Global Distribution of mcr Gene Variants in 214K Metagenomic Samples
ABSTRACT Since the initial discovery of a mobilized colistin resistance gene (mcr-1), several other variants have been reported, some of which might have circulated a while beforehand. Publicly available metagenomic data provide an opportunity to reanalyze samples to understand the evolutionary hist...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-04-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00105-22 |
| _version_ | 1818115920934993920 |
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| author | Hannah-Marie Martiny Patrick Munk Christian Brinch Judit Szarvas Frank M. Aarestrup Thomas Nordahl Petersen |
| author_facet | Hannah-Marie Martiny Patrick Munk Christian Brinch Judit Szarvas Frank M. Aarestrup Thomas Nordahl Petersen |
| author_sort | Hannah-Marie Martiny |
| collection | DOAJ |
| description | ABSTRACT Since the initial discovery of a mobilized colistin resistance gene (mcr-1), several other variants have been reported, some of which might have circulated a while beforehand. Publicly available metagenomic data provide an opportunity to reanalyze samples to understand the evolutionary history of recently discovered antimicrobial resistance genes (ARGs). Here, we present a large-scale metagenomic study of 442 Tbp of sequencing reads from 214,095 samples to describe the dissemination and emergence of nine mcr gene variants (mcr-1 to mcr-9). Our results show that the dissemination of each variant is not uniform. Instead, the source and location play a role in the spread. However, the genomic context and the genes themselves remain primarily unchanged. We report evidence of new subvariants occurring in specific environments, such as a highly prevalent and new variant of mcr-9. This work emphasizes the importance of sharing genomic data for the surveillance of ARGs in our understanding of antimicrobial resistance. IMPORTANCE The ever-growing collection of metagenomic samples available in public data repositories has the potential to reveal new details on the emergence and dissemination of mobilized colistin resistance genes. Our analysis of metagenomes deposited online in the last 10 years shows that the environmental distribution of mcr gene variants depends on sampling source and location, possibly leading to the emergence of new variants, although the contig on which the mcr genes were found remained consistent. |
| first_indexed | 2024-12-11T04:14:18Z |
| format | Article |
| id | doaj.art-152fab56b7ea49538294fade94d6fabe |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-11T04:14:18Z |
| publishDate | 2022-04-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-152fab56b7ea49538294fade94d6fabe2022-12-22T01:21:17ZengAmerican Society for MicrobiologymSystems2379-50772022-04-017210.1128/msystems.00105-22Global Distribution of mcr Gene Variants in 214K Metagenomic SamplesHannah-Marie Martiny0Patrick Munk1Christian Brinch2Judit Szarvas3Frank M. Aarestrup4Thomas Nordahl Petersen5Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, DenmarkResearch Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, DenmarkResearch Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, DenmarkResearch Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, DenmarkResearch Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, DenmarkResearch Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, DenmarkABSTRACT Since the initial discovery of a mobilized colistin resistance gene (mcr-1), several other variants have been reported, some of which might have circulated a while beforehand. Publicly available metagenomic data provide an opportunity to reanalyze samples to understand the evolutionary history of recently discovered antimicrobial resistance genes (ARGs). Here, we present a large-scale metagenomic study of 442 Tbp of sequencing reads from 214,095 samples to describe the dissemination and emergence of nine mcr gene variants (mcr-1 to mcr-9). Our results show that the dissemination of each variant is not uniform. Instead, the source and location play a role in the spread. However, the genomic context and the genes themselves remain primarily unchanged. We report evidence of new subvariants occurring in specific environments, such as a highly prevalent and new variant of mcr-9. This work emphasizes the importance of sharing genomic data for the surveillance of ARGs in our understanding of antimicrobial resistance. IMPORTANCE The ever-growing collection of metagenomic samples available in public data repositories has the potential to reveal new details on the emergence and dissemination of mobilized colistin resistance genes. Our analysis of metagenomes deposited online in the last 10 years shows that the environmental distribution of mcr gene variants depends on sampling source and location, possibly leading to the emergence of new variants, although the contig on which the mcr genes were found remained consistent.https://journals.asm.org/doi/10.1128/msystems.00105-22antimicrobial resistancemetagenomicsmicrobiome |
| spellingShingle | Hannah-Marie Martiny Patrick Munk Christian Brinch Judit Szarvas Frank M. Aarestrup Thomas Nordahl Petersen Global Distribution of mcr Gene Variants in 214K Metagenomic Samples mSystems antimicrobial resistance metagenomics microbiome |
| title | Global Distribution of mcr Gene Variants in 214K Metagenomic Samples |
| title_full | Global Distribution of mcr Gene Variants in 214K Metagenomic Samples |
| title_fullStr | Global Distribution of mcr Gene Variants in 214K Metagenomic Samples |
| title_full_unstemmed | Global Distribution of mcr Gene Variants in 214K Metagenomic Samples |
| title_short | Global Distribution of mcr Gene Variants in 214K Metagenomic Samples |
| title_sort | global distribution of mcr gene variants in 214k metagenomic samples |
| topic | antimicrobial resistance metagenomics microbiome |
| url | https://journals.asm.org/doi/10.1128/msystems.00105-22 |
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