, a massive screening of 384 ARGs using a high-throughput qPCR in pooled healthy mother-infant pairs feces from the MAMI cohort was carried out to identify the most abundant and prevalent ARGs in infants and in mothers. This pre-analysis allowed for later targeted profiling in a large number of infants in a longitudinal manner during the first 4 months of life. 16S rRNA V3-V4 amplicon sequencing was performed to asses microbial composition longitudinally. Potential factors influencing the microbiota and ARGs in this period were also considered, such as mode of birth and breastfeeding type.ResultsFollowing the massive screening, the top 45 abundant ARGs and mobile genetic elements were identified and studied in 72 infants during their first months of life (7 days, 1, 2, and 4 months). These genes were associated with resistance to aminoglycosides, beta-lactams and tetracyclines, among others, as well as integrons, and other mobile genetic elements. Changes in both ARG composition and quantity were observed during the first 4 months of life: most ARGs abundance increased over time, but mobile genetic elements decreased significantly. Further exploration of modulating factors highlighted the effect on ARG composition of specific microbial genus, and the impact of mode of birth at 7 days and 4 months. The influence of infant formula feeding was observed at 4-month-old infants, who exhibited a distinctive resistome composition.ConclusionsThis study illustrates the ARG evolution and dynamics in the infant gut by use of a targeted, high-throughput, quantitative PCR-based method. An increase in antibiotic resistance over the first months of life were observed with a fundamental role of delivery mode in shaping resistance profiles. Further, we highlighted the influence of feeding methods on the resistome development. These findings offer pivotal insights into dynamics of and factors influencing early-life resistome, with potential avenues for intervention strategies.BMC2024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://incliva.portalinvestigacion.com/publicaciones/18470Annals of Clinical Microbiology and AntimicrobialsISSN: 14760711reponame:r-INCLIVA. Repositorio Institucional de Producción Científica de INCLIVAinstname:INCLIVAInglésinfo:eu-repo/semantics/openAccessoai:incliva.fundanetsuite.com:p184702026-06-07T16:35:31Z
dc.title.none.fl_str_mv Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
title Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
spellingShingle Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
Samarra, A
Antibiotic resistance
Infant
Gut
Breastfeeding
Microbiota
title_short Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
title_full Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
title_fullStr Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
title_full_unstemmed Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
title_sort Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life
dc.creator.none.fl_str_mv Samarra, A
Cabrera-Rubio, R
Martínez-Costa, C
Collado, MC
author Samarra, A
author_facet Samarra, A
Cabrera-Rubio, R
Martínez-Costa, C
Collado, MC
author_role author
author2 Cabrera-Rubio, R
Martínez-Costa, C
Collado, MC
author2_role author
author
author
dc.subject.none.fl_str_mv Antibiotic resistance
Infant
Gut
Breastfeeding
Microbiota
topic Antibiotic resistance
Infant
Gut
Breastfeeding
Microbiota
description BackgroundAlongside microbiota development, the evolution of the resistome is crucial in understanding the early-life acquisition and persistence of Antibiotic Resistance Genes (ARGs). Therefore, the aim of this study is to provide a comprehensive view of the evolution and dynamics of the neonatal resistome from 7 days to 4 months of age using a high-throughput qPCR platform.MethodsIn the initial phase, a massive screening of 384 ARGs using a high-throughput qPCR in pooled healthy mother-infant pairs feces from the MAMI cohort was carried out to identify the most abundant and prevalent ARGs in infants and in mothers. This pre-analysis allowed for later targeted profiling in a large number of infants in a longitudinal manner during the first 4 months of life. 16S rRNA V3-V4 amplicon sequencing was performed to asses microbial composition longitudinally. Potential factors influencing the microbiota and ARGs in this period were also considered, such as mode of birth and breastfeeding type.ResultsFollowing the massive screening, the top 45 abundant ARGs and mobile genetic elements were identified and studied in 72 infants during their first months of life (7 days, 1, 2, and 4 months). These genes were associated with resistance to aminoglycosides, beta-lactams and tetracyclines, among others, as well as integrons, and other mobile genetic elements. Changes in both ARG composition and quantity were observed during the first 4 months of life: most ARGs abundance increased over time, but mobile genetic elements decreased significantly. Further exploration of modulating factors highlighted the effect on ARG composition of specific microbial genus, and the impact of mode of birth at 7 days and 4 months. The influence of infant formula feeding was observed at 4-month-old infants, who exhibited a distinctive resistome composition.ConclusionsThis study illustrates the ARG evolution and dynamics in the infant gut by use of a targeted, high-throughput, quantitative PCR-based method. An increase in antibiotic resistance over the first months of life were observed with a fundamental role of delivery mode in shaping resistance profiles. Further, we highlighted the influence of feeding methods on the resistome development. These findings offer pivotal insights into dynamics of and factors influencing early-life resistome, with potential avenues for intervention strategies.
publishDate 2024
dc.date.none.fl_str_mv 2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://incliva.portalinvestigacion.com/publicaciones/18470
url https://incliva.portalinvestigacion.com/publicaciones/18470
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BMC
publisher.none.fl_str_mv BMC
dc.source.none.fl_str_mv Annals of Clinical Microbiology and Antimicrobials
ISSN: 14760711
reponame:r-INCLIVA. Repositorio Institucional de Producción Científica de INCLIVA
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