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Guo J, Brassard D, Adam N, Verster AJ, Shay JA, Miville-Godin C, Janta-Polczynski M, Ferreira J, Mounier M, Pilar AV, Tapp K, Classen A, Shiu M, Charlebois D, Petronella N, Weedmark K, Corneau N, Veres T. Automated centrifugal microfluidic system for the preparation of adaptor-ligated sequencing libraries. LAB ON A CHIP 2024; 24:182-196. [PMID: 38044704 DOI: 10.1039/d3lc00781b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The intensive workload associated with the preparation of high-quality DNA libraries remains a key obstacle toward widespread deployment of sequencing technologies in remote and resource-limited areas. We describe the development of single-use microfluidic devices driven by an advanced pneumatic centrifugal microfluidic platform, the PowerBlade, to automate the preparation of Illumina-compatible libraries based on adaptor ligation methodology. The developed on-chip workflow includes enzymatic DNA fragmentation coupled to end-repair, adaptor ligation, first DNA cleanup, PCR amplification, and second DNA cleanup. This complex workflow was successfully integrated into simple thermoplastic microfluidic devices that are amenable to mass production with injection molding. The system was validated by preparing, on chip, libraries from a mixture of genomic DNA extracted from three common foodborne pathogens (Listeria monocytogenes, Escherichia coli and Salmonella enterica serovar Typhimurium) and comparing them with libraries made via a manual procedure. The two types of libraries were found to exhibit similar quality control metrics (including genome coverage, assembly, and relative abundances) and led to nearly uniform coverage independent of GC content. This microfluidic technology offers a time-saving and cost-effective alternative to manual procedures and robotic-based automation, making it suitable for deployment in remote environments where technical expertise and resources might be scarce. Specifically, it facilitates field practices that involve mid- to low-throughput sequencing, such as tasks related to foodborne pathogen detection, characterization, and microbial profiling.
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Affiliation(s)
- Jimin Guo
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Daniel Brassard
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Nadine Adam
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Adrian J Verster
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Julie A Shay
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Caroline Miville-Godin
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Mojra Janta-Polczynski
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Jason Ferreira
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Maxence Mounier
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Ana V Pilar
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Kyle Tapp
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Adam Classen
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Matthew Shiu
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
| | - Denis Charlebois
- Canadian Space Agency, 6767 Route de l'Aéroport, Saint-Hubert, QC J3Y 8Y9, Canada
| | - Nicholas Petronella
- Bureau of Food Surveillance and Science Integration, Bioinformatics High-Capacity Computing Laboratory, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Kelly Weedmark
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Nathalie Corneau
- Bureau of Microbial Hazards, Microbiology Research Division, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
| | - Teodor Veres
- Medical Devices Research Center, Life Sciences Division, National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC, J4B 6Y4, Canada.
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Poates A, Truong J, Lindsey R, Griswold T, Williams-Newkirk AJ, Carleton H, Trees E. Sequencing of Enteric Bacteria: Library Preparation Procedure Matters for Accurate Identification and Characterization. Foodborne Pathog Dis 2022; 19:569-578. [PMID: 35861967 DOI: 10.1089/fpd.2022.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Enzymatic library preparation kits are increasingly used for bacterial whole genome sequencing. While they offer a rapid workflow, the transposases used in the kits are recognized to be somewhat biased. The aim of this study was to optimize and validate a protocol for the Illumina DNA Prep kit (formerly Nextera DNA Flex) for sequencing enteric pathogens and compare its performance against the Nextera XT kit. One hundred forty-three strains of Campylobacter, Escherichia, Listeria, Salmonella, Shigella, and Vibrio were prepared with both methods and sequenced on the Illumina MiSeq using 300 and/or 500 cycle chemistries. Sequences were compared using core genome multilocus sequence typing (cgMLST), 7-gene multilocus sequence typing (MLST), and detection of markers encoding serotype, virulence, and antimicrobial resistance. Sequences for one Escherichia strain were downsampled to determine the minimum coverage required for the analyses. While organism-specific differences were observed, the Prep libraries generated longer average read lengths and less fragmented assemblies compared to the XT libraries. In downstream analysis, the most notable difference between the kits was observed for Escherichia, particularly for the 300 cycle sequences. The O group was not predicted in 32% and 4% of XT sequences when using blast and kmer algorithms, respectively, while the O group was predicted from all Prep sequences regardless of the algorithm. In addition, the ehxA gene was not detected in 6% of XT sequences and 34% were missing one or more of the type III secretion systems and/or plasmid-associated genes, which were detected in the Prep sequences. The coverage downsampling revealed that acceptable assembly quality and allele detection was achieved at 30 × coverage with the Prep libraries, whereas 40-50 × coverage was required for the XT libraries. The better performance of the Prep libraries was attributed to more even coverage, particularly in genome regions low in GC content.
