Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics
Antibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge abo...
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| Format: | Article |
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MDPI AG
2021-04-01
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| Series: | Antibiotics |
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| Online Access: | https://www.mdpi.com/2079-6382/10/4/378 |
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| author | Inka Marie Willms Maja Grote Melissa Kocatürk Lukas Singhoff Alina Andrea Kraft Simon Henning Bolz Heiko Nacke |
| author_facet | Inka Marie Willms Maja Grote Melissa Kocatürk Lukas Singhoff Alina Andrea Kraft Simon Henning Bolz Heiko Nacke |
| author_sort | Inka Marie Willms |
| collection | DOAJ |
| description | Antibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge about their diversity, mobility and encoded resistance spectra gained increasing public attention. This knowledge offers opportunities with respect to improved risk prediction and development of strategies to tackle antibiotic resistance, and might help to direct the design of novel antibiotics, before further resistances reach hospital settings or the animal sector. Here, metagenomic libraries, which comprise genes of cultivated microorganisms, but, importantly, also those carried by the uncultured microbial majority, were screened for novel ARGs from forest and grassland soils. We detected three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes. These ARGs were derived from phylogenetically diverse soil bacteria and predicted to encode antibiotic inactivation, antibiotic efflux, or alternative variants of target enzymes. Moreover, deduced gene products show a minimum identity of ~21% to reference database entries and confer high-level resistance. This highlights the vast potential of functional metagenomics for the discovery of novel ARGs from soil ecosystems. |
| first_indexed | 2024-03-10T12:37:45Z |
| format | Article |
| id | doaj.art-7a33300ef2df4073a3591242acc24b9b |
| institution | Directory Open Access Journal |
| issn | 2079-6382 |
| language | English |
| last_indexed | 2024-03-10T12:37:45Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antibiotics |
| spelling | doaj.art-7a33300ef2df4073a3591242acc24b9b2023-11-21T14:06:31ZengMDPI AGAntibiotics2079-63822021-04-0110437810.3390/antibiotics10040378Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional MetagenomicsInka Marie Willms0Maja Grote1Melissa Kocatürk2Lukas Singhoff3Alina Andrea Kraft4Simon Henning Bolz5Heiko Nacke6Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, GermanyDepartment of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, GermanyDepartment of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, GermanyDepartment of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, GermanyDepartment of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, GermanyDepartment of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, GermanyDepartment of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, D-37077 Göttingen, GermanyAntibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge about their diversity, mobility and encoded resistance spectra gained increasing public attention. This knowledge offers opportunities with respect to improved risk prediction and development of strategies to tackle antibiotic resistance, and might help to direct the design of novel antibiotics, before further resistances reach hospital settings or the animal sector. Here, metagenomic libraries, which comprise genes of cultivated microorganisms, but, importantly, also those carried by the uncultured microbial majority, were screened for novel ARGs from forest and grassland soils. We detected three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes. These ARGs were derived from phylogenetically diverse soil bacteria and predicted to encode antibiotic inactivation, antibiotic efflux, or alternative variants of target enzymes. Moreover, deduced gene products show a minimum identity of ~21% to reference database entries and confer high-level resistance. This highlights the vast potential of functional metagenomics for the discovery of novel ARGs from soil ecosystems.https://www.mdpi.com/2079-6382/10/4/378antibiotic resistance genessoilfunctional metagenomicsbeta-lactam resistancechloramphenicol resistancefosfomycin resistance |
| spellingShingle | Inka Marie Willms Maja Grote Melissa Kocatürk Lukas Singhoff Alina Andrea Kraft Simon Henning Bolz Heiko Nacke Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics Antibiotics antibiotic resistance genes soil functional metagenomics beta-lactam resistance chloramphenicol resistance fosfomycin resistance |
| title | Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics |
| title_full | Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics |
| title_fullStr | Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics |
| title_full_unstemmed | Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics |
| title_short | Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics |
| title_sort | novel soil derived beta lactam chloramphenicol fosfomycin and trimethoprim resistance genes revealed by functional metagenomics |
| topic | antibiotic resistance genes soil functional metagenomics beta-lactam resistance chloramphenicol resistance fosfomycin resistance |
| url | https://www.mdpi.com/2079-6382/10/4/378 |
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