Microbiology
Understanding organisms, behavior, resistance mechanisms, and clinical significance across viral, bacterial, and fungal infections.
What We Do
Our approach: science, systems, and strategy.
Theiagen operationalizes pathogen genomics by aligning scientific depth, technology infrastructure, and an engagement strategy built around where each organization is starting.
Science
The full range of bioinformatics disciplines - working together.
Theiagen’s scientific depth spans microbiology, bioinformatics, epidemiology, and software systems - the complete range of disciplines required to understand and operationalize pathogens at a genomic level. Most organizations have one or two. We have all of them, and what is essential is we know how they work together.
Bioinformatics
Processing, analyzing, and interpreting genomic sequence data at scale.
Epidemiology
Connecting genomic findings to population-level patterns, transmission, and public health response.
Software systems
Building tools, NGS pipelines, and platforms that make genomic programs operational, scalable, and sustainable.
Science
Sequencing capabilities
Theiagen supports the sequencing approaches needed to answer pathogen questions across isolated organisms and complex samples.
Isolate Sequencing (WGS)
Whole genome sequencing of individual strains for deep characterization, including antimicrobial resistance, virulence factors, phylogenetics, and strain classification.
Targeted Metagenomics
Selective enrichment using multiplex amplicon or hybrid-capture methods to detect and characterize critical pathogens, antimicrobial resistance genes, or other microbial targets in complex samples.
Full Metagenomics
Community-level sequencing that reveals microbial diversity, functional potential, and ecological dynamics across clinical, food, and environmental samples.
Science
Pathogen expertise in practice
Bacterial Infections
Expertise
- Antimicrobial resistance surveillance (AMR)
- Foodborne pathogen investigations
- Healthcare-associated infections (HAI)
- Nontuberculous Mycobacteria (NTM) investigations
Our Work
- NTM healthcare-associated transmission investigation case study
- Accelerating Bioinformatics Implementation in Public Health (2023)
Viral Infections
Expertise
- SARS-CoV-2 surveillance
- Emerging viral threats
- Population-scale genomic epidemiology
Fungal Infections
Expertise
- Candida auris surveillance
- Antifungal resistance monitoring
- Outbreak investigations
Science
Example applications
- Surveillance
SARS-CoV-2, influenza, enterics, healthcare-associated infections (HAIs), and emerging bacterial, viral, and fungal pathogens
- Outbreak Response
Healthcare-associated infections and foodborne outbreaks
- Antimicrobial Resistance
Bacterial and fungal resistance monitoring
- Laboratory Modernization
Workflow implementation, workforce enablement, and quality management systems
- Data Standards & Interoperability
Containerized bioinformatics workflows, INSDC, Pathogen Data Object Model, and NCBI data submissions
- Genomic Epidemiology
Facility, local, regional, national, and international investigations
Systems
The technology layer that connects genomic science to real decisions.
Theiagen builds and integrates the pipelines, platforms, and data infrastructure - Nextflow, WDL, Terra, Manifold, cloud and on-premises environments - that turn raw sequencing data into clear, defensible outputs. Our cloud-based genomic analysis capabilities scale from single-lab deployments to statewide surveillance networks. We work within what you already have rather than asking you to start over.
NGS pipeline automation
Standardized, reproducible workflows that reduce manual handling and make analysis sustainable at scale.
Cloud-based genomic analysis
Infrastructure that scales from single-lab deployments to statewide surveillance networks.
Data management software
Configuration and integration that support QC, reporting, collaboration, and defensible decisions.
Strategy
Every engagement is structured around exactly what you need.
Because every client’s situation is different, we listen first. Then we structure an approach - using Build, Train, or Support, or a combination of all three - around what your organization actually requires. Nothing more, nothing less.
Need the right starting point?
We can help assess where your science, systems, and strategy are aligned - and where they need support.