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Gauthier NPG, Chan W, Locher K, Smailus D, Coope R, Charles M, Jassem A, Kopetzky J, Chorlton SD, Manges AR. Validation of an automated, end-to-end metagenomic sequencing assay for agnostic detection of respiratory viruses. J Infect Dis 2024:jiae226. [PMID: 38696336 DOI: 10.1093/infdis/jiae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/16/2024] [Accepted: 04/26/2024] [Indexed: 05/04/2024] Open
Abstract
BACKGROUND Current molecular diagnostics are limited in the number and type of detectable pathogens. Metagenomic next generation sequencing (mNGS) is an emerging, and increasingly feasible, pathogen-agnostic diagnostic approach. Translational barriers prohibit the widespread adoption of this technology in clinical laboratories. We validate an end-to-end mNGS assay for detection of respiratory viruses. Our assay is optimized to reduce turnaround time, lower cost-per-sample, increase throughput, and deploy secure and actionable bioinformatic results. METHODS We validated our assay using residual nasopharyngeal swab specimens from Vancouver General Hospital (n = 359), RT-PCR-positive, or negative for Influenza, SARS-CoV-2, and RSV. We quantified sample stability, assay precision, the effect of background nucleic acid levels, and analytical limits of detection. Diagnostic performance metrics were estimated. RESULTS We report that our mNGS assay is highly precise, semi-quantitative, with analytical limits of detection ranging from 103-104 copies/mL. Our assay is highly specific (100%) and sensitive (61.9% Overall: 86.8%; RT-PCR Ct < 30). Multiplexing capabilities enable processing of up to 55-specimens simultaneously on an Oxford Nanopore GridION device, with results reported within 12-hours. CONCLUSIONS This study outlines the diagnostic performance and feasibility of mNGS for respiratory viral diagnostics, infection control, and public health surveillance. We addressed translational barriers to widespread mNGS adoption.
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Affiliation(s)
- Nick P G Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wilson Chan
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia
| | - Kerstin Locher
- Division of Medical Microbiology, Vancouver General Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Duane Smailus
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Robin Coope
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Marthe Charles
- Division of Medical Microbiology, Vancouver General Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Agatha Jassem
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Jennifer Kopetzky
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | | | - Amee R Manges
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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Chorlton SD. Ten common issues with reference sequence databases and how to mitigate them. Front Bioinform 2024; 4:1278228. [PMID: 38560517 PMCID: PMC10978663 DOI: 10.3389/fbinf.2024.1278228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Metagenomic sequencing has revolutionized our understanding of microbiology. While metagenomic tools and approaches have been extensively evaluated and benchmarked, far less attention has been given to the reference sequence database used in metagenomic classification. Issues with reference sequence databases are pervasive. Database contamination is the most recognized issue in the literature; however, it remains relatively unmitigated in most analyses. Other common issues with reference sequence databases include taxonomic errors, inappropriate inclusion and exclusion criteria, and sequence content errors. This review covers ten common issues with reference sequence databases and the potential downstream consequences of these issues. Mitigation measures are discussed for each issue, including bioinformatic tools and database curation strategies. Together, these strategies present a path towards more accurate, reproducible and translatable metagenomic sequencing.
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Ritchie G, Chorlton SD, Matic N, Bilawka J, Gowland L, Leung V, Stefanovic A, Romney MG, Lowe CF. WGS of a cluster of MDR Shigella sonnei utilizing Oxford Nanopore R10.4.1 long-read sequencing. J Antimicrob Chemother 2024; 79:55-60. [PMID: 37965757 DOI: 10.1093/jac/dkad346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
OBJECTIVES To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR). METHODS WGS was performed on S. sonnei isolates identified from stool and blood between September 2021 and October 2022. Bacterial DNA from clinical isolates was extracted on the MagNA Pure 24 and sequenced on the GridION utilizing R10.4.1 flowcells. Phenotypic antimicrobial susceptibility testing was interpreted based on CLSI breakpoints. Sequencing data were processed with BugSeq, and AMR was assessed with BugSplit and ResFinder. RESULTS Fifty-six isolates were sequenced, including 53 related to the cluster of cases. All cluster isolates were identified as S. sonnei by sequencing, with global genotype 3.6.1.1.2 (CipR.MSM5), MLST 152 and PopPUNK cluster 3. Core genome MLST (cgMLST, examining 2513 loci) and reference-based MLST (refMLST, examining 4091 loci) both confirmed the clonality of the isolates. Cluster isolates were resistant to ampicillin (blaTEM-1), trimethoprim/sulfamethoxazole (dfA1, dfrA17; sul1, sul2), azithromycin (ermB, mphA) and ciprofloxacin (gyrA S83L, gyrA D87G, parC S80I). No genomic predictors of resistance to carbapenems were identified. CONCLUSIONS WGS with R10.4.1 enabled rapid sequencing and identification of an MDR S. sonnei community cluster. Genetic predictors of AMR were concordant with phenotypic antimicrobial susceptibility testing.
