Accelerating the implementation of genomics technologies for actionable insights
We are a dedicated team of experts determined to enhance public health outcomes through the innovative implementation of NGS and bioinformatics technologies. Together, we draw upon experience from academic, governmental, and industry careers to deliver a world-leading service across a diverse range of microbial genomics applications, including infectious disease, food safety, molecular diagnostics, and environmental monitoring.
Pathogen genomics is crucial to many modern public health, diagnostics, environmental monitoring and food safety approaches. It enables the identification and tracking of disease-causing microbes while aiding in the development of effective treatments, policies and disease prevention strategies.
Next-generation sequencing (NGS) plays a pivotal role in pathogen genomics. It offers a means to read the genetic code of disease-causing microbes and it provides critical insights into microbial diversity, evolution and key virulence factors.
Here at Theiagen Genomics, we utilize the latest NGS approaches, develop helpful resources and train personnel to the highest level. We seamlessly integrate technology and build capacity in your workflows as your expert partner in pathogen genomics.
Pathogen genomics requires highly technical expertise to be done well. That’s why we offer personalized training in the latest sequencing and bioinformatics technologies tailored to your needs.
Whether it’s on-site or remote, one hour or one week, our training experts can equip your team with the skills they need to excel.
Our comprehensive support goes beyond technical assistance – it includes a deep understanding of your data, providing flexible terms and generating key insights for workflow innovation.
Whether your project is large or small, we offer the same support regardless of your scale or throughput needs.
Team up with Theiagen today and leverage our expertise for your success.
Upload your data directly or import it from your sequencing instrument for a seamless transfer, or retrieve it from a public or private repository.
We piece together genetic information from your data to form a genome assembly. Then, we conduct Quality Control (QC), functional characterization, drug resistance and virulence prediction and pathogen specific characterization steps.
We generate comprehensive reports to serve as your project guide. We present your results and findings in an easy-to-read format that supports further research and proactive decision-making.
We map the evolutionary history and relationships between different organisms within your sample. We guide you to evaluate pathogen risk and pinpoint optimal solutions.
Share your data with the wider scientific community by depositing it into a public repository to ensure that your findings contribute to the broader body of knowledge. Our experts can help with the complex challenge to best practices.
Read about how our work has enabled peer-reviewed scientific papers.
"This study sought to detect and characterize persistent infection cases in California using routine epidemiologic and genomic surveillance data. We identified 69 persistent infection cases with collection dates between January 2021 and July 2023 ranging from 21 to 400 days in duration, with an average of 44 days."
"This study sought to detect and characterize persistent infection cases in California using routine epidemiologic and genomic surveillance data. We identified 69 persistent infection cases with collection dates between January 2021 and July 2023 ranging from 21 to 400 days in duration, with an average of 44 days."
"Colorectal cancer (CRC) is the fourth most common cancer and the third leading cause of cancer-related mortality worldwide, with incidence rising among younger populations. The significant clinical and economic burden highlights the need for minimally invasive technologies capable of detecting pre-malignant and early-stage disease."
"Colorectal cancer (CRC) is the fourth most common cancer and the third leading cause of cancer-related mortality worldwide, with incidence rising among younger populations. The significant clinical and economic burden highlights the need for minimally invasive technologies capable of detecting pre-malignant and early-stage disease."
"We conducted a retrospective study to explore molecular insights into human respiratory syncytial virus (HRSV) group B strains among patients attending outpatient clinics at government medical facilities both prior and during the onset of Influenza A/H1N1/2009 pandemic outbreak."
"We conducted a retrospective study to explore molecular insights into human respiratory syncytial virus (HRSV) group B strains among patients attending outpatient clinics at government medical facilities both prior and during the onset of Influenza A/H1N1/2009 pandemic outbreak."
"To address the challenges of sharing lower quality datasets, PHA4GE has developed a set of standardized contextual data tags, namely fields and terms, that can be included in public repository submissions as a means of flagging pathogen sequence data with known quality issues, increasing their discoverability."
"To address the challenges of sharing lower quality datasets, PHA4GE has developed a set of standardized contextual data tags, namely fields and terms, that can be included in public repository submissions as a means of flagging pathogen sequence data with known quality issues, increasing their discoverability."
