Efficiently sequence key microbial targets

Using targeted NGS to reduce cost and accelerate analysis

What is targeted microbial sequencing?

Within complex samples, targeted microbial sequencing is an efficient way to resolve microbial DNA/RNA sequences from non-microbial DNA/RNA while allowing researchers to efficiently identify and characterize microbes of interest. With the power of next-generation sequencing (NGS), techniques such as amplicon sequencing and hybridization (hybrid) capture enrichment are effective methods that can reduce the cost of sequencing and streamline data analysis.

On a lab bench, a scientist pipetting using a single channel tube, filled, part of a library prep workflow. Reagent cartridge and tray in the background.

Amplicon vs hybrid capture enrichment

Amplicon sequencing and hybrid capture are popular methods to perform targeted sequencing. Each approach has different considerations based on the goals of the study. Amplicon sequencing is a highly targeted method to analyze genetic variation in specific genomic regions. This method uses oligonucleotide primers designed to target and amplify small genomes or specific regions of interest, followed by NGS. Hybrid capture is a method that uses biotinylated probes specific to a genomic region of interest. Once bound, these hybridized genomic fragments can be captured by streptavidin for amplification and sequencing.

  Amplicon sequencing Hybrid capture
Targets

Smaller number of targets

Larger number of targets

Example use cases

Single virus variant tracking
Tuberculosis drug resistance

Broad pathogen surveillance
Antimicrobial resistance surveillance

Workflow

Simpler and faster turnaround times

More complex and time-consuming

Applications of targeted microbial sequencing

Wastewater surveillance

Wastewater surveillance is a method to detect, identify and characterize pathogens found in wastewater. This method provides data to help monitor outbreaks and other threats at the community level.

Tuberculosis surveillance

Learn about integrative NGS-based solutions for tuberculosis detection, characterization, and analysis.

Infectious disease identification

Learn how NGS-based methods can improve infectious disease characterization and surveillance of viruses, bacteria, fungi, and parasites.

Genomic surveillance

Learn how researchers use genomic surveillance to study pathogens at a molecular level, providing insights into their behavior and evolution in populations around the world.

Targeted microbial sequencing workflows

1
Prep
2
Sequence
3
Analyze

Interactive visualization and easy interpretation of results from the Deeplex Myc-TB targeted amplicon kit.

1
Prep
2
Sequence
3
Analyze

Related methods

Shotgun metagenomic sequencing

See how this method enables microbiologists to evaluate bacterial diversity, detect the abundance of microbes in various environments, and study unculturable microorganisms that are otherwise difficult or impossible to analyze.

Whole-genome microbial sequencing

Learn how microbial whole-genome sequencing is an important tool for mapping genomes of novel organisms, finishing genomes of known organisms, or comparing genomes across multiple samples.

Additional resources

Download this eBook to see how NGS is fueling the future of drug-resistant TB (DR-TB) research. Learn about the global implications of DR-TB, how NGS is being used to advance the WHO goal of ending TB, and Illumina targeted and whole-genome sequencing workflows.

This Application Note details methods to detect SARS-CoV-2 variants and other respiratory viruses using the Illumina COVIDSeq Assay and Respiratory Virus Enrichment Kit in wastewater samples.

This webinar covers the use of NGS-powered tools to evaluate chronic infections such as urinary tract infections (UTIs) and wound infections that continue to impact everyday life from antimicrobial resistant pathogens.

See this Application Note to learn more about a comprehensive and rapid target enrichment sequencing workflow for highly sensitive detection and characterization of common respiratory viruses, including COVID-19 strains.

Video resources

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Fast, flexible library prep with IMAP

In this video, Illumina Scientist Jeff Koble provides an overview of the Illumina Microbial Amplicon Prep assay, detailing tips and tricks to help ensure successful preparation of libraries.

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Simple and efficient IMAP analysis with DRAGEN Targeted Microbial App

Illumina Bioinformatics Scientist Soo Bin Kwon demonstrates how DRAGEN Target Microbial enables comprehensive analysis of microbial targets sequenced with IMAP.

Get in touch

Interested in learning more about targeted microbial sequencing?