Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere

Clonal complex 5 methicillin-resistant Staphylococcus aureus (CC5-MRSA) includes multiple prevalent clones that cause hospital-associated infections in the Western Hemisphere. Here, we present a phylogenomic study of these MRSA to reveal their phylogeny, spatial and temporal population structure, an...

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Autores:
Challagundla, Lavanya
Reyes, Jinnethe
Rafiqullah, Iftekhar
Sordelli, Daniel O.
Echaniz-Aviles, Gabriela
Velazquez-Meza, Maria E.
Castillo-Ramírez, Santiago
Fittipaldi, Nahuel
Feldgarden, Michael
Chapman, Sinéad B.
Calderwood, Michael S.
Carvajal Ortiz, Lina Paola
Rincón, Sandra
Hanson, Blake
Planet, Paul J.
Arias, César A.
Díaz, Lorena
Robinson, D. Ashley
Tipo de recurso:
Fecha de publicación:
2018
Institución:
Universidad El Bosque
Repositorio:
Repositorio U. El Bosque
Idioma:
eng
OAI Identifier:
oai:repositorio.unbosque.edu.co:20.500.12495/1608
Acceso en línea:
http://hdl.handle.net/20.500.12495/1608
https://doi.org/10.3389/fmicb.2018.01901
Palabra clave:
Infección hospitalaria
Virulencia
Farmacorresistencia microbiana
Methicillin-resistant staphylococcus aureus
MRSA
Phylogenomics
Rights
License
Attribution 4.0 International
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dc.title.spa.fl_str_mv Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
title Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
spellingShingle Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
Infección hospitalaria
Virulencia
Farmacorresistencia microbiana
Methicillin-resistant staphylococcus aureus
MRSA
Phylogenomics
title_short Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
title_full Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
title_fullStr Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
title_full_unstemmed Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
title_sort Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemisphere
dc.creator.fl_str_mv Challagundla, Lavanya
Reyes, Jinnethe
Rafiqullah, Iftekhar
Sordelli, Daniel O.
Echaniz-Aviles, Gabriela
Velazquez-Meza, Maria E.
Castillo-Ramírez, Santiago
Fittipaldi, Nahuel
Feldgarden, Michael
Chapman, Sinéad B.
Calderwood, Michael S.
Carvajal Ortiz, Lina Paola
Rincón, Sandra
Hanson, Blake
Planet, Paul J.
Arias, César A.
Díaz, Lorena
Robinson, D. Ashley
dc.contributor.author.none.fl_str_mv Challagundla, Lavanya
Reyes, Jinnethe
Rafiqullah, Iftekhar
Sordelli, Daniel O.
Echaniz-Aviles, Gabriela
Velazquez-Meza, Maria E.
Castillo-Ramírez, Santiago
Fittipaldi, Nahuel
Feldgarden, Michael
Chapman, Sinéad B.
Calderwood, Michael S.
Carvajal Ortiz, Lina Paola
Rincón, Sandra
Hanson, Blake
Planet, Paul J.
Arias, César A.
Díaz, Lorena
Robinson, D. Ashley
dc.contributor.orcid.none.fl_str_mv Carvajal Ortiz, Lina Paola [0000-0001-8301-8836]
dc.subject.decs.spa.fl_str_mv Infección hospitalaria
Virulencia
Farmacorresistencia microbiana
topic Infección hospitalaria
Virulencia
Farmacorresistencia microbiana
Methicillin-resistant staphylococcus aureus
MRSA
Phylogenomics
dc.subject.keywords.spa.fl_str_mv Methicillin-resistant staphylococcus aureus
MRSA
Phylogenomics
description Clonal complex 5 methicillin-resistant Staphylococcus aureus (CC5-MRSA) includes multiple prevalent clones that cause hospital-associated infections in the Western Hemisphere. Here, we present a phylogenomic study of these MRSA to reveal their phylogeny, spatial and temporal population structure, and the evolution of selected traits. We studied 598 genome sequences, including 409 newly generated sequences, from 11 countries in Central, North, and South America, and references from Asia and Europe. An early-branching CC5-Basal clade is well-dispersed geographically, is methicillin-susceptible and MRSA predominantly of ST5-IV such as the USA800 clone, and includes separate subclades for avian and porcine strains. In the early 1970s and early 1960s, respectively, two clades appeared that subsequently underwent major expansions in the Western Hemisphere: a CC5-I clade in South America and a CC5-II clade largely in Central and North America. The CC5-I clade includes the ST5-I Chilean/Cordobes clone, and the ST228-I South German clone as an early offshoot, but is distinct from other ST5-I clones from Europe that nest within CC5-Basal. The CC5-II clade includes divergent strains of the ST5-II USA100 clone, various other clones, and most known vancomycin-resistant strains of S. aureus, but is distinct from ST5-II strain N315 from Japan that nests within CC5-Basal. The recombination rate of CC5 was much lower than has been reported for other S. aureus genetic backgrounds, which indicates that recurrence of vancomycin resistance in CC5 is not likely due to an enhanced promiscuity. An increased number of antibiotic resistances and decreased number of toxins with distance from the CC5 tree root were observed. Of note, the expansions of the CC5-I and CC5-II clades in the Western Hemisphere were preceded by convergent gains of resistance to fluoroquinolone, macrolide, and lincosamide antibiotics, and convergent losses of the staphylococcal enterotoxin p (sep) gene from the immune evasion gene cluster of phage ϕSa3. Unique losses of surface proteins were also noted for these two clades. In summary, our study has determined the relationships of different clades and clones of CC5 and has revealed genomic changes for increased antibiotic resistance and decreased virulence associated with the expansions of these MRSA in the Western Hemisphere.