"In the face of scarce public health resources, it is critical to understand which disease surveillance strategies are effective, yet such validation has historically been difficult. From May 1 to December 31, 2021, a cohort study was carried out in Santa Clara County, California, in which 10,131 high-quality genomic sequences from COVID-19 polymerase chain reaction tests were merged with disease surveillance data."
"In the face of scarce public health resources, it is critical to understand which disease surveillance strategies are effective, yet such validation has historically been difficult. From May 1 to December 31, 2021, a cohort study was carried out in Santa Clara County, California, in which 10,131 high-quality genomic sequences from COVID-19 polymerase chain reaction tests were merged with disease surveillance data."
"Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens."
"Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens."
"A Candida auris outbreak has been ongoing in Southern Nevada since August 2021. In this manuscript we describe the sequencing of over 200 C. auris isolates from patients at several facilities."
"A Candida auris outbreak has been ongoing in Southern Nevada since August 2021. In this manuscript we describe the sequencing of over 200 C. auris isolates from patients at several facilities."
"The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations."
"The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations."
" We invite readers to consider the content that has been generated. Specifically: levels of quality, comprehensiveness, textual accuracy and the AI’s reasoning of the ethical implications of its own existence."
" We invite readers to consider the content that has been generated. Specifically: levels of quality, comprehensiveness, textual accuracy and the AI’s reasoning of the ethical implications of its own existence."
"The coronavirus disease 2019 (COVID-19) pandemic has provided a stage to illustrate that there is considerable value in obtaining rapid, whole-genome–based information about pathogens. This article describes the utility of a commercially available, automated severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) library preparation, genome sequencing, and a bioinformatics analysis pipeline to provide rapid, near–real-time SARS-CoV-2 variant description."
"The coronavirus disease 2019 (COVID-19) pandemic has provided a stage to illustrate that there is considerable value in obtaining rapid, whole-genome–based information about pathogens. This article describes the utility of a commercially available, automated severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) library preparation, genome sequencing, and a bioinformatics analysis pipeline to provide rapid, near–real-time SARS-CoV-2 variant description."
"Whole genome sequencing (WGS) of clinical bacterial isolates has the potential to transform the fields of diagnostics and public health. To realize this potential, bioinformatic software that reports identification results needs to be developed that meets the quality standards of a diagnostic test. We developed GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) using k-mer based strategies for identification of bacteria based on WGS reads."
"Whole genome sequencing (WGS) of clinical bacterial isolates has the potential to transform the fields of diagnostics and public health. To realize this potential, bioinformatic software that reports identification results needs to be developed that meets the quality standards of a diagnostic test. We developed GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) using k-mer based strategies for identification of bacteria based on WGS reads."
"Staphylococcus aureus is a major cause of bacteremia and other hospital-acquired infections. The cell-wall active antibiotic vancomycin is commonly used to treat both methicillin-resistant (MRSA) and sensitive (MSSA) infections. Vancomycin intermediate S. aureus (VISA) variants can arise through de novo mutations. Here, we performed pilot experiments to develop a combined PCR/long-read sequencing-based method for detection of previously known VISA-causing mutations."
"Staphylococcus aureus is a major cause of bacteremia and other hospital-acquired infections. The cell-wall active antibiotic vancomycin is commonly used to treat both methicillin-resistant (MRSA) and sensitive (MSSA) infections. Vancomycin intermediate S. aureus (VISA) variants can arise through de novo mutations. Here, we performed pilot experiments to develop a combined PCR/long-read sequencing-based method for detection of previously known VISA-causing mutations."
"Cases of reinfection with SARS-CoV-2 are well-documented. Efforts to determine the frequency of the phenomenon have been made and have shown that the occurrence may be rare to date. The true incidence of reinfection is difficult to determine due to the possibility that secondary infections are harder to detect due to decreased or absent symptoms or less testing. The frequency of reinfection cases will increase over time, as more cases in the human population denotes more opportunities for the phenomenon, but also because genomic variation in the virus over the course of pandemic time can lead to variants that can evade immunities "
"Cases of reinfection with SARS-CoV-2 are well-documented. Efforts to determine the frequency of the phenomenon have been made and have shown that the occurrence may be rare to date. The true incidence of reinfection is difficult to determine due to the possibility that secondary infections are harder to detect due to decreased or absent symptoms or less testing. The frequency of reinfection cases will increase over time, as more cases in the human population denotes more opportunities for the phenomenon, but also because genomic variation in the virus over the course of pandemic time can lead to variants that can evade immunities "
"We aimed to estimate the frequency of mcr-9 among CRE cases within the GA EIP catchment area and to compare clinical outcomes and microbiological, genomic, and clinical characteristics of mcr-9-positive and mcr-9-negative cases."
