Microbial Genomics
Microbial Genomics

Microbial whole-genome sequencing

Generate accurate and complete microbial genomes, and perform comprehensive analysis of microbes

What is whole-genome sequencing of microbial isolates?

Whole-genome sequencing (WGS) 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 bacterial, viral, and other 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 application resources

Benchtop applications ebook

Download this eBook to learn how benchtop sequencers support a broad range of applications while delivering exceptional data quality and accuracy.

NGS workflow finder
NGS Workflow Finder

Use the NGS Workflow Finder to get recommendations for your application workflows of interest so you can sequence with confidence.

NGS library prep
Empowering new sequencing possibilities

Watch this webinar unveiling the MiSeq i100 Series. View application data in oncology, microbiology, and infectious disease, and gain insights from early-access users.

Featured applications

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

1
Prep

Illumina DNA Prep

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

2
Sequence

MiSeq i100 Series

Our fastest, simplest benchtop system for microbial whole-genome sequencing.

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.

3
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.

Surveillance of healthcare-acquired infections with bacterial genome sequencing

Outbreak detection is possible through comprehensive isolate discrimination and characterization through microbial WGS.

Read technical note

Get in touch

Interested in learning more about microbial whole-genome sequencing?

Additional resources

References

  1. 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
  2. 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
  3. 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. 
  4. 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.
  5. 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 
  6. 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
  7. 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 
  8. 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.
  9. 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
  10. 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
  11. 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
  12. 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.