Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants

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Reviewed Marked as Reviewed by Atrayees on 2023-7-6
study design
prospective cohort
Citation
PMID PubMed identifier for scientific articles.
31337807
DOI Digital object identifier for electronic documents.
10.1038/s41598-019-46964-5
URI
Authors
Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM, Tejesvi MV
Journal
Scientific reports
Year
2019
Altogether, 20-30% of women receive intrapartum antibiotic prophylaxis (IAP) to prevent sepsis in infants and 2-5% of newborn infants receive antibiotics due to suspected sepsis. Caesarean section has a long-term impact on the intestinal microbiome but the effects of perinatal antibiotics on gut microbiome in vaginally delivered infants are not well known. We compared the impact of IAP, postnatal antibiotics, or their combination on the gut microbiome and emergence of antimicrobial resistance in a controlled study of 149 newborn infants recruited within 24 hours after birth. We collected 659 fecal samples, including 426 daily samples from infants before discharge from the hospital and 111 follow-up samples at six months. Penicillin was mostly used for IAP and the combination of penicillin and aminoglycoside for postnatal treatment. Postnatal antibiotic groups received Lactobacillus reuteri probiotic. Newborn gut colonization differed in both IAP and postnatal antibiotics groups as compared to that in control group. The effect size of IAP was comparable to that caused by postnatal antibiotics. The observed differences were still present at six months and not prevented by lactobacilli consumption. Given the present clinical results, the impact of perinatal antibiotics on the subsequent health of newborn infants should be further evaluated.

Experiment 1


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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-18

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Subjects

Location of subjects
Finland
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
Group 0 name Corresponds to the control (unexposed) group for case-control studies
control group
Group 1 name Corresponds to the case (exposed) group for case-control studies
Postnatal antibiotic group (2-day old infant)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Term, vaginally delivered infants
Group 0 sample size Number of subjects in the control (unexposed) group
47
Group 1 sample size Number of subjects in the case (exposed) group
29

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4-V5
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Kruskall-Wallis
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

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Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: Figure 5, Figure 3

Description: The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: increased abundance in Postnatal antibiotic group (2-day old infant)

NCBI Quality ControlLinks
Lactobacillus   
Bacillota   

Revision editor(s): WikiWorks, Atrayees

Signature 2

EditHistoryDelete
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Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: Figure 5, Figure 3

Description: The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: decreased abundance in Postnatal antibiotic group (2-day old infant)

NCBI Quality ControlLinks
Bacteroides   

Revision editor(s): WikiWorks, Atrayees

Experiment 2


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Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IAP group (4-day old infant)
Group 1 sample size Number of subjects in the case (exposed) group
44

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

Source: Figure 5

Description: The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: decreased abundance in IAP group (4-day old infant)

NCBI Quality ControlLinks
Bacteroides   

Revision editor(s): WikiWorks

Experiment 3


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Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IAP group (6-month old infant)

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: Figure 5, Figure 3

Description: The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: increased abundance in IAP group (6-month old infant)

NCBI Quality ControlLinks
Clostridium   
Bacillota   

Revision editor(s): WikiWorks, Atrayees

Signature 2

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Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2023/07/06

Curator: Atrayees

Revision editor(s): Atrayees

Source: Figure 3, Figure 5

Description: The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: decreased abundance in IAP group (6-month old infant)

NCBI Quality ControlLinks
Bacteroidia   

Revision editor(s): Atrayees

Experiment 4


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Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IAP+postnatal antibiotic group (2-day old infant)
Group 1 sample size Number of subjects in the case (exposed) group
29

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

Source: Figure 5

Description: The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: increased abundance in IAP+postnatal antibiotic group (2-day old infant)

NCBI Quality ControlLinks
Lactobacillus   

Revision editor(s): WikiWorks

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks, Atrayees

Source: Figure 5, Figure 3

Description: The relative abundances of the bacterial genera and phyla mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: decreased abundance in IAP+postnatal antibiotic group (2-day old infant)

NCBI Quality ControlLinks
Bacteroides   
Bacteroidia   

Revision editor(s): WikiWorks, Atrayees

Experiment 5


EditHistoryDelete
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Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IAP+postnatal antibiotic group (4-day old infant)

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

Source: Figure 5

Description: The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: decreased abundance in IAP+postnatal antibiotic group (4-day old infant)

NCBI Quality ControlLinks
Bacteroides   

Revision editor(s): WikiWorks

Experiment 6


EditHistoryDelete
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Your review change was submittedDuplicate this ExperimentAdd a new Signature
Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
IAP+postnatal antibiotic group (6-month old infant)

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

Source: Figure 5

Description: The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: increased abundance in IAP+postnatal antibiotic group (6-month old infant)

NCBI Quality ControlLinks
Clostridium   

Revision editor(s): WikiWorks

Signature 2

EditHistoryDelete
Flag for review
Your review change was submitted
Reviewed Marked as Reviewed by Atrayees on 2023-7-6

Curated date: 2023/07/06

Curator: Atrayees

Revision editor(s): Atrayees

Source: Figure 3, Figure 5

Description: The relative abundances of the bacterial genera mainly explaining the observed phylum level changes after perinatal antibiotic exposure

Abundance in Group 1: decreased abundance in IAP+postnatal antibiotic group (6-month old infant)

NCBI Quality ControlLinks
Bacteroidia   

Revision editor(s): Atrayees

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