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Affiliation(s)
- Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Samuel D Chorlton
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jennifer Bilawka
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
| | - Leah Gowland
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Providence Health Care, 1081 Burrard St., Vancouver, BC V6Z 1Y6, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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Ritchie G, Leung V, Himsworth CG, Byers KA, Lee LKF, Chorlton SD, Stefanovic A, Romney MG, Matic N, Lowe CF. No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community. Microbiol Spectr 2023; 11:e0477722. [PMID: 37255425 PMCID: PMC10434041 DOI: 10.1128/spectrum.04777-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/03/2023] [Indexed: 06/01/2023] Open
Abstract
During an investigation into a cluster of Shigella flexneri serotype 2a cases in an underserved community, we assessed the relatedness of human and rat S. flexneri isolates utilizing a novel PCR targeting insertion sites (IS-PCR) of mobile elements in the Shigella genome characteristic of the cluster strain. Whole-genome sequences of S. flexneri (n = 50) associated with the cluster were analyzed. De novo genome assemblies were analyzed by a Geneious V10.2.6 motif search, and two unique IS were identified in all human Shigella sequences of the local cluster. Hydrolysis probe PCR assays were designed to detect these sequences consisting of forward and reverse primers to amplify across each insertion site and a hydrolysis probe spanning the insertion site. IS-PCR was performed for three Shigella PCR-positive culture-negative rat intestine specimens from this community. Both insertion sites were detected in the de novo genome assemblies of all clinical S. flexneri isolates (n = 50). Two of the three PCR-positive culture-negative rat samples were positive for both unique ISs identified in the human S. flexneri isolates, suggesting that the rat Shigella species strains were closely related to the human strains in the cluster. The cycle threshold (Ct) values were >35, indicating that the bacterial load was very low in the rat samples. Two unique IS were identified in clinical isolates from a community S. flexneri cluster. Both IS targets were identified in PCR-positive (Shigella spp.), culture-negative rat tissue and clinical isolates from humans, indicating relatedness. IMPORTANCE This article describes a novel molecular method to show relatedness between bacterial infections, which may not be able to grow in the laboratory due to treatment with antibiotics or for bacteria requiring unique conditions to grow well. Uniquely, we applied this technique to Shigella isolates from human cases associated with a local cluster in an underserved community, as well as rat samples from the same community. We believe that this novel approach can serve as a complementary method to support outbreak/cluster investigation for Shigella spp.
