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Updated: May 30, 2026

Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow

Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow

Published on: August 15, 2025

Hybrid selection for sequencing pathogen genomes from clinical samples.

Alexandre Melnikov¹, Kevin Galinsky, Peter Rogov

¹Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA 02142, USA.

|August 13, 2011

Summary

This summary is machine-generated.

We developed a hybrid selection method to boost pathogen DNA in clinical samples. This technique significantly enriches malaria parasite DNA, enabling efficient pathogen genome sequencing.

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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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Published on: August 20, 2021

Area of Science:

Genomics
Molecular Biology
Parasitology

Background:

Clinical samples often contain a vast excess of host DNA, hindering pathogen genetic analysis.
Sequencing low-abundance pathogen DNA from complex biological mixtures is challenging.

Purpose of the Study:

To adapt and validate a solution hybrid selection protocol for enriching pathogen DNA from human genetic material.
To enable efficient whole-genome sequencing of pathogens directly from clinical specimens.

Main Methods:

Utilized a solution hybrid selection protocol.
Tested the protocol using mock mixtures of human and Plasmodium falciparum DNA.
Applied the protocol to clinical samples from malaria-infected patients.

Main Results:

Achieved an average of approximately 40-fold enrichment of Plasmodium falciparum parasite DNA.
Demonstrated successful enrichment in both artificial mixtures and real-world clinical samples.

Conclusions:

The adapted hybrid selection protocol effectively enriches pathogen DNA from human genetic material.
This method facilitates efficient genome sequencing of pathogens and endosymbiotic organisms from clinical samples.