Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis
The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but a...
Main Authors: | , , , , , , , , , , , , , , , , , , , , |
---|---|
Format: | Dataset |
Language: | English |
Published: |
Dryad
2020
|
Subjects: | |
Online Access: | https://doi.org/10.5061/dryad.82jq4 |
id |
fttriple:oai:gotriple.eu:50|dedup_wf_001::91085a98593a7382a3628eccfcbd0b7a |
---|---|
record_format |
openpolar |
spelling |
fttriple:oai:gotriple.eu:50|dedup_wf_001::91085a98593a7382a3628eccfcbd0b7a 2023-05-15T16:51:44+02:00 Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis Méric, Guillaume Miragaia, Maria De Been, Mark Yahara, Koji Pascoe, Ben Mageiros, Leonardos Mikhail, Jane Harris, Llinos G. Wilkinson, Thomas S. Rolo, Joana Lamble, Sarah Bray, James E. Jolley, Keith A. Hanage, William P. Bowden, Rory Maiden, Martin C. J. Mack, Dietrich De Lencastre, Hermínia Feil, Edward J. Corander, Jukka Sheppard, Samuel K. 2020-06-25 https://doi.org/10.5061/dryad.82jq4 en eng Dryad http://dx.doi.org/10.5061/dryad.82jq4 https://dx.doi.org/10.5061/dryad.82jq4 lic_creative-commons 10.5061/dryad.82jq4 oai:easy.dans.knaw.nl:easy-dataset:89199 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89199 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c recombination Staphylococcus epidermidis nosocomial infections Evolution Life sciences medicine and health care Ecology Portugal Argentina Bulgary Colombia Cape Verde Denmark Greece Hungary Iceland Italy Japan Mexico Taiwan Uruguay FOS: Biological sciences envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2020 fttriple https://doi.org/10.5061/dryad.82jq4 2023-01-22T17:23:46Z The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species. Meric et al. 2015 GBE: 83 novel Staphylococcus epidermidis genome assembliesZIP archive containing contigs for 83 whole genome sequences of S. epidermidis. Metadata is attached to the Dryad submission. Contact: Prof Samuel Sheppard s.k.sheppard@swansea.ac.ukMeric_2015_GBE_83_Sepi_genomes.zip Dataset Iceland Unknown Argentina Sheppard ENVELOPE(-56.967,-56.967,-63.367,-63.367) Uruguay |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
recombination Staphylococcus epidermidis nosocomial infections Evolution Life sciences medicine and health care Ecology Portugal Argentina Bulgary Colombia Cape Verde Denmark Greece Hungary Iceland Italy Japan Mexico Taiwan Uruguay FOS: Biological sciences envir geo |
spellingShingle |
recombination Staphylococcus epidermidis nosocomial infections Evolution Life sciences medicine and health care Ecology Portugal Argentina Bulgary Colombia Cape Verde Denmark Greece Hungary Iceland Italy Japan Mexico Taiwan Uruguay FOS: Biological sciences envir geo Méric, Guillaume Miragaia, Maria De Been, Mark Yahara, Koji Pascoe, Ben Mageiros, Leonardos Mikhail, Jane Harris, Llinos G. Wilkinson, Thomas S. Rolo, Joana Lamble, Sarah Bray, James E. Jolley, Keith A. Hanage, William P. Bowden, Rory Maiden, Martin C. J. Mack, Dietrich De Lencastre, Hermínia Feil, Edward J. Corander, Jukka Sheppard, Samuel K. Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis |
topic_facet |
recombination Staphylococcus epidermidis nosocomial infections Evolution Life sciences medicine and health care Ecology Portugal Argentina Bulgary Colombia Cape Verde Denmark Greece Hungary Iceland Italy Japan Mexico Taiwan Uruguay FOS: Biological sciences envir geo |
description |
The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species. Meric et al. 2015 GBE: 83 novel Staphylococcus epidermidis genome assembliesZIP archive containing contigs for 83 whole genome sequences of S. epidermidis. Metadata is attached to the Dryad submission. Contact: Prof Samuel Sheppard s.k.sheppard@swansea.ac.ukMeric_2015_GBE_83_Sepi_genomes.zip |
format |
Dataset |
author |
Méric, Guillaume Miragaia, Maria De Been, Mark Yahara, Koji Pascoe, Ben Mageiros, Leonardos Mikhail, Jane Harris, Llinos G. Wilkinson, Thomas S. Rolo, Joana Lamble, Sarah Bray, James E. Jolley, Keith A. Hanage, William P. Bowden, Rory Maiden, Martin C. J. Mack, Dietrich De Lencastre, Hermínia Feil, Edward J. Corander, Jukka Sheppard, Samuel K. |
author_facet |
Méric, Guillaume Miragaia, Maria De Been, Mark Yahara, Koji Pascoe, Ben Mageiros, Leonardos Mikhail, Jane Harris, Llinos G. Wilkinson, Thomas S. Rolo, Joana Lamble, Sarah Bray, James E. Jolley, Keith A. Hanage, William P. Bowden, Rory Maiden, Martin C. J. Mack, Dietrich De Lencastre, Hermínia Feil, Edward J. Corander, Jukka Sheppard, Samuel K. |
author_sort |
Méric, Guillaume |
title |
Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis |
title_short |
Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis |
title_full |
Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis |
title_fullStr |
Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis |
title_full_unstemmed |
Data from: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis |
title_sort |
data from: ecological overlap and horizontal gene transfer in staphylococcus aureus and staphylococcus epidermidis |
publisher |
Dryad |
publishDate |
2020 |
url |
https://doi.org/10.5061/dryad.82jq4 |
long_lat |
ENVELOPE(-56.967,-56.967,-63.367,-63.367) |
geographic |
Argentina Sheppard Uruguay |
geographic_facet |
Argentina Sheppard Uruguay |
genre |
Iceland |
genre_facet |
Iceland |
op_source |
10.5061/dryad.82jq4 oai:easy.dans.knaw.nl:easy-dataset:89199 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89199 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.82jq4 https://dx.doi.org/10.5061/dryad.82jq4 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.82jq4 |
_version_ |
1766041838850932736 |