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Affiliation(s)
- Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University British Columbia, Vancouver, British Columbia, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University British Columbia, Vancouver, British Columbia, Canada
| | - Chelsea G. Himsworth
- British Columbia Regional Centre, Canadian Wildlife Health Cooperative, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kaylee A. Byers
- British Columbia Regional Centre, Canadian Wildlife Health Cooperative, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- Pacific Institute on Pathogens, Pandemics and Society, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Lisa K. F. Lee
- British Columbia Regional Centre, Canadian Wildlife Health Cooperative, Abbotsford, British Columbia, Canada
- Department of Veterinary Pathology, Western College of Veterinary Medicine, Saskatoon, Saskatchewan, Canada
| | - Samuel D. Chorlton
- Department of Pathology and Laboratory Medicine, University British Columbia, Vancouver, British Columbia, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University British Columbia, Vancouver, British Columbia, Canada
| | - Marc G. Romney
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University British Columbia, Vancouver, British Columbia, Canada
| | - Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University British Columbia, Vancouver, British Columbia, Canada
| | - Christopher F. Lowe
- Division of Medical Microbiology and Virology, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University British Columbia, Vancouver, British Columbia, Canada
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Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
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Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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Coope RJN, Matic N, Pandoh PK, Corbett RD, Smailus DE, Pleasance S, Lowe CF, Ritchie G, Chorlton SD, Young M, Ally AA, Asano JK, Carlsen RE, Chahal SS, Zhao Y, Holmes DT, Romney MG, Jones SJM, Marra MA. Automated Library Construction and Analysis for High-Throughput Nanopore Sequencing of SARS-CoV-2. J Appl Lab Med 2022; 7:1025-1036. [PMID: 35723286 PMCID: PMC9384306 DOI: 10.1093/jalm/jfac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/23/2022] [Indexed: 11/23/2022]
Abstract
Background To support the implementation of high-throughput pipelines suitable for SARS-CoV-2 sequencing and analysis in a clinical laboratory, we developed an automated sample preparation and analysis workflow. Methods We used the established ARTIC protocol with approximately 400 bp amplicons sequenced on Oxford Nanopore’s MinION. Sequences were analyzed using Nextclade, assigning both a clade and quality score to each sample. Results A total of 2179 samples on twenty-five 96-well plates were sequenced. Plates of purified RNA were processed within 12 h, sequencing required up to 24 h, and analysis of each pooled plate required 1 h. The use of samples with known threshold cycle (Ct) values enabled normalization, acted as a quality control check, and revealed a strong correlation between sample Ct values and successful analysis, with 85% of samples with Ct < 30 achieving a “good” Nextclade score. Less abundant samples responded to enrichment with the fraction of Ct > 30 samples achieving a “good” classification rising by 60% after addition of a post-ARTIC PCR normalization. Serial dilutions of 3 variant of concern samples, diluted from approximately Ct = 16 to approximately Ct = 50, demonstrated successful sequencing to Ct = 37. The sample set contained a median of 24 mutations per sample and a total of 1281 unique mutations with reduced sequence read coverage noted in some regions of some samples. A total of 10 separate strains were observed in the sample set, including 3 variants of concern prevalent in British Columbia in the spring of 2021. Conclusions We demonstrated a robust automated sequencing pipeline that takes advantage of input Ct values to improve reliability.
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Affiliation(s)
- Robin J N Coope
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Nancy Matic
- Department of Pathology and Laboratory Medicine, Saint Paul’s Hospital , Vancouver, BC , Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC , Canada
| | - Pawan K Pandoh
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Richard D Corbett
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Duane E Smailus
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Stephen Pleasance
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Christopher F Lowe
- Department of Pathology and Laboratory Medicine, Saint Paul’s Hospital , Vancouver, BC , Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC , Canada
| | - Gordon Ritchie
- Department of Pathology and Laboratory Medicine, Saint Paul’s Hospital , Vancouver, BC , Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC , Canada
| | - Samuel D Chorlton
- Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC , Canada
| | - Matthew Young
- Department of Pathology and Laboratory Medicine, Saint Paul’s Hospital , Vancouver, BC , Canada
| | - Adrian A Ally
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Jennifer K Asano
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Rebecca E Carlsen
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Sundeep S Chahal
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
| | - Daniel T Holmes
- Department of Pathology and Laboratory Medicine, Saint Paul’s Hospital , Vancouver, BC , Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC , Canada
| | - Marc G Romney
- Department of Pathology and Laboratory Medicine, Saint Paul’s Hospital , Vancouver, BC , Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia , Vancouver, BC , Canada
| | - Steven J M Jones
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
- Department of Medical Genetics, University of British Columbia , Vancouver, BC , Canada
| | - Marco A Marra
- Canada’s Michael Smith Genome Sciences Centre at BC Cancer , Vancouver, BC , Canada
- Department of Medical Genetics, University of British Columbia , Vancouver, BC , Canada
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Gauthier NPG, Nelson C, Bonsall MB, Locher K, Charles M, MacDonald C, Krajden M, Chorlton SD, Manges AR. Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples. PLoS One 2021; 16:e0259712. [PMID: 34793508 PMCID: PMC8601544 DOI: 10.1371/journal.pone.0259712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES The COVID-19 pandemic has underscored the need for rapid novel diagnostic strategies. Metagenomic Next-Generation Sequencing (mNGS) may allow for the detection of pathogens that can be missed in targeted assays. The goal of this study was to assess the performance of nanopore-based Sequence-Independent Single Primer Amplification (SISPA) for the detection and characterization of SARS-CoV-2. METHODS We performed mNGS on clinical samples and designed a diagnostic classifier that corrects for barcode crosstalk between specimens. Phylogenetic analysis was performed on genome assemblies. RESULTS Our assay yielded 100% specificity overall and 95.2% sensitivity for specimens with a RT-PCR cycle threshold value less than 30. We assembled 10 complete, and one near-complete genomes from 20 specimens that were classified as positive by mNGS. Phylogenetic analysis revealed that 10/11 specimens from British Columbia had a closest relative to another British Columbian specimen. We found 100% concordance between phylogenetic lineage assignment and Variant of Concern (VOC) PCR results. Our assay was able to distinguish between the Alpha and Gamma variants, which was not possible with the current standard VOC PCR being used in British Columbia. CONCLUSIONS This study supports future work examining the broader feasibility of nanopore mNGS as a diagnostic strategy for the detection and characterization of viral pathogens.
