Real-time infectious disease outbreak investigations with nanopore sequencing and BugSeq analysis
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Infectious disease outbreaks continue to pose significant challenges to public health, and solutions are needed that enable real-time, comprehensive genomic characterisation of pathogens and antimicrobial resistance.
In this webinar, we will hear from medical microbiologists sharing their experiences detecting and tracking bacterial outbreaks by implementing real-time sequencing with Oxford Nanopore and analysis with BugSeq, as an end to end solution. Discover how rapid, accessible sequencing and analysis in microbiology laboratories enables swift and accurate investigation of bacterial community clusters, antimicrobial resistance profiling, and contributes to outbreak management.
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Meet the speakers
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Christopher Lowe, Medical Microbiologist, Providence Health CareDr. Lowe completed medical school at the University of British Columbia, and residency in Medical Microbiology at the University of Toronto. He has been a Medical Microbiologist and Infection Prevention and Control physician at Providence Health Care since 2013. Within Microbiology, his area of focus has been in clinical virology and molecular diagnostics, including clinical applications of next-generation sequencing. In addition to his clinical responsibilities, he has been the Program Director for the UBC Medical Microbiology Residency Training Program since 2015, and a Clinical Professor in the Department of Pathology and Laboratory Medicine at UBC.
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Sherif Nour, Director of Sales & Marketing, BugSeqSherif leads Sales and Customer Success with BugSeq. His main focus is in enabling labs to adopt and scale their sequencing through BugSeq's premium bioinformatics platform and in house expert support.
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Gordon Ritchie, Molecular Scientist,, Providence Health CareGordon Ritchie (Ph.D., DABCC, FNACB) is a Clinical Scientist at St. Paul’s Hospital in Vancouver, and a Clinical Associate Professor at UBCThe University of British Columbia (UBC). After completing his Ph.D. in Experimental Medicine from UBC, Gordon spent six years at SKMC Hospital, Abu Dhabi, UAE as a Molecular Scientist and has been St. Paul’s Hospital for the past 16 years. Gordon has over 10 years’ experience using NGS next-generation sequencing (NGS) techniques for molecular diagnostics and has several publications using NGS for bacterial and viral whole genome sequencing, and targeted amplicon sequencing for antiviral drug resistance testing.
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Aaron Pomerantz, Associate Director, Segment Marketing - Infectious and Applied Markets, Oxford Nanopore TechnologiesAaron received his PhD from UC Berkeley in the Department of Integrative Biology, employing genomics, genome editing, and bioimaging techniques in non-model organisms, as well as in-field nanopore sequencing in the Amazon rainforest. In his role as Associate Director of Global Segment Marketing at Oxford Nanopore, he covers synthetic biology, microbiology and infectious disease.
Mobile genetic elements are considered to be the most efficient intra- and interspecies transfer of antimicrobial resistance determinants in bacteria. We investigated the clonality and genetic background of four NDM-5 positive Escherichia coli isolates within a German hospital using short-read (MiSeq, Ilumina) and long-read sequencing (MinION™, Oxford Nanopore Technologies), cgMLST analysis (Ridom SeqSphere+) and MOB-suite integrated into BugSeq (https://bugseq.com/), an automated bioinformatics platform. Our results showed that the clinical E. coli isolates were unrelated and NDM-5 was plasmid-encoded. In addition, the backbone of two NDM-5-encoding plasmids aligned and had the same cluster ID, while the remaining plasmids had different backbones and cluster IDs, which were confirmed by the BugSeq platform and our in-house workflow. These data underline the critical contribution of whole genome sequencing in tracking plasmid dissemination as well as a user-friendly application of bioinformatics pipelines for analysing bacterial genomes and plasmids.
Mobile genetic elements are considered to be the most efficient intra- and interspecies transfer of antimicrobial resistance determinants in bacteria. We investigated the clonality and genetic background of four NDM-5 positive Escherichia coli isolates within a German hospital using short-read (MiSeq, Ilumina) and long-read sequencing (MinION™, Oxford Nanopore Technologies), cgMLST analysis (Ridom SeqSphere+) and MOB-suite integrated into BugSeq (https://bugseq.com/), an automated bioinformatics platform. Our results showed that the clinical E. coli isolates were unrelated and NDM-5 was plasmid-encoded. In addition, the backbone of two NDM-5-encoding plasmids aligned and had the same cluster ID, while the remaining plasmids had different backbones and cluster IDs, which were confirmed by the BugSeq platform and our in-house workflow. These data underline the critical contribution of whole genome sequencing in tracking plasmid dissemination as well as a user-friendly application of bioinformatics pipelines for analysing bacterial genomes and plasmids.
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Kyriaki Xanthopoulou, Postdoctoral research fellow, University of Cologne
