Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing
Abstract Background Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance an...
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doaj-f9912318a90e48c5bf06ecb79f8c98ac2020-11-24T22:09:12ZengBMCMicrobiome2049-26182017-10-015111310.1186/s40168-017-0361-8Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencingNoelle R. Noyes0Maggie E. Weinroth1Jennifer K. Parker2Chris J. Dean3Steven M. Lakin4Robert A. Raymond5Pablo Rovira6Enrique Doster7Zaid Abdo8Jennifer N. Martin9Kenneth L. Jones10Jaime Ruiz11Christina A. Boucher12Keith E. Belk13Paul S. Morley14Department of Microbiology, Immunology and Pathology, Colorado State UniversityDepartment of Animal Sciences, Colorado State UniversityDepartment of Clinical Sciences, Colorado State UniversityDepartment of Computer Sciences, Colorado State UniversityDepartment of Clinical Sciences, Colorado State UniversityDepartment of Computer Sciences, Colorado State UniversityDepartment of Animal Sciences, Colorado State UniversityDepartment of Clinical Sciences, Colorado State UniversityDepartment of Microbiology, Immunology and Pathology, Colorado State UniversityDepartment of Animal Sciences, Colorado State UniversityDepartment of Pediatrics, Section of Hematology Oncology and Bone Marrow Transplant, University of Colorado School of MedicineDepartment of Computer and Information Science and Engineering, University of FloridaDepartment of Computer and Information Science and Engineering, University of FloridaDepartment of Animal Sciences, Colorado State UniversityDepartment of Clinical Sciences, Colorado State UniversityAbstract Background Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. Results The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. Conclusions These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.http://link.springer.com/article/10.1186/s40168-017-0361-8ResistomeAntimicrobial resistanceMolecular enrichmentMicrobial ecologyRare microbiome |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Noelle R. Noyes Maggie E. Weinroth Jennifer K. Parker Chris J. Dean Steven M. Lakin Robert A. Raymond Pablo Rovira Enrique Doster Zaid Abdo Jennifer N. Martin Kenneth L. Jones Jaime Ruiz Christina A. Boucher Keith E. Belk Paul S. Morley |
spellingShingle |
Noelle R. Noyes Maggie E. Weinroth Jennifer K. Parker Chris J. Dean Steven M. Lakin Robert A. Raymond Pablo Rovira Enrique Doster Zaid Abdo Jennifer N. Martin Kenneth L. Jones Jaime Ruiz Christina A. Boucher Keith E. Belk Paul S. Morley Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing Microbiome Resistome Antimicrobial resistance Molecular enrichment Microbial ecology Rare microbiome |
author_facet |
Noelle R. Noyes Maggie E. Weinroth Jennifer K. Parker Chris J. Dean Steven M. Lakin Robert A. Raymond Pablo Rovira Enrique Doster Zaid Abdo Jennifer N. Martin Kenneth L. Jones Jaime Ruiz Christina A. Boucher Keith E. Belk Paul S. Morley |
author_sort |
Noelle R. Noyes |
title |
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing |
title_short |
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing |
title_full |
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing |
title_fullStr |
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing |
title_full_unstemmed |
Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing |
title_sort |
enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing |
publisher |
BMC |
series |
Microbiome |
issn |
2049-2618 |
publishDate |
2017-10-01 |
description |
Abstract Background Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. Results The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. Conclusions These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics. |
topic |
Resistome Antimicrobial resistance Molecular enrichment Microbial ecology Rare microbiome |
url |
http://link.springer.com/article/10.1186/s40168-017-0361-8 |
work_keys_str_mv |
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