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Updated: May 9, 2025

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Integrated population clustering and genomic epidemiology with PopPIPE.

Martin P McHugh1,2, Samuel T Horsfield3, Johanna von Wachsmann3

  • 1Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.

Microbial Genomics
|April 28, 2025
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Summary

A new Population analysis PIPEline (PopPIPE) uses rapid, reference-free methods for bacterial genome analysis. It effectively clusters bacterial populations and identifies transmission events, improving upon existing methods for outbreak investigations.

Keywords:
clusteringgenomic epidemiologypipelinestransmission

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Genetic distances in bacterial DNA aid in population clustering and transmission event detection.
  • Reference-free methods offer sensitive detection of genetic differences, particularly in outbreak samples.
  • Recombination challenges analysis across longer genetic distances, demanding bioinformatic expertise.

Purpose of the Study:

  • To introduce a Population analysis PIPEline (PopPIPE) for analyzing bacterial genomes at both population-wide and outbreak scales.
  • To provide a user-friendly, rapid, and reproducible pipeline for bacterial population structure and transmission analysis.
  • To enhance the detection of transmission events and subpopulation clustering using reference-free methods.

Main Methods:

  • Utilizes k-mer sketching for initial population splitting into strains.
  • Employs split k-mer analysis and recombination removal for alignment and subcluster creation.
  • Combines rapid reference-free genome analysis techniques for comprehensive bacterial genome analysis.

Main Results:

  • PopPIPE successfully generates high-quality subclusters on a population-wide dataset of *Streptococcus pneumoniae*.
  • Analysis of vancomycin-resistant *Enterococcus faecium* samples revealed more epidemiologically plausible transmission clusters compared to core genome and MLST approaches.
  • The pipeline demonstrates speed, reproducibility, and the creation of interactive visualizations.

Conclusions:

  • PopPIPE offers a user-friendly solution for bacterial genome analysis, from species-wide clustering to outbreak investigations.
  • The pipeline effectively addresses challenges posed by variable gene content, order, and recombination in bacterial genomes.
  • PopPIPE enhances the ability to detect transmission clusters and understand population dynamics in bacterial pathogens.