Generate accurate and complete microbial genomes

Whole-genome sequencing for comprehensive analysis of microbes

What is whole-genome sequencing of microbial isolates?

Whole-genome sequencing of microbial isolates is an important tool for mapping genomes of novel organisms, finishing genomes of known organisms, or comparing genomes across multiple samples. Sequencing entire microbial genomes is important for generating accurate reference genomes, for microbial identification, and for other comparative genomic studies. ^1-6

Unlike traditional methods, NGS-based microbial genome sequencing doesn’t rely on labor-intensive cloning steps, saving time and simplifying the workflow. NGS can identify low-frequency variants and genome rearrangements that may be missed or are too expensive to identify using other methods.

Male scientist, back side view, pipetting into 8 lane plate in wet lab, plates and tubes in background, other scientist blurry in the foreground

De novo microbial genome sequencing

De novo whole-genome sequencing involves assembling a genome without the use of a genomic reference and is often used to sequence novel microbial genomes.⁷ Illumina sequencers provide unparalleled raw read accuracy and read depth for high-quality draft and microbial whole-genome assemblies.⁸

Microbial whole-genome reference based mapping

Microbial whole-genome resequencing involves sequencing the entire genome of a bacteria, virus, or other microbe, and comparing the sequence to that of a known reference. Generating rapid and accurate microbial reference genome sequence information is critical for detecting low frequency mutations, finding key deletions and insertions, and discovering other genetic changes among microbial strains. ^9-12

Featured applications

Healthcare-associated infection surveillance

See how NGS is used to identify the genetic makeup of pathogens for more precise identification and tracking of outbreaks and transmission routes than ever before.

Food safety surveillance

NGS is paving the way for substantial improvements in food safety by providing sensitive detection coupled with high-throughput capabilities. Using laboratory networks, scientists and health professionals can collect and share genomic data across the globe.

Tuberculosis surveillance

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

Antimicrobial resistance

Learn more about how NGS is empowering antimicrobial resistance research in areas of early detection, outbreak responses, and clinical studies.

Recommended workflow for microbial whole-genome sequencing

Prep

Illumina DNA Prep

A fast, integrated workflow for preparing libraries for use in sequencing applications such as microbial whole-genome sequencing.

Sequence

iSeq 100 System

NGS technology in an easy-to-use, inexpensive ecosystem for microbial whole-genome sequencing applications.

MiniSeq System

Simple, accessible benchtop sequencing for microbial whole-genome sequencing applications.

MiSeq System

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

Analyze

SRST2

The SRST2 app reports the presence of STs (sequence types) from a MLST database and/or reference genes from a sequence database of virulence genes, resistance genes, and plasmid replicons.

Get in touch

Interested in learning more about microbial whole-genome sequencing?

References

Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ, et al. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med. 2013; 369(3):290–2. doi: 10.1056/NEJMc1215305
Harrison EM, Paterson GK, Holden MT, Larsen J, Stegger M, et al. Whole-genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC. EMBO Mol Med. 2013; 5(4):509–15. doi: 10.1002/emmm.201202413
Pérez-Cobas AE, Gomez-Valero L, Buchrieser C. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microb Genom. 2020; 6(8). doi: 10.1099/mgen.0.000409.
Sundermann AJ, Chen J, Miller JK, et al. Whole-genome sequencing surveillance and machine learning for healthcare outbreak detection and investigation: A systematic review and summary. Antimicrob Steward Healthc Epidemiol. 2022; 2(1). doi: 10.1017/ash.2021.241.
Peterson SW, Demczuk W, Martin I, et al. Identification of bacterial and fungal pathogens directly from clinical blood cultures using whole genome sequencing. Genomics. 2023;115(2). doi: 10.1016/j.ygeno.2023.110580
Mitchell PK, Wang L, Stanhope BJ, et al. Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria. Microb Genom. 2022; 8(2). doi: 10.1099/mgen.0.000717
Lee CY, Lee YF, Lai LC, et al. MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes. N Biotechnol. 2021; Nov 25:65. doi: 10.1016/j.nbt.2021.08.002
Bruzek S, Vestal G, Lasher A, et al. Bacterial Whole Genome Sequencing on the Illumina iSeq 100 for Clinical and Public Health Laboratories. J Mol Diagn. 2020 Dec;22(12):1419-1429. doi: 10.1016/j.jmoldx.2020.09.003.
Valiente-Mullor C, Beamud B, Ansari I, et al. One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads. PLoS Comput Biol. 2021; Jan 17(1). doi: 10.1371/journal.pcbi.1008678
Shea J, Halse TA, Kohlerschmidt D, et al. Low-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York. J Clin Microbiol. 2021;59(4). doi: 10.1128/JCM.01885-2
Aggarwal SK, Singh A, Choudhary M, et al. Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives. Genes (Basel). 2022; Mar 27;13(4):598. doi: 10.3390/genes13040598
Maladan Y, Krismawati H, Wahyuni T, et al. The whole-genome sequencing in predicting Mycobacterium tuberculosis drug susceptibility and resistance in Papua, Indonesia. BMC Genomics. 2021 Nov 22;22(1):844. doi: 10.1186/s12864-021-08139-3.

Generate accurate and complete microbial genomes

What is whole-genome sequencing of microbial isolates?

De novo microbial genome sequencing

Microbial whole-genome reference based mapping

Featured applications

Healthcare-associated infection surveillance

Food safety surveillance

Tuberculosis surveillance

Antimicrobial resistance

Recommended workflow for microbial whole-genome sequencing

Prep

Sequence

Analyze

Get in touch

Additional resources

Push-button de novo microbial genome sequence assembly

Direct bacterial colony sequencing

De novo bacterial sequencing overview

Empowering healthcare–associated infection surveillance with bacterial genome sequencing

References

For every lab, everywhere

NextSeq 1000 and NextSeq 2000 Reagents

NGS Workflow Finder

DRAGEN v4.3 now available on-premises and on-cloud

Illumina Proactive Instrument Performance Service

Do more, faster than ever

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

This is the Genome Era

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

Generate accurate and complete microbial genomes

What is whole-genome sequencing of microbial isolates?

De novo microbial genome sequencing

Microbial whole-genome reference based mapping

NGS Workflow Finder

Featured applications

Recommended workflow for microbial whole-genome sequencing

Prep

Sequence

Analyze

Surveillance of healthcare-acquired infections with bacterial genome sequencing

Get in touch

Additional resources

References