publishDate 2018
dc.date.issued.none.fl_str_mv 2018
dc.date.accessioned.none.fl_str_mv 2019-08-14T16:10:52Z
dc.date.available.none.fl_str_mv 2019-08-14T16:10:52Z
dc.type.spa.fl_str_mv article
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dc.type.local.spa.fl_str_mv artículo
dc.identifier.issn.none.fl_str_mv 1664-302X
dc.identifier.uri.none.fl_str_mv http://hdl.handle.net/20.500.12495/1608
dc.identifier.doi.none.fl_str_mv https://doi.org/10.3389/fmicb.2018.01901
dc.identifier.instname.spa.fl_str_mv instname:Universidad El Bosque
dc.identifier.reponame.spa.fl_str_mv reponame:Repositorio Institucional Universidad El Bosque
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identifier_str_mv 1664-302X
instname:Universidad El Bosque
reponame:Repositorio Institucional Universidad El Bosque
repourl:https://repositorio.unbosque.edu.co
url http://hdl.handle.net/20.500.12495/1608
https://doi.org/10.3389/fmicb.2018.01901
dc.language.iso.none.fl_str_mv eng
language eng
dc.relation.ispartofseries.spa.fl_str_mv Frontiers in microbiology, 1664-302X, 2018
dc.relation.uri.none.fl_str_mv https://www.frontiersin.org/articles/10.3389/fmicb.2018.01901/full
dc.rights.*.fl_str_mv Attribution 4.0 International
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_abf2
dc.rights.uri.*.fl_str_mv http://creativecommons.org/licenses/by/4.0/
dc.rights.local.spa.fl_str_mv Acceso abierto
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dc.rights.creativecommons.none.fl_str_mv 2018
rights_invalid_str_mv Attribution 4.0 International
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Acceso abierto
http://purl.org/coar/access_right/c_abf451
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http://purl.org/coar/access_right/c_abf2
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dc.publisher.spa.fl_str_mv Frontiers
dc.publisher.journal.spa.fl_str_mv Frontiers in microbiology
institution Universidad El Bosque
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spelling Challagundla, LavanyaReyes, JinnetheRafiqullah, IftekharSordelli, Daniel O.Echaniz-Aviles, GabrielaVelazquez-Meza, Maria E.Castillo-Ramírez, SantiagoFittipaldi, NahuelFeldgarden, MichaelChapman, Sinéad B.Calderwood, Michael S.Carvajal Ortiz, Lina PaolaRincón, SandraHanson, BlakePlanet, Paul J.Arias, César A.Díaz, LorenaRobinson, D. AshleyCarvajal Ortiz, Lina Paola [0000-0001-8301-8836]2019-08-14T16:10:52Z2019-08-14T16:10:52Z20181664-302Xhttp://hdl.handle.net/20.500.12495/1608https://doi.org/10.3389/fmicb.2018.01901instname:Universidad El Bosquereponame:Repositorio Institucional Universidad El Bosquerepourl:https://repositorio.unbosque.edu.coapplication/pdfengFrontiersFrontiers in microbiologyFrontiers in microbiology, 1664-302X, 2018https://www.frontiersin.org/articles/10.3389/fmicb.2018.01901/fullAttribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/Acceso abiertohttp://purl.org/coar/access_right/c_abf4512018http://purl.org/coar/access_right/c_abf2Phylogenomic classification and the evolution of clonal complex 5 Methicillin-Resistant Staphylococcus aureus in the Western Hemispherearticleartículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_6501Infección hospitalariaVirulenciaFarmacorresistencia microbianaMethicillin-resistant staphylococcus aureusMRSAPhylogenomicsClonal complex 5 methicillin-resistant Staphylococcus aureus (CC5-MRSA) includes multiple prevalent clones that cause hospital-associated infections in the Western Hemisphere. Here, we present a phylogenomic study of these MRSA to reveal their phylogeny, spatial and temporal population structure, and the evolution of selected traits. We studied 598 genome sequences, including 409 newly generated sequences, from 11 countries in Central, North, and