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Affiliation(s)
- Nick P G Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cassidy Nelson
- Mathematical Ecology Research Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Michael B Bonsall
- Mathematical Ecology Research Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kerstin Locher
- Division of Medical Microbiology, Vancouver General Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marthe Charles
- Division of Medical Microbiology, Vancouver General Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Clayton MacDonald
- Division of Medical Microbiology, Vancouver General Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Samuel D Chorlton
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- BugSeq Bioinformatics Inc, Vancouver, British Columbia, Canada
| | - Amee R Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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Chorlton SD, Ritchie G, Lawson T, McLachlan E, Romney MG, Matic N, Lowe CF. Next-generation sequencing for cytomegalovirus antiviral resistance genotyping in a clinical virology laboratory. Antiviral Res 2021; 192:105123. [PMID: 34174249 DOI: 10.1016/j.antiviral.2021.105123] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 11/26/2022]
Abstract
INTRODUCTION The identification of CMV antiviral drug resistance (AVDR) is a critical diagnostic test for immunocompromised patients with CMV infection and a failure of virologic response on optimal antiviral treatment. We developed a next-generation sequencing (NGS) assay for CMV AVDR testing and compared the AVDR mutations identified by NGS to Sanger sequencing. METHODS Retrospective review of CMV AVDR testing requests for UL97 and UL54 at our laboratory from 2014 to 2019 was conducted. NGS was performed on the MinION and compared to Sanger sequencing performed at the national reference laboratory. Analysis of the sequences was completed with a novel cloud bioinformatics platform (BugSeq). RESULTS Twenty patient samples previously characterized were included for study on the MinION. NGS captured all of the CMV AVDR mutations identified by Sanger, and identified additional mutations in UL97 and/or UL54 in 8/13 (62%) of the samples. An analysis of the depth of coverage at which we no longer detected minority single nucleotide variants (SNVs) detected in the original data was conducted, estimating a recall of 95% at 1800 fold coverage. CONCLUSION NGS utilizing MinION technology for the detection of CMV AVDR mutations identified additional minority variants in UL97 and UL54 as compared with Sanger sequencing. Through the application of a bioinformatics pipeline available online, our NGS process eliminates barriers associated with the use of the MinION and NGS in clinical laboratories.
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Affiliation(s)
- Samuel D Chorlton
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Gordon Ritchie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada
| | - Elizabeth McLachlan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Marc G Romney
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada
| | - Nancy Matic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada
| | - Christopher F Lowe
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada.
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Abstract
Readhead et al. recently reported in Neuron the detection and association of human herpesviruses 6A (HHV6A) and 7 (HHV7) with Alzheimer's disease by shotgun sequencing. I was skeptical of the specificity of their modified Viromescan bioinformatics method and subsequent analysis for numerous reasons. Using their supplementary data, the prevalence of variola virus, the etiological agent of the eradicated disease smallpox, can be calculated at 97.5% of their Mount Sinai Brain Bank dataset. Reanalysis of Readhead et al.'s data using highly sensitive and specific alternative methods finds no HHV7 reads in their samples; HHV6A reads were found in only 2 out of their top 15 samples sorted by reported HHV6A abundance. Finally, recreation of Readhead et al.'s modified Viromescan method identifies reasons for its low specificity.
