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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Related Experiment Video

Updated: May 27, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates.

Yu Wan1,2,3, Rachel Pike4, Alessandra Harley4

  • 1HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, United Kingdom. yu.wan@liverpool.ac.uk.

BMC Genomic Data
|February 15, 2025
PubMed
Summary

This study provides complete genomes and antimicrobial resistance data for 22 Staphylococcus capitis isolates, including the multidrug-resistant NRCS-A clone. This resource aids future research on S. capitis genomics and antimicrobial resistance.

Keywords:
Staphylococcus capitisAntibiogramsAntimicrobial resistanceAntimicrobial susceptibilityBioresourceGenomicsHybrid genome assemblyNRCS-A cloneNanopore MinION sequencingReference genomes

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Area of Science:

  • Microbiology
  • Genomics
  • Infectious Diseases

Background:

  • Staphylococcus capitis is an opportunistic pathogen causing various infections, with increasing detection in sterile sites.
  • A multidrug-resistant clone, NRCS-A, has been identified in neonatal intensive care units in England.
  • Public databases lack comprehensive genomes and antibiograms for S. capitis.

Purpose of the Study:

  • To generate complete genome assemblies and antimicrobial susceptibility data for diverse S. capitis isolates.
  • To address the gap in public genomic and resistance data for S. capitis.
  • To provide a resource for understanding S. capitis evolution and antimicrobial resistance.

Main Methods:

  • Performed long- and short-read whole-genome sequencing and hybrid genome assembly for 22 S. capitis isolates.
  • Conducted antimicrobial susceptibility testing for 13 antimicrobials.
  • Included two type strains and 20 clinical isolates, with 10 being the NRCS-A clone.

Main Results:

  • Presented complete genome assemblies (2.4-2.7 Mbp, 33% GC content) for 22 S. capitis isolates.
  • Identified plasmids in 20 isolates.
  • Documented resistance to various antimicrobials including teicoplanin, daptomycin, and ciprofloxacin in 1-10 isolates.

Conclusions:

  • The generated genomic and antimicrobial resistance data serve as a valuable resource for future studies.
  • This work enhances the understanding of S. capitis genomics and evolution.
  • Facilitates research into the antimicrobial resistance mechanisms of S. capitis.