Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats

Autores
Azziz, Gastón; Gimentz, Matìas; Romero, Hèctor; Valdespino Castillo, P.; Falcòn, Luisa I.; Ruberto, Lucas Adolfo Mauro; Mac Cormack, Walter Patricio; Batista, Silvia
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
Fil: Azziz, Gastón. Universidad de la República; Uruguay
Fil: Gimentz, Matìas. Universidad de la República; Uruguay
Fil: Romero, Hèctor. Universidad de la República; Uruguay
Fil: Valdespino Castillo, P.. Lawrence Berkeley National Laboratory; Estados Unidos
Fil: Falcòn, Luisa I.. Universidad Nacional Autónoma de México; México
Fil: Ruberto, Lucas Adolfo Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; Argentina
Fil: Mac Cormack, Walter Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; Argentina
Fil: Batista, Silvia. Universidad de la República; Uruguay
Materia
BETA-LACTAMASE
MICROBIAL MATS
ANTARCTICA
METAGENOMES
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/121509
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/121509
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial matsAzziz, GastónGimentz, MatìasRomero, HèctorValdespino Castillo, P.Falcòn, Luisa I.Ruberto, Lucas Adolfo MauroMac Cormack, Walter PatricioBatista, SilviaBETA-LACTAMASEMICROBIAL MATSANTARCTICAMETAGENOMEShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Analysis 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.Fil: Azziz, Gastón. Universidad de la República; UruguayFil: Gimentz, Matìas. Universidad de la República; UruguayFil: Romero, Hèctor. Universidad de la República; UruguayFil: Valdespino Castillo, P.. Lawrence Berkeley National Laboratory; Estados UnidosFil: Falcòn, Luisa I.. Universidad Nacional Autónoma de México; MéxicoFil: Ruberto, Lucas Adolfo Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: Mac Cormack, Walter Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: Batista, Silvia. Universidad de la República; UruguayHigher Education Press2019-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/121509Azziz, Gastón; Gimentz, Matìas; Romero, Hèctor; Valdespino Castillo, P.; Falcòn, Luisa I.; et al.; Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats; Higher Education Press; Frontiers of Environmental Science and Engineering; 13; 3; 6-2019; 1-121673-74152095-221XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1007/s11783-019-1128-1info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs11783-019-1128-1info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:42:11Zoai:ri.conicet.gov.ar:11336/121509instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 14:42:11.609CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats
title Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats
spellingShingle Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats
Azziz, Gastón
BETA-LACTAMASE
MICROBIAL MATS
ANTARCTICA
METAGENOMES
title_short Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats
title_full Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats
title_fullStr Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats
title_full_unstemmed Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats
title_sort Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats
dc.creator.none.fl_str_mv Azziz, Gastón
Gimentz, Matìas
Romero, Hèctor
Valdespino Castillo, P.
Falcòn, Luisa I.
Ruberto, Lucas Adolfo Mauro
Mac Cormack, Walter Patricio
Batista, Silvia
author Azziz, Gastón
author_facet Azziz, Gastón
Gimentz, Matìas
Romero, Hèctor
Valdespino Castillo, P.
Falcòn, Luisa I.
Ruberto, Lucas Adolfo Mauro
Mac Cormack, Walter Patricio
Batista, Silvia
author_role author
author2 Gimentz, Matìas
Romero, Hèctor
Valdespino Castillo, P.
Falcòn, Luisa I.
Ruberto, Lucas Adolfo Mauro
Mac Cormack, Walter Patricio
Batista, Silvia
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv BETA-LACTAMASE
MICROBIAL MATS
ANTARCTICA
METAGENOMES
topic BETA-LACTAMASE
MICROBIAL MATS
ANTARCTICA
METAGENOMES
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv 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.
Fil: Azziz, Gastón. Universidad de la República; Uruguay
Fil: Gimentz, Matìas. Universidad de la República; Uruguay
Fil: Romero, Hèctor. Universidad de la República; Uruguay
Fil: Valdespino Castillo, P.. Lawrence Berkeley National Laboratory; Estados Unidos
Fil: Falcòn, Luisa I.. Universidad Nacional Autónoma de México; México
Fil: Ruberto, Lucas Adolfo Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; Argentina
Fil: Mac Cormack, Walter Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; Argentina
Fil: Batista, Silvia. Universidad de la República; Uruguay
description 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.
publishDate 2019
dc.date.none.fl_str_mv 2019-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/121509
Azziz, Gastón; Gimentz, Matìas; Romero, Hèctor; Valdespino Castillo, P.; Falcòn, Luisa I.; et al.; Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats; Higher Education Press; Frontiers of Environmental Science and Engineering; 13; 3; 6-2019; 1-12
1673-7415
2095-221X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/121509
identifier_str_mv Azziz, Gastón; Gimentz, Matìas; Romero, Hèctor; Valdespino Castillo, P.; Falcòn, Luisa I.; et al.; Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats; Higher Education Press; Frontiers of Environmental Science and Engineering; 13; 3; 6-2019; 1-12
1673-7415
2095-221X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1007/s11783-019-1128-1
info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs11783-019-1128-1
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Higher Education Press
publisher.none.fl_str_mv Higher Education Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.22299

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