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Affiliation(s)
- Samuel D Chorlton
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
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10
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Fan J, Huang S, Chorlton SD. BugSeq: a highly accurate cloud platform for long-read metagenomic analyses. BMC Bioinformatics 2021; 22:160. [PMID: 33765910 PMCID: PMC7993542 DOI: 10.1186/s12859-021-04089-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/18/2021] [Indexed: 12/21/2022] Open
Abstract
Background As the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification (ie. determining the composition of a sample) in a fast and accurate manner are needed. Existing tools were either designed for short-read data (eg. Centrifuge), take days to analyse modern sequencer outputs (eg. MetaMaps) or suffer from suboptimal accuracy (eg. CDKAM). Additionally, all tools require command line expertise and do not scale in the cloud. Results We present BugSeq, a novel, highly accurate metagenomic classifier for nanopore reads. We evaluate BugSeq on simulated data, mock microbial communities and real clinical samples. On the ZymoBIOMICS Even and Log communities, BugSeq (F1 = 0.95 at species level) offers better read classification than MetaMaps (F1 = 0.89–0.94) in a fraction of the time. BugSeq significantly improves on the accuracy of Centrifuge (F1 = 0.79–0.93) and CDKAM (F1 = 0.91–0.94) while offering competitive run times. When applied to 41 samples from patients with lower respiratory tract infections, BugSeq produces greater concordance with microbiological culture and qPCR compared with “What’s In My Pot” analysis. Conclusion BugSeq is deployed to the cloud for easy and scalable long-read metagenomic analyses. BugSeq is freely available for non-commercial use at https://bugseq.com/free. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04089-5.
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Affiliation(s)
- Jeremy Fan
- BugSeq Bioinformatics Inc, Vancouver, BC, Canada
| | - Steven Huang
- BugSeq Bioinformatics Inc, Vancouver, BC, Canada
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Zou J, Chorlton SD, Romney MG, Payne M, Lawson T, Wong A, Champagne S, Ritchie G, Lowe CF. Phenotypic and Genotypic Correlates of Penicillin Susceptibility in Nontoxigenic Corynebacterium diphtheriae, British Columbia, Canada, 2015-2018. Emerg Infect Dis 2021; 26:97-103. [PMID: 31855139 PMCID: PMC6924910 DOI: 10.3201/eid2601.191241] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In 2015, the Clinical and Laboratory Standards Institute (CLSI) updated its breakpoints for penicillin susceptibility in Corynebacterium species from <1 mg/L to <0.12 mg/L. We assessed the effect of this change on C. diphtheriae susceptibility reported at an inner city, tertiary care center in Vancouver, British Columbia, Canada, during 2015–2018 and performed whole-genome sequencing to investigate phenotypic and genotypic resistance to penicillin. We identified 44/45 isolates that were intermediately susceptible to penicillin by the 2015 breakpoint, despite meeting previous CLSI criteria for susceptibility. Sequencing did not reveal β-lactam resistance genes. Multilocus sequence typing revealed a notable predominance of sequence type 76. Overall, we saw no evidence of penicillin nonsusceptibility at the phenotypic or genotypic level in C. diphtheriae isolates from our institution. The 2015 CLSI breakpoint change could cause misclassification of penicillin susceptibility in C. diphtheriae isolates, potentially leading to suboptimal antimicrobial treatment selection.
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Chorlton SD. Adjunctive bradyzoite-directed therapy for reducing complications of congenital toxoplasmosis. Med Hypotheses 2019; 133:109376. [PMID: 31472369 DOI: 10.1016/j.mehy.2019.109376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/18/2019] [Indexed: 11/25/2022]
Abstract
Congenital toxoplasmosis is caused by in utero infection of the fetus with the intracellular parasite Toxoplasma gondii. Upon infection, the parasite forms life-long cysts in fetal brain and eyes which are resistant to the currently accepted therapy of pyrimethamine and sulfadiazine. These cysts commonly reactivate later in life causing chorioretinitis and visual impairment, and rarely cause neurological complications. I hypothesize that adjunctive, bradyzoite-directed therapies have the potential to alleviate a significant burden of disease by reducing cyst burden in neonatal brain and eyes. Atovaquone is perhaps the most promising drug for further evaluation given its low side-effect profile, established safety, and efficacy in animal models reducing cyst burden. Very limited observational data in humans suggests atovaquone may prevent Toxoplasma-associated chorioretinitis recurrence. Clinical trials are needed to evaluate it and other potential drugs as adjunctive treatment in congenital toxoplasmosis.
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Affiliation(s)
- Samuel D Chorlton
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
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