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.

Our Favorites¶

Increased Severity of Multidrug-Resistant Shigella sonnei Infections in People Experiencing Homelessness¶

Increased Severity of Multidrug-Resistant Shigella sonnei Infections in People Experiencing Homelessness published in November 2024 in Clinical Infectious Diseases, and from the diagnostic laboratory at Providence Health Care, used BugSeq to investigate an outbreak of Shigella sonnei in Vancouver, British Columbia.

Through this study the authors found that:

The primary population characteristics in people experiencing shigellosis shifted from sexual transmission, to likely environmental transmission in people experiencing homelessness
This shift corresponded to an increased severity of disease over time
More severe disease was associated with a particular clade of S. sonnei that was resistant to first- and second-line antimicrobials

The authors utilized BugSeq’s refMLST outbreak analysis feature and showed that the maximum allelic distance between any two isolates within the clade of specimens that was associated with increased disease severity was 19 alleles, indicating clonality of these isolates. Furthermore, the authors were able to determine the genotypic determinants of resistance for many isolates within the clade associated with increased severity and used BugSeq to determine whether AMR genes were conserved in plasmids for isolates within this clade.

Stefanovic et al:

“Isolates belonging to the 3.6.1.1.2 genotype exhibited conserved plasmid composition and AMR mutations.”

Validation of an Automated, End-to-End Metagenomic Sequencing Assay for Agnostic Detection of Respiratory Viruses¶

The BugSeq team was excited to publish the results of our first BARDA-funded project, where we collaborated with researchers at the University of British Columbia, Vancouver Coastal Health, and the BC Centre for Disease Control to develop and validate an automated end-to-end metagenomic sequencing assay for agnostic detection of viral pathogens.

The study, published in April 2024 in The Journal of Infectious Diseases, outlined the optimization and automation of the RAPID-mNGS assay; an ONT-powered metagenomic sequencing assay that is optimized for use with BugSeq analysis. We showed that we could achieve sample-to-result in less than 12-hours at comparable cost to multiplex molecular diagnostic panels. Our team performed a robust analytical and clinical validation study, where we demonstrated the ability of RAPID-mNGS to detect novel or emerging pathogens through an in silico exercise, and showed that the assay is highly specific and sensitive for detection of respiratory viruses. Further details are also covered in our webinar with ONT.

Figure 3 from Gauthier et al. highlights the results from the clinical validation study on over 350 upper respiratory specimens collected from Vancouver General Hospital. Specificity was 100% overall, and we found that RAPID-mNGS demonstrated high sensitivity up to RT-PCR Ct 30. Furthermore, we showed that mNGS can be used semi-quanititatively for determination of viral loads when viral sequence reads are normalized to a quantified internal control.

Optimized bacterial community characterization through full-length 16S rRNA gene sequencing utilizing MinION nanopore technology¶

Sequencing of the 16S rRNA gene can be used for both characterization of microbial communities, as well as a robust method for microbial identification from isolates or clinical samples. In this study published in February 2024 in BMC Microbiology, Bertolo and colleagues compared different sample preparation and analysis methods (including BugSeq) and compared performance for taxonomic classification of 16S rRNA sequences from a defined microbial community.

The authors validated BugSeq and found that our 16S classification workflow performed very well against comparator pipelines in terms of classification accuracy.

Bertolo, Valido & Stoyanov:

“At the species taxonomic level, the BugSeq workflow was superior, with a Pearson correlation coefficient of 0.92.”

This paper highlights the value of long-read 16S rRNA sequencing for taxonomic classification of bacterial species, demonstrating the utility of this technology for rapid, direct-from-sample sequencing to classify bacterial species. The accuracy and clinically interpretable reports provided by BugSeq’s workflow provides clinical users with confidence using BugSeq to power their sequencing needs.

An outlook on 2025¶

We were amazed at the applications that infectious disease researchers and clinical laboratories chose to use sequencing for in 2024. 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 2025 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!