"We aimed to estimate the frequency of mcr-9 among CRE cases within the GA EIP catchment area and to compare clinical outcomes and microbiological, genomic, and clinical characteristics of mcr-9-positive and mcr-9-negative cases."
The purpose of this pilot study was to evaluate the effectiveness of mold sanitation in homes that suffered hurricane-related water damage.
The purpose of this pilot study was to evaluate the effectiveness of mold sanitation in homes that suffered hurricane-related water damage.
A case report is presented of an individual who had two distinct COVID-19 illnesses from genetically distinct SARS-CoV-2 agents.
A case report is presented of an individual who had two distinct COVID-19 illnesses from genetically distinct SARS-CoV-2 agents.
Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs. To determine the variants of SARS-CoV-2 circulating in the state of Nevada, specimens from 200 COVID-19 patients were sequenced through our robust sequencing platform, which enabled sequencing of SARS-CoV-2 from specimens with even very low viral loads, without the need of culture-based amplification.
Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs. To determine the variants of SARS-CoV-2 circulating in the state of Nevada, specimens from 200 COVID-19 patients were sequenced through our robust sequencing platform, which enabled sequencing of SARS-CoV-2 from specimens with even very low viral loads, without the need of culture-based amplification.
Kalamari is a resource that supports genomic epidemiology and pathogen surveillance. It consists of representative genomes and common contaminants. Kalamari also contains a custom taxonomy and software for downloading and formatting the data.
Kalamari is a resource that supports genomic epidemiology and pathogen surveillance. It consists of representative genomes and common contaminants. Kalamari also contains a custom taxonomy and software for downloading and formatting the data.
Abstract The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants constitute a challenge for public health authorities worldwide. Recombinant variants, composed of two or more SARS-CoV-2 lineages, often have unknown impacts on transmission, immune escape, and virulence in the early stages of emergence. We examined 4213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 in California to describe regional and statewide trends in prevalence.
Abstract The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants constitute a challenge for public health authorities worldwide. Recombinant variants, composed of two or more SARS-CoV-2 lineages, often have unknown impacts on transmission, immune escape, and virulence in the early stages of emergence. We examined 4213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 in California to describe regional and statewide trends in prevalence.
Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather than for surveillance or interventions.
Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather than for surveillance or interventions.
California COVIDNet, a collaborative initiative for SARS-CoV-2 genomic surveillance, involved 50 partners and overcame data and computational challenges. Since March 2021, it has sequenced over 450,000 genomes, contributing to nearly 800,000 in total, covering all California regions and representing over 5% of the state's positive tests.
California COVIDNet, a collaborative initiative for SARS-CoV-2 genomic surveillance, involved 50 partners and overcame data and computational challenges. Since March 2021, it has sequenced over 450,000 genomes, contributing to nearly 800,000 in total, covering all California regions and representing over 5% of the state's positive tests.
Public health labs rapidly adopted whole-genome sequencing for SARS-CoV-2, leading to the development of COVIDNet by the California Department of Public Health. This scalable, cloud-based initiative serves as a model for worldwide public health labs, offering insights into bioinformatics, genomic surveillance, best practices for data sharing, and enhancing collaboration between laboratory scientists and epidemiologists.
Public health labs rapidly adopted whole-genome sequencing for SARS-CoV-2, leading to the development of COVIDNet by the California Department of Public Health. This scalable, cloud-based initiative serves as a model for worldwide public health labs, offering insights into bioinformatics, genomic surveillance, best practices for data sharing, and enhancing collaboration between laboratory scientists and epidemiologists.
We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories (PHLs). Bioinformatics implementation for public health requires practitioners to undertake standardized bioinformatic analyses and generate reproducible, validated and auditable results.
We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories (PHLs). Bioinformatics implementation for public health requires practitioners to undertake standardized bioinformatic analyses and generate reproducible, validated and auditable results.
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