Genomic diversity of antibiotic multi-resistant Staphylococcus epidermidis isolated from a tertiary care hospital in México City
A peer-reviewed article of this Preprint also exists.
Author and article information
Abstract
Staphylococcus epidermidis is a human commensal and opportunistic pathogen worldwide distributed. To ascertain which pathogenic S. epidermidis clones are circulating in a local tertiary hospital setting, we sequenced the complete genomes of 17 S. epidermidis isolates obtained from neonatal infections at a Hospital Care Unit in México City. Genomic comparisons between S. epidermidis isolates revealed high pairwise whole genome nucleotide identities of about 97% to 99% and essentially a clonal structure. We inferred eight Multilocus Sequence Types (MLST´s), six of them of worldwide distribution, and two showing allelic variants, not in MLST databases. The profile of virulence includes genes involved in biofilm and modulin formation; most of the strains are multi-resistant to methicillin and several other beta-lactams, fluoroquinolones, and macrolides. 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 frequent than the mutation rate and affected the whole genome. Therefore, recombination properties shape the population structure of local nosocomial S. epidermidis strains, formed by pathogenic and probably, non-pathogenic clones.
Cite this as
2019. Genomic diversity of antibiotic multi-resistant Staphylococcus epidermidis isolated from a tertiary care hospital in México City. PeerJ Preprints 7:e27693v1 https://doi.org/10.7287/peerj.preprints.27693v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This is a submission to PeerJ for review.
Sections
Supplemental Information
Genome identity (ANIm) between pairs of SE INPer strains
Pairwise whole genome alignments were done with Mummer within the JSspecies program (Richter et al., 2016). The percent of average nucleotide alignment (ANI) was illustrated by a heat-map constructed with ggPlot2 in R (see methods). ANI > 99% are in red color. S. epidermidis ATCC 12228 was included for comparison. S10 strain had ANI = 97% respect all the other SE strains.
Pangenome model of SE strains
The pangenome model of 29 SE strains was performe with GET_HOMOLOGUES (Contreras-Moreira and Vinuesa, 2013) as described in methods. A. Pangenome size (number of gene family clusters, Y axis) as a function of the number of SE genomes (X axis). B. Core genome according to the Tettelin equations.
Clonal relationships of the STs detected in INPer strains respect to the ST database
Alleles for the seven proteins used in the S. epidermidisMLST scheme (Thomas et al., 2007) were looked at the Staphylococcus epidermidis MLST database ( https://pubmlst.org/sepidermidis/ ; Table 1; see methods) (Feil et al., 2004). The clonal relationships among STs were determined by eBURST( http://eburst.mlst.net ). Six out of 8 ST complexes assigned to the SEINPer strains are denoted by numbers in violet color.
Genomes of SEfrom the GenBank used in this work
Prophage sequences and their homologs found in SEINPer genomes
CRISPR-Cas elements present in SE INPer strains
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Roberto Cabrera-Contreras conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Rosa I Santamaría performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.
Patricia Bustos performed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.
Irma Martínez-Flores performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.
Enrique Meléndez performed the experiments, contributed reagents/materials/analysis tools, approved the final draft, literature searching.
Rubén Morelos performed the experiments, contributed reagents/materials/analysis tools, approved the final draft, literature searching.
Martín Barbosa-Amezcua performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.
Vanessa González-Covarrubias performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.
Xavier Soberón conceived and designed the experiments, contributed reagents/materials/analysis tools, approved the final draft.
Víctor González conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
S. epidermidis of the INPer collection used in this work were uploaded in GenBank with the following Biosample identifiers: SAMN11086744, SAMN11086745, SAMN11086746, SAMN11086747, SAMN11086748, SAMN11086749, SAMN11086750, SAMN11086751, SAMN11086752, SAMN11086753, SAMN11086754, SAMN11086755, SAMN11086756, SAMN11086757, SAMN11086758, SAMN11086759, SAMN11086760. The accession numbers for the genomes of reference S. epidermidis strains are listed in Table S3.
Data Deposition
The following information was supplied regarding data availability:
There is no raw data other than the sequences deposited in GenBank.
Funding
This work was supported by a research grant from PAPIIT-DGAPA, UNAM No. IN214019 and partially from a research budget from: “Departamento de Salud Pública, Facultad de Medicina, UNAM, México”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
