Genomic analysis of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated during eight years in a single children 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 pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study. Resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides were included. 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 (MLST´s) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). However, half of the S. epidermidis analyzed lacked the icaoperon 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.
Cite this as
2019. Genomic analysis of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated during eight years in a single children hospital in México City. PeerJ Preprints 7:e27693v2 https://doi.org/10.7287/peerj.preprints.27693v2note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
In the previous version, we try to answer a general question about what are the S. epidermidis flowing in the children hospital during 8 years. The reviewers main concern was that we use a limited number of isolates and how these isolates were selected. We also lack of a clear explanation of why we performed the experiments with multidrug-resistant strains. Then, the question was not adequately responded. These and other details were addressed in the new reviewed version.
The new version focus on the study of the frequency of the multi resistant isolates during eight years, and if these isolates correspond to one or few clones, and if they are pathogenic or commensal. We added data on a survey of staphylococci along eight years. The results showed that S. epidermidis multi resistant to more than 8 antibiotics were the most common found in these years. Our results indicate that multiresistance is a property shared by pathogenic and commensal isolates. Then, it could the factor that explain the permanency of clones along thee years in the same hospital setting.
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Supplemental Information
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
Survey of staphylococci at Instituto Nacional de Perinatología, México City Alone eight years
A. Species classification and proportion. B. Origin of the isolates and proportion. C. Isolation sites proportion.
Frequency cumulation of antibiotic resistant strains in Staphylococcus
A. S. epidermidis. B. S. aureus. The absolute number of antibiotic resistances (x-axis) by the number of strains (y-axis) was counted from 2006 to 2013.
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.
Phylogenetic tree of the SCCmec recombinases
A. ccrA. B. ccrB. C. ccrB
Proposed structure of the combined cassette SCCmec IV-VIII
The segment corresponding to SCCmec cassettes contained within the contig 12 of the S07 strain is annotated according to the best blastN matches against the nr database of the Genebank
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.
Eugenia Silva-Herzog analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft, analysis of the data from a survey of S. epidermidis along eight years.
Xavier Soberón conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, 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.