South America, and references from Asia and Europe. An early-branching CC5-Basal clade is well-dispersed geographically, is methicillin-susceptible and MRSA predominantly of ST5-IV such as the USA800 clone, and includes separate subclades for avian and porcine strains. In the early 1970s and early 1960s, respectively, two clades appeared that subsequently underwent major expansions in the Western Hemisphere: a CC5-I clade in South America and a CC5-II clade largely in Central and North America. The CC5-I clade includes the ST5-I Chilean/Cordobes clone, and the ST228-I South German clone as an early offshoot, but is distinct from other ST5-I clones from Europe that nest within CC5-Basal. The CC5-II clade includes divergent strains of the ST5-II USA100 clone, various other clones, and most known vancomycin-resistant strains of S. aureus, but is distinct from ST5-II strain N315 from Japan that nests within CC5-Basal. The recombination rate of CC5 was much lower than has been reported for other S. aureus genetic backgrounds, which indicates that recurrence of vancomycin resistance in CC5 is not likely due to an enhanced promiscuity. An increased number of antibiotic resistances and decreased number of toxins with distance from the CC5 tree root were observed. Of note, the expansions of the CC5-I and CC5-II clades in the Western Hemisphere were preceded by convergent gains of resistance to fluoroquinolone, macrolide, and lincosamide antibiotics, and convergent losses of the staphylococcal enterotoxin p (sep) gene from the immune evasion gene cluster of phage ϕSa3. Unique losses of surface proteins were also noted for these two clades. In summary, our study has determined the relationships of different clades and clones of CC5 and has revealed genomic changes for increased antibiotic resistance and decreased virulence associated with the expansions of these MRSA in the Western Hemisphere.ORIGINALChallagundla L., Reyes J., Rafiqullah I., Sordelli D.O., Echaniz-Aviles G., Velazquez-Meza M.E._2016.pdfChallagundla L., Reyes J., Rafiqullah I., Sordelli D.O., Echaniz-Aviles G., Velazquez-Meza M.E._2016.pdfapplication/pdf1516266https://repositorio.unbosque.edu.co/bitstreams/61fbd955-f612-4ef5-9966-d43d4fa649d7/download741333e913e66f6580c41a78b1a979acMD51CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8908https://repositorio.unbosque.edu.co/bitstreams/b7b87bd6-401c-41bb-84e1-841b21ee4efa/download0175ea4a2d4caec4bbcc37e300941108MD52LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://repositorio.unbosque.edu.co/bitstreams/69654293-59c8-42c5-b3ce-e5a3373479b7/download8a4605be74aa9ea9d79846c1fba20a33MD53THUMBNAILChallagundla L., Reyes J., Rafiqullah I., Sordelli D.O., Echaniz-Aviles G., Velazquez-Meza M.E._2016.pdf.jpgChallagundla L., Reyes J., Rafiqullah I., Sordelli D.O., Echaniz-Aviles G., Velazquez-Meza M.E._2016.pdf.jpgIM Thumbnailimage/jpeg13101https://repositorio.unbosque.edu.co/bitstreams/32af727c-4902-4114-97af-66bae0b3307d/download2a7bda80dc2f9449183b3d338359bd58MD54TEXTChallagundla L., Reyes J., Rafiqullah I., Sordelli D.O., Echaniz-Aviles G., Velazquez-Meza M.E._2016.pdf.txtChallagundla L., Reyes J., Rafiqullah I., Sordelli D.O., Echaniz-Aviles G., Velazquez-Meza M.E._2016.pdf.txtExtracted texttext/plain88107https://repositorio.unbosque.edu.co/bitstreams/4c08a77c-7df5-4509-a83c-ee232bca41c3/download40188786174d6fdd71d3ff04ffa5b66aMD5520.500.12495/1608oai:repositorio.unbosque.edu.co:20.500.12495/16082024-02-07 10:15:41.591http://creativecommons.org/licenses/by/4.0/Attribution 4.0 Internationalopen.accesshttps://repositorio.unbosque.edu.coRepositorio Institucional Universidad El Bosquebibliotecas@biteca.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