2025¶

Our Favorite Publications of 2025

2025 has been a definitive year for the adoption of next-generation sequencing (NGS) in clinical microbiology. We have moved beyond asking if sequencing should be used, to demonstrating how it solves problems that traditional microbiology cannot.

As we look forward to 2026, we took the opportunity to look back at some of our favorite publications from the past year. These studies showcase the versatility of BugSeq, from untangling diagnostic discrepancies to tracking high-priority fungal threats and characterizing emerging pathogens.

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

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.

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).

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.

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.

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.