Genomic diversity of antibiotic multi-resistant Staphylococcus epidermidis isolated from a tertiary care hospital in México City
- Published
- Accepted
- Subject Areas
- Genomics, Microbiology, Infectious Diseases
- Keywords
- Staphylococcus epidermidis, genomes, pangenome, prophages, CRISPR, Recombination, antibiotic resistance, insertion sequences, clonal structure
- Copyright
- © 2019 Cabrera-Contreras et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 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.27693v1
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.
Author Comment
This is a submission to PeerJ for review.
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.