Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates

Manoshi S. Datta, Idan Yelin, Ori Hochwald, Imad Kassis, Liron Borenstein-Levin, Amir Kugelman and Roy Kishony ()
Additional contact information
Manoshi S. Datta: Technion—Israel Institute of Technology
Idan Yelin: Technion—Israel Institute of Technology
Ori Hochwald: Rambam Medical Center
Imad Kassis: Rambam Medical Center
Liron Borenstein-Levin: Rambam Medical Center
Amir Kugelman: Rambam Medical Center
Roy Kishony: Technion—Israel Institute of Technology

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: Abstract Early in life, infants are colonized with multiple bacterial strains whose differences in gene content can have important health consequences. Metagenomics-based approaches have revealed gene content differences between different strains co-colonizing newborns, but less is known about the rate, mechanism, and phenotypic consequences of gene content diversification within strains. Here, focusing on Staphylococcus epidermidis, we whole-genome sequence and phenotype more than 600 isolates from newborns. Within days of birth, infants are co-colonized with a highly personalized repertoire of S. epidermidis strains, which are spread across the newborn body. Comparing the genomes of multiple isolates of each strain, we find very little evidence of adaptive evolution via single-nucleotide polymorphisms. By contrast, we observe gene content differences even between otherwise genetically identical cells, including variation of the clinically important methicillin resistance gene, mecA, suggesting rapid gene gain and loss events at rates higher than point mutations. Mapping the genomic architecture of structural variants by long-read Nanopore sequencing, we find that deleted regions were always flanked by direct repeats, consistent with site-specific recombination. However, we find that even within a single genetic background, recombination occurs at multiple, often non-canonical repeats, leading to the rapid evolution of patient-specific diverse structural variants in the SCCmec island and to differences in antibiotic resistance.

Date: 2021
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-021-26392-8 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26392-8

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-021-26392-8

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().