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  • 4 min read

Bringing Precision Medicine to the ICU: Insights from BugSeq Grant Recipient Dr. Georgios Kitsios

UPMC In 2024, BugSeq awarded a research grant to Dr. Georgios Kitsios, physician-scientist and Associate Professor of Medicine at the University of Pittsburgh. Dr. Kitsios leads innovative research in applying metagenomic sequencing to critical care medicine—specifically, tackling the challenge of ventilator-associated pneumonia (VAP), a life-threatening infection that affects up to half of mechanically ventilated patients. Our team at BugSeq was excited by his team’s VAP-MAPS project, which is harnessing cutting-edge nanopore sequencing and advanced bioinformatics to bring rapid, actionable diagnostics to the ICU. We caught up with Dr. Kitsios to learn more about the project and how his team is using BugSeq to advance VAP diagnostics.

  • 10 min read

Enabling Phenotypic AMR Prediction from NGS Data with Expert-Augmented Machine Learning and Curated Databases

Detecting and understanding antimicrobial resistance (AMR) is a critical challenge in modern microbiology, with far-reaching implications for public health and clinical decision-making. In a previous blog post, BugSeq’s Approach to AMR, we outlined the importance of combining genomic insights with machine learning (ML) to enhance AMR detection. However, not all computational approaches to AMR prediction enable the same accuracy, insight, and power. In this post, we discuss the advantages and limitations of different approaches and demonstrate how the approach BugSeq takes—expert-augmented machine learning combined with a curated AMR database—offers a more robust, interpretable, and powerful path for phenotypic AMR prediction (genomic AST).

  • 7 min read

H1 2025 Platform Update: AI-Driven Insights, Phenotypic AMR Prediction, Advanced Fungal Genomics, and Next-Generation Surveillance Tools from BugSeq

The first half of 2025 marked a significant leap forward for the BugSeq platform, delivering powerful new capabilities to tackle the most pressing challenges in infectious disease. We’re introducing AI-powered report summaries to accelerate interpretation, leading accuracy AMR phenotype prediction (coming in a separate blog post), advanced fungal diagnostics to combat emerging pathogens, and next-generation surveillance tools that fuse genomic and epidemiological data. These updates are engineered to empower laboratories with deeper insights, greater accuracy, and faster time to action.

  • 4 min read

Data-Driven Infection Control Using BugSeq’s Isolate Clustering and Insights

Infection control poses a daunting challenge for clinical microbiology labs: pathogens are constantly evolving, and outbreaks can spread with alarming speed. Timely, accurate insights are the key to staying ahead, preventing outbreaks before they happen and rapidly mitigating them when they do. BugSeq’s Infection Control solutions currently help hundreds of labs be proactive about infection control. By harnessing advanced clustering methods and real-time insights, we empower laboratories and healthcare facilities to detect, track, and prevent the spread of infectious diseases more efficiently than ever.

  • 5 min read

Supporting Bioinformatics in a Regulated Environment

Next-generation sequencing is enabling a new paradigm of microbiology assays within the clinical and public health laboratory. These assays are enabling identification of microorganisms from culture or directly from sample, study of antimicrobial resistance, and investigation of relatedness between isolates.While many of these assays are used for surveillance purposes, with global changes to many regulatory frameworks, there is a growing need for assays that can be used in a regulated environment. BugSeq is invested in enabling reporting from our results to improve human health. Below, we detail some of the unique capabilities of BugSeq to enable integration into mission-critical assays.

  • 5 min read

Our Favorite Publications of 2024

2024 was another incredible year for sequencing in diagnostic and public health labs. As sequencing moves closer to routine use for clinical and public health microbiology, we are amazed by the breadth of sequencing applications that microbiologists, epidemiologists, and laboratory scientists are using to reduce the burden of infectious diseases.

As we approach 2025, and what will assuredly be another year of innovation for sequencing in the infectious disease field, we took the opportunity to look back at some of our favorite publications of 2024. We were amazed by the range of applications that public health professionals were choosing to use sequencing for; this list includes studies using sequencing for outbreak investigation, antimicrobial resistance prediction, and agnostic pathogen detection.

  • 3 min read

In 2023, Trust for America’s Health (TFAH) released “The Impact of Chronic Underfunding on America’s Public Health System: Trends, Risks and Recommendations”. This report highlights the important role that public health systems, and the laboratories that underpin them, play in the protection and improvement of well-being and prosperity for the nation and the world. Yet, according to the report, “for over two decades, the country’s public health system has not received the level of funding needed to ensure it meets the nation’s public health needs.” Public health laboratories continue to fight for reduction of morbidity and mortality in their communities despite reduced resources. Here, we detail how BugSeq is enabling public health laboratories to achieve this goal using the policy recommendations of the TFAH report.

  • 7 min read

BugSeq’s Approach to AMR

Introduction

Antimicrobial resistance (AMR) poses a major threat to human and animal health. In 2019 alone, there were an estimated 1.27 million deaths attributable to AMR, and that number has likely grown since. For each person with an infection, AMR reduces the likelihood that they are treated with effective antimicrobials and recover from infection. Faster, more accurate detection of AMR from clinical, biothreat and surveillance samples is of paramount importance to curb the global burden of disease attributable to AMR. Prediction of phenotypic AMR using DNA (and RNA!) sequencing is a promising avenue to achieve this goal. At BugSeq, we have focused on combating AMR since our inception; to date, we have predicted AMR for hundreds of thousands of genomes. We often get questions about how our AMR analysis works; below, we detail our goals, latest approaches and updated thinking to bioinformatic analysis for AMR prediction.

  • 3 min read

BugSeq Bioinformatics Inc. Collaborative Effort to Develop and Validate an end-to-end Agnostic Diagnostic Assay Published

Introduction

BugSeq partnered with University of British Columbia Researchers, along with clinical and public health collaborators at Vancouver Coastal Health, BC Centre for Disease Control, and Canada’s Michael Smith Genome Sciences Centre to develop, automate, and validate an end-to-end metagenomic sequencing assay for agnostic detection of respiratory viral pathogens within 12-hours. The work was funded by the Biomedical Advanced Research and Development Authority (BARDA), part of the Administration for Strategic Preparedness and Response within the U.S. Department of Health and Human Services under contract number 75A50122C00027.

The results of this collaborative project were published last week in The Journal of Infectious Diseases. Gauthier et al. outlined the development and validation of a metagenomic sequencing assay, termed Rapid Pathogen Identification through Metagenomic Next-Generation Sequencing (RAPID-mNGS).