Antibiotic resistance potential of the healthy preterm infant gut microbiome
Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy i...
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PeerJ Inc.
2017-01-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/2928.pdf |
| _version_ | 1797419825567367168 |
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| author | Graham Rose Alexander G. Shaw Kathleen Sim David J. Wooldridge Ming-Shi Li Saheer Gharbia Raju Misra John Simon Kroll |
| author_facet | Graham Rose Alexander G. Shaw Kathleen Sim David J. Wooldridge Ming-Shi Li Saheer Gharbia Raju Misra John Simon Kroll |
| author_sort | Graham Rose |
| collection | DOAJ |
| description | Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities. |
| first_indexed | 2024-03-09T06:52:52Z |
| format | Article |
| id | doaj.art-182981b5879b476f9ff96078791d6a70 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:52:52Z |
| publishDate | 2017-01-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-182981b5879b476f9ff96078791d6a702023-12-03T10:15:33ZengPeerJ Inc.PeerJ2167-83592017-01-015e292810.7717/peerj.2928Antibiotic resistance potential of the healthy preterm infant gut microbiomeGraham Rose0Alexander G. Shaw1Kathleen Sim2David J. Wooldridge3Ming-Shi Li4Saheer Gharbia5Raju Misra6John Simon Kroll7Genomics Research Unit, Public Health England, London, United KingdomDepartment of Medicine, Imperial College London, London, United KingdomDepartment of Medicine, Imperial College London, London, United KingdomGenomics Research Unit, Public Health England, London, United KingdomDepartment of Medicine, Imperial College London, London, United KingdomGenomics Research Unit, Public Health England, London, United KingdomGenomics Research Unit, Public Health England, London, United KingdomSection of Paediatrics, Department of Medicine, Imperial College London, London, United KingdomBackground Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.https://peerj.com/articles/2928.pdfPreterm infantsShotgun metagenomicsAntibiotic resistanceGut microbiome |
| spellingShingle | Graham Rose Alexander G. Shaw Kathleen Sim David J. Wooldridge Ming-Shi Li Saheer Gharbia Raju Misra John Simon Kroll Antibiotic resistance potential of the healthy preterm infant gut microbiome PeerJ Preterm infants Shotgun metagenomics Antibiotic resistance Gut microbiome |
| title | Antibiotic resistance potential of the healthy preterm infant gut microbiome |
| title_full | Antibiotic resistance potential of the healthy preterm infant gut microbiome |
| title_fullStr | Antibiotic resistance potential of the healthy preterm infant gut microbiome |
| title_full_unstemmed | Antibiotic resistance potential of the healthy preterm infant gut microbiome |
| title_short | Antibiotic resistance potential of the healthy preterm infant gut microbiome |
| title_sort | antibiotic resistance potential of the healthy preterm infant gut microbiome |
| topic | Preterm infants Shotgun metagenomics Antibiotic resistance Gut microbiome |
| url | https://peerj.com/articles/2928.pdf |
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