eCommons

 

Supplemental Data from: Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide

Other Titles

Abstract

The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1,666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity singlecell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.

Journal / Series

Volume & Issue

Description

Recommended citation for this dataset: Peter Diebold, Rhee, Matthew, Shi, Qiaojuan, Nguyen, Vinh Trung, Umrani, Fayaz, Ahmed, Sheraz, Kulkarni, Vandana, Deshpande, Prasad, Alexander, Mallika, Ngo, Thi Hoa, Christakis, Nicholas, Iqbal, Najeeha, Ali, Asad, Mathad, Jyoti, Ilana Brito. (2023) Supplemental Data from: Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. [dataset] Cornell University eCommons Repository. https://doi.org/10.7298/aq1k-vf97

Sponsorship

This work was supported by funding from the U.S. National Institutes of Health (1R01AI151059, 1DP2HL141007), the National Sciences Foundation (1650122, 1661338), the Gates Foundation (OPP1161064), the NOMIS Foundation (GR108454-CON-80002144) and SCENERI project funded by AXA (to N.T.H.).

Date Issued

2023-11

Publisher

Keywords

microbiome; antibiotic resistance; microbiology; metagenomics; ARG

Location

Effective Date

Expiration Date

Sector

Employer

Union

Union Local

NAICS

Number of Workers

Committee Chair

Committee Co-Chair

Committee Member

Degree Discipline

Degree Name

Degree Level

Related Version

Related DOI

Related To

Related Part

Based on Related Item

Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong D, Beghini F, Malik F, Ramos M, Dowd J, Huttenhower C, Morgan M, Segata N, Waldron L (2017). Accessible, curated metagenomic data through ExperimentHub. Nat. Methods, 14 (11), 1023-1024. ISSN 1548-7091, 1548-7105, doi: 10.1038/nmeth.4468.

Has Other Format(s)

Part of Related Item

Related To

Related Publication(s)

Peter Diebold, Rhee, Matthew, Shi, Qiaojuan, Nguyen, Vinh Trung, Umrani, Fayaz, Ahmed, Sheraz, Kulkarni, Vandana, Deshpande, Prasad, Alexander, Mallika, Ngo, Thi Hoa, Christakis, Nicholas, Iqbal, Najeeha, Ali, Asad, Mathad, Jyoti, Ilana Brito. (2023) Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nature Communications (submitted)

Link(s) to Related Publication(s)

References

Link(s) to Reference(s)

Previously Published As

Government Document

ISBN

ISMN

ISSN

Other Identifiers

Rights

CC0 1.0 Universal

Types

dataset

Accessibility Feature

Accessibility Hazard

none

Accessibility Summary

Link(s) to Catalog Record