Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats
Por:
Azziz G., Giménez M., Romero H., Valdespino-Castillo P.M., Falcón L.I., Ruberto, Lucas A. M., Mac Cormack W.P., Batista S.
Publicada:
1 jun 2019
Categoría:
Environmental science (miscellaneous)
Resumen:
Analysis of environmental samples for bacterial antibiotic resistance
genes may have different objectives and analysis strategies. In some
cases, the purpose was to study diversity and evolution of genes that
could be grouped within a mechanism of antibiotic resistance. Different
protocols have been designed for detection and confirmation that a
functional gene was found. In this study, we present a sequence-based
screening of candidate genes encoding beta-lactamases in 14 metagenomes
of Antarctic microbial mats. The samples were obtained from different
sites, representing diverse biogeographic regions of maritime and
continental Antarctica. A protocol was designed based on generation of
Hidden Markov Models from the four beta-lactamase classes by Ambler
classification, using sequences from the Comprehensive Antibiotic
Resistance Database (CARD). The models were used as queries for
metagenome analysis and recovered contigs were subsequently annotated
using RAST. According to our analysis, 14 metagenomes analyzed contain
A, B and C beta-lactamase genes. Class D genes, however, were identified
in 11 metagenomes. The most abundant was class C (46.8%), followed by
classes B (35.5%), A (14.2%) and D (3.5%). A considerable number of
sequences formed clusters which included, in some cases, contigs from
different metagenomes. These assemblies are clearly separated from
reference clusters, previously identified using CARD beta-lactamase
sequences. While bacterial antibiotic resistance is a major challenge of
public health worldwide, our results suggest that environmental
diversity of beta-lactamase genes is higher than that currently
reported, although this should be complemented with gene function
analysis.
Filiaciones:
Azziz G.:
Clemente Estable Biol Res Insitute, Mol Microbiol Unit, Montevideo 11600, Uruguay
UdelaR, Microbiol Lab, Fac Agron, Montevideo 12900, Uruguay
Molecular Microbiology Unit, Clemente Estable Biological Research Insitute, Montevideo, 11600, Uruguay
Microbiology Laboratory, Faculty of Agronomy, UdelaR, Montevideo, 12900, Uruguay
Giménez M.:
Clemente Estable Biol Res Insitute, Mol Microbiol Unit, Montevideo 11600, Uruguay
Molecular Microbiology Unit, Clemente Estable Biological Research Insitute, Montevideo, 11600, Uruguay
Romero H.:
UdelaR, Genome Org & Evolut Lab, Dept Ecol & Evolut, Fac Sci, Montevideo 11400, Uruguay
Genome Organization and Evolution Laboratory, Ecology and Evolution Department, Faculty of Sciences, UdelaR, Montevideo, 11400, Uruguay
Valdespino-Castillo P.M.:
Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging, BSISB Imaging Program, Berkeley, CA 94720 USA
Molecular Biophysics and Integrated Bioimaging, BSISB Imaging Program, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
Falcón L.I.:
Univ Nacl Autonoma Mexico, Bacteial Ecol Lab, Inst Ecol, Cdmx 04510, DF, Mexico
UNAM, Yucatan Technol & Sci Pk, Merida 97302, Mexico
Bacteial Ecology Laboratory, Ecology Institute, National Autonomous University of Mexico, CDMX, 04510, Mexico
UNAM, Yucatan Technology and Science Park, Merida, 97302, Mexico
Ruberto, Lucas A. M.:
Argentine Antarctic Inst, RA-1650 Buenos Aires, DF, Argentina
UBA, Biotechnol Unit, Fac Pharm & Biochem, Nanobiotec Inst,CONICET, RA-1113 Buenos Aires, DF, Argentina
Mac Cormack W.P.:
Argentine Antarctic Inst, RA-1650 Buenos Aires, DF, Argentina
UBA, Biotechnol Unit, Fac Pharm & Biochem, Nanobiotec Inst,CONICET, RA-1113 Buenos Aires, DF, Argentina
Argentine Antarctic Institute, Buenos Aires, 1650, Argentina
Biotechnology Unit, Faculty of Pharmacy and Biochemistry, Nanobiotec Institute UBA-CONICET, Buenos Aires, 1113, Argentina
Batista S.:
Clemente Estable Biol Res Insitute, Mol Microbiol Unit, Montevideo 11600, Uruguay
Molecular Microbiology Unit, Clemente Estable Biological Research Insitute, Montevideo, 11600, Uruguay
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