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

Amplicon sequencing
Hybrid capture

Prep

COVIDSeq Assay

A low- to mid-throughput NGS assay to identify and track the emergence and prevalence of novel  SARS-CoV-2 variants.

Illumina Microbial Amplicon Prep–Influenza A/B

A streamlined whole-genome NGS library prep kit for high-impact research and public health surveillance of influenza A and B viruses.

Illumina Microbial Amplicon Prep (IMAP)

A flexible and streamlined NGS library prep kit that enables various public health surveillance and microbial research applications.

Urinary Pathogen ID/AMR Enrichment Kit

A targeted NGS-based assay for sequencing mycobacterium, M. tuberculosis complex (MTBC) strains, and antimicrobial resistance markers.

Sequence

MiniSeq System

Simple, accessible benchtop sequencing for targeted sequencing applications.

MiSeq System

A powerful and compact system ideal for rapid, cost-effective microbial sequencing applications.

NextSeq 550 System

Combine proven NGS technology with tunable output to enable sequencing and array capabilities across a range of applications.

NextSeq 1000 and 2000 Systems

Empower discoveries with a comprehensive workflow from start to finish.

Analyze

DRAGEN Targeted Microbial

This app is designed to analyze sequencing libraries generated from Illumina hybrid capture (enrichment) panels or tiled amplicon panels (ie COVIDseq).

Deeplex Myc-TB Web App

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

Prep

Illumina Respiratory Virus Enrichment Kit

A streamlined workflow offering highly sensitive detection and characterization of common respiratory viruses, including SARS-CoV-2 strains.

Viral Surveillance Panel v2

Whole-genome sequencing of over 200 RNA and DNA viruses and subtypes identified as high-risk to public health.

Respiratory Pathogen ID/AMR Enrichment Panel Kit

Library prep and enrichment kit that delivers highly sensitive, comprehensive respiratory pathogen identification and antimicrobial resistance insights.

Urinary Pathogen ID/AMR Enrichment Kit

A library prep and enrichment kit that enables sensitive, culture-free detection and analysis of common and underrecognized uropathogens and AMR genes.

Sequence

NextSeq 550 System

Combine proven NGS technology with tunable output to enable sequencing and array capabilities across a range of applications.

NextSeq 1000 and 2000 Systems

Empower discoveries with a comprehensive workflow from start to finish.

NovaSeq X Series

Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput, and scalability.

Analyze

DRAGEN Microbial Enrichment Plus

This app is designed to analyze sequencing libraries generated from Illumina microbiology enrichment based (hybrid-capture) panels, including the Viral Surveillance Panel v2 and Respiratory Pathogen ID/AMR Enrichment Panel Kit.

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.

Surveillance of infectious disease through wastewater sequencing

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.

Targeted enrichment for disease and AMR detection

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.

Find and characterize respiratory viruses with target enrichment

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

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.

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.

Primer design for the IMAP protocol with PrimalScheme3

Christopher Kent from the University of Birmingham introduces PrimalScheme3 and discusses best practices for primer design to help optimize IMAP experiments.

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Efficiently sequence key microbial targets

What is targeted microbial sequencing?

NGS Workflow Finder

Amplicon vs hybrid capture enrichment

Precision Metagenomics eBook

Applications of targeted microbial sequencing

Targeted microbial sequencing workflows

Prep

Sequence

Analyze

Prep

Sequence

Analyze

Related methods

Additional resources

Video resources

Fast, flexible library prep with IMAP