Article (Scientific journals)
Expanding the repertoire of carbapenem-hydrolyzing metallo-β-lactamases by functional metagenomic analysis of soil microbiota
Gudeta, D. D.; Bortolaia, V.; Pollini, S. et al.
2016In Frontiers in Microbiology, 7 (DEC)
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Keywords :
Antibiotic resistance; Carbapenems; Functional metagenomics; Metallo-β-lactamases; Soil; Article; DNA sequence; Escherichia coli
Abstract :
[en] Carbapenemases are bacterial enzymes that hydrolyze carbapenems, a group of last-resort β-lactam antibiotics used for treatment of severe bacterial infections. They belong to three β-lactamase classes based amino acid sequence (A, B, and D). The aim of this study was to elucidate occurrence, diversity and functionality of carbapenemase-encoding genes in soil microbiota by functional metagenomics. Ten plasmid libraries were generated by cloning metagenomic DNA from agricultural (n = 6) and grassland (n = 4) soil into Escherichia coli. The libraries were cultured on amoxicillin-containing agar and up to 100 colonies per library were screened for carbapenemase production by CarbaNP test. Presumptive carbapenemases were characterized with regard to DNA sequence, minimum inhibitory concentration (MIC) of β-lactams, and imipenem hydrolysis. Nine distinct class B carbapenemases, also known as metallo-beta-lactamases (MBLs), were identified in six soil samples, including two subclass B1 (GRD23-1 and SPN79-1) and seven subclass B3 (CRD3-1, PEDO-1, GRD33-1, ESP-2, ALG6-1, ALG11-1, and DHT2-1). Except PEDO-1 and ESP-2, these enzymes were distantly related to any previously described MBLs (33 to 59% identity). RAIphy analysis indicated that six enzymes (CRD3-1, GRD23-1, DHT2-1, SPN79-1, ALG6-1, and ALG11-1) originated from Proteobacteria, two (PEDO-1 and ESP-2) from Bacteroidetes and one (GRD33-1) from Gemmatimonadetes. All MBLs detected in soil microbiota were functional when expressed in E. coli, resulting in detectable imipenem-hydrolyzing activity and significantly increased MICs of clinically relevant β-lactams. Interestingly, the MBLs yielded by functional metagenomics generally differed from those detected in the same soil samples by antibiotic selective culture, showing that the two approaches targeted different subpopulations in soil microbiota. © 2016 Gudeta, Bortolaia, Pollini, Docquier, Rossolini, Amos, Wellington and Guardabassi.
Disciplines :
Microbiology
Author, co-author :
Gudeta, D. D.;  Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark, Department of Microbiology and Immunology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
Bortolaia, V.;  Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
Pollini, S.;  Department of Medical Biotechnology, University of Siena, Siena, Italy
Docquier, Jean-Denis ;  Université de Liège - ULiège > Département des sciences de la vie > Centre d'ingénierie des protéines
Rossolini, G. M.;  Department of Medical Biotechnology, University of Siena, Siena, Italy, Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy, Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy, Don Carlo Gnocchi Foundation, Florence, Italy
Amos, Gregory C.A.;  School of Life Sciences, University of Warwick, Coventry, United Kingdom, Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
Wellington, Elizabeth M. H.;  School of Life Sciences, University of Warwick, Coventry, United Kingdom
Guardabassi, L.;  Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark, Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts, West Indies, Saint Kitts and Nevis
Language :
English
Title :
Expanding the repertoire of carbapenem-hydrolyzing metallo-β-lactamases by functional metagenomic analysis of soil microbiota
Publication date :
2016
Journal title :
Frontiers in Microbiology
eISSN :
1664-302X
Publisher :
Frontiers Research Foundation
Volume :
7
Issue :
DEC
Peer reviewed :
Peer Reviewed verified by ORBi
Name of the research project :
Grant HEALTH-F3-2011-282004(EvoTAR)
Funders :
UE - Union Européenne [BE]
UniversityofCopenhagen
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since 19 November 2020

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