Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey
Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, includin...
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PeerJ Inc.
2019-11-01
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| author | Roberto Cabrera-Contreras Rosa I. Santamaría Patricia Bustos Irma Martínez-Flores Enrique Meléndez-Herrada Rubén Morelos-Ramírez Martín Barbosa-Amezcua Vanessa González-Covarrubias Eugenia Silva-Herzog Xavier Soberón Víctor González |
| author_facet | Roberto Cabrera-Contreras Rosa I. Santamaría Patricia Bustos Irma Martínez-Flores Enrique Meléndez-Herrada Rubén Morelos-Ramírez Martín Barbosa-Amezcua Vanessa González-Covarrubias Eugenia Silva-Herzog Xavier Soberón Víctor González |
| author_sort | Roberto Cabrera-Contreras |
| collection | DOAJ |
| description | Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings. |
| first_indexed | 2024-03-09T06:52:48Z |
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| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:52:48Z |
| publishDate | 2019-11-01 |
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| spelling | doaj.art-0a8a4de429ce4b9aa215d54d995565a02023-12-03T10:16:19ZengPeerJ Inc.PeerJ2167-83592019-11-017e806810.7717/peerj.8068Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years surveyRoberto Cabrera-Contreras0Rosa I. Santamaría1Patricia Bustos2Irma Martínez-Flores3Enrique Meléndez-Herrada4Rubén Morelos-Ramírez5Martín Barbosa-Amezcua6Vanessa González-Covarrubias7Eugenia Silva-Herzog8Xavier Soberón9Víctor González10Laboratorio de Patogenicidad Bacteriana, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, MéxicoCentro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, MéxicoCentro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, MéxicoCentro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, MéxicoLaboratorio de Patogenicidad Bacteriana, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, MéxicoLaboratorio de Patogenicidad Bacteriana, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, MéxicoInstituto Nacional de Medicina Genómica, Ciudad de México, MéxicoInstituto Nacional de Medicina Genómica, Ciudad de México, MéxicoInstituto Nacional de Medicina Genómica, Ciudad de México, MéxicoInstituto Nacional de Medicina Genómica, Ciudad de México, MéxicoCentro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, MéxicoStaphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.https://peerj.com/articles/8068.pdfGenomesPangenomeProphagesCRISPRRecombinationAntibiotic resistance |
| spellingShingle | Roberto Cabrera-Contreras Rosa I. Santamaría Patricia Bustos Irma Martínez-Flores Enrique Meléndez-Herrada Rubén Morelos-Ramírez Martín Barbosa-Amezcua Vanessa González-Covarrubias Eugenia Silva-Herzog Xavier Soberón Víctor González Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey PeerJ Genomes Pangenome Prophages CRISPR Recombination Antibiotic resistance |
| title | Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey |
| title_full | Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey |
| title_fullStr | Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey |
| title_full_unstemmed | Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey |
| title_short | Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey |
| title_sort | genomic diversity of prevalent staphylococcus epidermidis multidrug resistant strains isolated from a children s hospital in mexico city in an eight years survey |
| topic | Genomes Pangenome Prophages CRISPR Recombination Antibiotic resistance |
| url | https://peerj.com/articles/8068.pdf |
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