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Genomic diversity of antibiotic multi-resistant Staphylococcus epidermidis isolated from a tertiary care hospital in México City

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RT @VictorG74402417: My preprint has been published today in @PeerJPreprints https://t.co/9nXx3imNUX #Genomics #Microbiology #InfectiousDis…
RT @VictorG74402417: My preprint has been published today in @PeerJPreprints https://t.co/9nXx3imNUX #Genomics #Microbiology #InfectiousDis…
My preprint has been published today in @PeerJPreprints https://t.co/9nXx3imNUX #Genomics #Microbiology #InfectiousDiseases
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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.

DOI: 10.7287/peerj.preprints.27693v1/supp-1

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.

DOI: 10.7287/peerj.preprints.27693v1/supp-2

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.

DOI: 10.7287/peerj.preprints.27693v1/supp-3

Completeness of SE INPer genome collection

DOI: 10.7287/peerj.preprints.27693v1/supp-5

Genomes of SEfrom the GenBank used in this work

DOI: 10.7287/peerj.preprints.27693v1/supp-6

Prophage sequences and their homologs found in SEINPer genomes

DOI: 10.7287/peerj.preprints.27693v1/supp-7

CRISPR-Cas elements present in SE INPer strains

DOI: 10.7287/peerj.preprints.27693v1/supp-8

Insertion sequences present in SEINPer strains

DOI: 10.7287/peerj.preprints.27693v1/supp-9

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.


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