Supplemental Data from: Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide
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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.
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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
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.).
microbiome; antibiotic resistance; microbiology; metagenomics; ARG
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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.
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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)
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