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.
Our Favorites¶
High-Throughput Surveillance of Candida auris¶
Yield of an Active Candida auris Molecular Surveillance Program at a Tertiary Care Cancer Center, from the team at Memorial Sloan Kettering Cancer Center and published in The Journal of Molecular Diagnostics, showcases the power of sequencing in infection prevention.
Candida auris remains a critical threat in healthcare settings. In this extensive surveillance program spanning several years, the authors combined PCR screening with whole-genome sequencing to monitor this pathogen in a high-risk population.
Using sequencing, the authors leveraged BugSeq to:
- Conclusively classify the majority of isolates as Clade I, with a single isolate identified as Clade III.
- Link molecular mechanisms of antifungal resistance with phenotype
- Demonstrate integration of genomic and epidemiologic investigation for infection control, with identification of probable transmission
This study also underscores BugSeq’s strength in fungal genomics. By enabling accurate identification and characterization, BugSeq enables microbiology laboratories to change the management of fungal infections beyond classic fungal culture.
Solving Diagnostic Mysteries: A blaCTX-M-27 Variant Discovery¶
Evaluation of the NG-Test® CTX-M MULTI lateral flow immunoassay and genomic discovery of a blaCTX-M-27 variant with a premature stop codon, published in Diagnostic Microbiology and Infectious Disease, highlights a critical strength of genomic analysis: understanding and resolving phenotypic-genotypic discordance.
In this study, the authors evaluated a lateral flow immunoassay for ESBL detection. When they encountered a discrepancy where the rapid test was negative but molecular signals suggested the presence of a resistance gene, they turned to sequencing.
Through genomic characterization, the team discovered:
- A blaCTX-M-27 variant harboring a premature stop codon.
- This mutation rendered the enzyme non-functional, explaining why the phenotypic and lateral flow tests were negative despite the gene’s presence.
This highlights BugSeq’s ability to go beyond simple “gene detection.” Our platform provides the granular, sequence-level detail necessary to understand the mechanism of resistance, ensuring that labs aren’t misled by the mere presence of a gene sequence. Read more about our AMR prediction in a recent blog post.
Characterizing Emerging Pathogens: Mycobacterium wolinskyi Endocarditis¶
Mycobacterium wolinskyi as an emerging cause of pacemaker pocket infection and lead endocarditis: a case report and genomic characterization, published in ASM Case Reports, demonstrates the necessity of NGS for rare and fastidious organisms.
The authors described a complex case of a pacemaker pocket infection caused by Mycobacterium wolinskyi, a rapidly growing non-tuberculous mycobacterium (NTM). In cases involving rare pathogens, traditional identification methods can be ambiguous or slow.
Through genomic characterization, the study provided:
- Definitive identification of the pathogen at the species level.
- Comprehensive genomic profiling to support clinical decision-making.
This study highlights BugSeq’s industry-leading taxonomic resolution - the authors performed a detailed investigation of the isolate’s identity and showed BugSeq came out on top with both 16S and WGS taxonomic accuracy. Whether it is a common pathogen or a rare NTM causing complex endocarditis, our workflow delivers the accurate identification clinicians need.
An Outlook for 2026¶
We were amazed at the applications that infectious disease researchers and clinical laboratories chose to use sequencing for in 2025. Together, these studies highlighted the range of applications that our users have utilized BugSeq for, including tracking outbreaks, detecting pathogens, monitoring antimicrobial resistance, and more!
As we look forward to the future of next-generation sequencing technology into 2026 and beyond, we believe that clinical and public health users will continue to expand their use of NGS technology for pathogen detection and public health surveillance. To this effect, BugSeq has made strides in bioinformatic accuracy, reproducibility, and reporting to power our users’ sequencing analysis in applied settings. Stay tuned in the new year for more exciting developments on how BugSeq is continuing to lead the way in providing accurate, comprehensive, and actionable bioinformatic solutions for infectious disease applications!
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A full list of publications citing BugSeq is available on the BugSeq website.