microbial genomics infectious disease

Genomic technologies have revolutionized microbiology research, enabling us to characterize microbial communities and reveal the diversity of microorganisms not seen before due to their inability to be isolated by culture. Genomics is expanding our knowledge of how pathogens interact with their hosts, how they relate to each other, and how drug resistance genes spread within a community.

Thermo Fisher Scientific offers a broad range of genomic technologies to characterize microbes. Our optimized platforms for next-generation sequencing, Sanger sequencing using capillary electrophoresis, and real-time PCR offer highly effective approaches to analyzing viruses, bacteria, fungi, and other eukaryotic microorganisms and microbial communities.

Instruments for infectious disease analysis

Adopting next-generation sequencing (NGS) in your lab is now simpler than ever. The Ion S5™ and Ion S5™ XL Systems enable a simple sequencing workflow for your lab with industry-leading speed and affordability. The systems support three chip formats, from 3 million to 80 million reads, and chemistry for 200 and 400 base pair reads, enabling a variety of applications from targeted amplicons to whole-genome sequencing. 

The Applied Biosystems™ 3500 Series Genetic Analyzer is part of a complete, integrated workflow for Sanger sequencing and fragment analysis applications. Designed with you in mind, the Applied Biosystems 3500 Series Genetic Analyzer gives you automated operation, easy-to-install consumables, electronic tracking of instrument performance and maintenance tasks, and integrated analysis software—so you can focus on the outcome.

The QuantStudio™ 12K Flex Real-Time PCR System is a high-throughput nanofluidic solution for microbial detection. Combining flexible throughput capabilities with a streamlined workflow, the QuantStudio System takes you from targeted discovery through confirmation and screening, all on a single platform. Multiple block formats are available for single tubes, 96- and 384- well plates, 384-well TaqMan™ Array Cards, and OpenArray™ Plates.

Viral identification and quantitation

Viruses can be identified by sequencing the viral RNA or DNA genome by next-generation sequencing or Sanger sequencing. In addition, presence or absence of specific viral genotypes in a sample can be determined by quantitative PCR approaches that target specific known viral sequences, including research assays that analyze microorganisms associated with common infectious diseases of the respiratory, gastrointestinal, and urogenital tracts.

Next-generation sequencing assays

Real-time PCR assays

Fighting Ebola from the ground up—sequencing in Sierra Leone

“We needed a workflow that is robust and is relatively straightforward, so the Ion AmpliSeq Ebola Research Panel was perfect for what we wanted to do.”
Professor Ian Goodfellow
University of Cambridge, United Kingdom

Emerging viruses

This group includes viruses that have not been reported in literature or that have substantially changed. Their genomic regions are best characterized by whole-genome sequencing. Bulk nucleic acids isolated from biological or cultured samples can be directly sequenced using the massively parallel Ion S5™ Next-Generation Sequencing System. The resulting sequencing reads can be filtered for human and known viral sequences, leaving previously unreported sequences. This approach has been used to characterize newly evolving Ebola strains and to detect new phage genera in oceanic water. A new relatively unexplored area, virome analysis catalogs the viral populations present in the environment directly from biological samples.

Next-generation sequencing products for total DNA or RNA analysis

Viral typing and epidemiology

Tracing the origins of specific viruses and determining the relatedness of viral strains can be done by sequencing the genomes of spatially and temporally related viral samples. Single nucleotide variant (SNV) differences between the isolates, determined by sequencing, are used to create minimum spanning trees based on the emergence of new SNVs.

Next-generation sequencing products

Bacterial identification

Genomic methods provide a clear and definitive approach to identify a bacterium. These methods can range from the most comprehensive approach based on de novo whole-genome sequencing to a simple and easy-to-use quantitative PCR assay. Both methods can be used to monitor the presence of potential pathogens in food, water, and other environmental samples. Traditional time- and labor-intensive microbiological identification methods are based on culturing individual organisms followed by phenotypic or genotypic analysis. Genomic methods have expanded the repertoire of known organisms by enabling the identification of difficult-to-culture or unculturable organisms.

Next-generation sequencing products

Sanger sequencing products

Real-time PCR assays

Antibiotic susceptibility and resistance research

Many mutations in the bacterial genome or episomal elements are associated with drug resistance. Surveying for these specific mutations may potentially be used to provide a clear indication of drug resistance in the future. Known mutations may be assessed by qPCR assays, Sanger sequencing assays, or next-generation sequencing assays. Novel variants associated with resistance are discovered by comparing the sequences of susceptible and resistant strains to find changes that may contribute to the resistance phenotype.

Next-generation sequencing products

Ion AmpliSeq TB Research Panel Variants identified by Ion AmpliSeq TB Research Panel from DNA isolated from archived pure M. tuberculosis cultures. WT indicates wild type. A red circle indicates presence of mutation. S531L (TCG/TTG) 761155

Infectious disease outbreak investigation research

Genomics has the potential to revolutionize infectious disease research that may be used to help trace the origin of outbreaks, monitor biologics manufacturing processes, and ensure food and beverage safety, and for clinical microbiology research applications. For these epidemiological research applications, whole-genome sequencing by NGS provides the highest data resolution. NGS may replace conventional approaches that were based on pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) by delivering single-base resolution across an entire bacterial genome. This high resolution can easily detect evolutionary changes at the highest level possible, distinguishing strains that may differ by as little as one variant. The standard approach involves whole-genome sequencing of isolates and then creating a minimum spanning tree using a gene-by-gene (allelic) approach.

MicroSEQ ID Software phylogenetic tree MicroSEQ ID Software phylogenetic tree.

Entire microbial communities can be profiled by extracting DNA from complex samples from sources such as deep ocean vents, soil, and the human gut, and then sequencing the bulk DNA. The introduction of next-generation sequencing to metagenome analysis has led to a new understanding of human metagenomes (Human Microbiome Project and MetaHIT) and has shed light on the relationship between human health and the microbiome.

Two primary approaches are used for metagenome analyses: targeted and shotgun metagenomics.

Targeted metagenomics

The 16S ribosomal RNA gene sequencing method is a highly effective and simple approach to identifying bacteria in a sample without the high background of host DNA sequences. 16S rDNA sequencing can effectively identify bacteria that may be missed by culture-based methods.

Next-generation sequencing products

Shotgun metagenomics

In the shotgun approach, the total nucleic acid is sequenced to get whole-genome sequences. Though whole-genome sequencing of the mixture of microbes provides higher resolution, it requires a substantially higher number of sequencing reads compared with targeted metagenomics, due to the sequencing reads contributed by the host organism and the computational effort required for the bioinformatics.

Next-generation sequencing products

The diversity of microbes

After decades of analyses and hundreds of studies, we’ve learned the diversity of microbes is even greater than imagined. And the diversity of these species tells us about the well-being of an ecosystem or how their interactions may be linked to diseases such as Inflammatory bowel disease, obesity, and chronic wounds. Hear how Dr. George Watts and Dr. Charles Li are using Ion 16S™ sequencing in their clinical and environmental research applications.

Microbial transcriptome analysis and metatranscriptomics

Sequencing all RNA species in a complex sample can provide an unbiased approach to detecting bacterial transcripts. With next-generation sequencing, unbiased information is obtained and novel transcripts can be detected.

Next-generation sequencing products

Publications