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Affiliation(s)
- Angela Poates
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jenny Truong
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Rebecca Lindsey
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Taylor Griswold
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Heather Carleton
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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3
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Segerman B, Ástvaldsson Á, Mustafa L, Skarin J, Skarin H. The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content. Front Microbiol 2022; 13:944770. [PMID: 35910628 PMCID: PMC9330563 DOI: 10.3389/fmicb.2022.944770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
Whole-genome sequencing (WGS) is becoming the new standard for bacterial high-resolution typing and the performance of laboratories is being evaluated in interlaboratory comparisons. The use of the Illumina Nextera XT library preparation kit has been found to be associated with poorer performance due to a GC-content-dependent coverage bias. The bias is especially strong when sequencing low GC-content species. Here, we have made an in-depth analysis of the Nextera XT coverage bias problem using data from a proficiency test of the low GC-content species Campylobacter jejuni. We have compared Nextera XT with Nextera Flex/DNA Prep and examined the consequences on downstream WGS analysis when using different quantities of raw data. We have also analyzed how the coverage bias relates to differential usage of tagmentation cleavage sites. We found that the tagmentation site was characterized by a symmetrical motif with a central AT-rich region surrounded by Gs and Cs. The Gs and Cs appeared to be the main determinant for cleavage efficiency and the genomic regions that were associated with low coverage only contained low-efficiency cleavage sites. This explains why low GC-content genomes and regions are more subjected to coverage bias. We furthermore extended our analysis to other datasets representing other bacterial species. We visualized how the coverage bias was large in low GC-content species such as C. jejuni, C. coli, Staphylococcus aureus, and Listeria monocytogenes, whereas species with neutral GC-content such as Salmonella enterica and Escherichia coli were only affected in certain regions. Species with high GC-content such as Mycobacterium tuberculosis and Pseudomonas aeruginosa were hardly affected at all. The coverage bias associated with Nextera XT was not found when Nextera Flex/DNA Prep had been used.
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Affiliation(s)
- Bo Segerman
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- *Correspondence: Bo Segerman,
| | - Ásgeir Ástvaldsson
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Linda Mustafa
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Joakim Skarin
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Biology, Swedish Food Agency, Uppsala, Sweden
| | - Hanna Skarin
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
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Distribution of Common and Rare Genetic Markers of Second-Line-Injectable-Drug Resistance in Mycobacterium tuberculosis Revealed by a Genome-Wide Association Study. Antimicrob Agents Chemother 2022; 66:e0207521. [PMID: 35532237 DOI: 10.1128/aac.02075-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Point mutations in the rrs gene and the eis promoter are known to confer resistance to the second-line injectable drugs (SLIDs) amikacin (AMK), capreomycin (CAP), and kanamycin (KAN). While mutations in these canonical genes confer the majority of SLID resistance, alternative mechanisms of resistance are not uncommon and threaten effective treatment decisions when using conventional molecular diagnostics. In total, 1,184 clinical Mycobacterium tuberculosis isolates from 7 countries were studied for genomic markers associated with phenotypic resistance. The markers rrs:A1401G and rrs:G1484T were associated with resistance to all three SLIDs, and three known markers in the eis promoter (eis:G-10A, eis:C-12T, and eis:C-14T) were similarly associated with kanamycin resistance (KAN-R). Among 325, 324, and 270 AMK-R, CAP-R, and KAN-R isolates, 274 (84.3%), 250 (77.2%), and 249 (92.3%) harbored canonical mutations, respectively. Thirteen isolates harbored more than one canonical mutation. Canonical mutations did not account for 103 of the phenotypically resistant isolates. A genome-wide association study identified three genes and promoters with mutations that, on aggregate, were associated with unexplained resistance to at least one SLID. Our analysis associated whiB7 5'-untranslated-region mutations with KAN resistance, supporting clinical relevance for this previously demonstrated mechanism of KAN resistance. We also provide evidence for the novel association of CAP resistance with the promoter of the Rv2680-Rv2681 operon, which encodes an exoribonuclease that may influence the binding of CAP to the ribosome. Aggregating mutations by gene can provide additional insight and therefore is recommended for identifying rare mechanisms of resistance when individual mutations carry insufficient statistical power.
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Yu MC, Hung CS, Huang CK, Wang CH, Liang YC, Lin JC. Integrative utility of long read sequencing-based whole genome analysis and phenotypic assay on differentiating isoniazid-resistant signature of Mycobacterium tuberculosis. J Biomed Sci 2021; 28:86. [PMID: 34922550 PMCID: PMC8684251 DOI: 10.1186/s12929-021-00783-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/18/2021] [Indexed: 11/10/2022] Open
Abstract
Background With the advancement of next generation sequencing technologies (NGS), whole-genome sequencing (WGS) has been deployed to a wide range of clinical scenarios. Rapid and accurate classification of drug-resistant Mycobacterium tuberculosis (MTB) would be advantageous in reducing the amplification of additional drug resistance and disease transmission. Methods In this study, a long-read sequencing approach was subjected to the whole-genome sequencing of clinical MTB clones with susceptibility test profiles, including isoniazid (INH) susceptible clones (n = 10) and INH resistant clones (n = 42) isolated from clinical specimens. Non-synonymous variants within the katG or inhA gene associated with INH resistance was identified using Nanopore sequencing coupled with a corresponding analytical workflow. Results In total, 54 nucleotide variants within the katG gene and 39 variants within the inhA gene associated with INH resistance were identified. Consistency among the results of genotypic profiles, susceptibility test, and minimal inhibitory concentration, the high-INH resistance signature was estimated using the area under the receiver operating characteristic curve with the existence of Ser315Thr (AUC = 0.822) or Thr579Asn (AUC = 0.875). Conclusions Taken together, we curated lists of coding variants associated with differential INH resistance using Nanopore sequencing, which may constitute an emerging platform for rapid and accurate identification of drug-resistant MTB clones.
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Affiliation(s)
- Ming-Chih Yu
- Division of Pulmonary Medicine, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Ching-Sheng Hung
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Chun-Kai Huang
- Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei, 11031, Taiwan
| | - Cheng-Hui Wang
- Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei, 11031, Taiwan
| | - Yu-Chih Liang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan. .,School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei, 11031, Taiwan.
| | - Jung-Chun Lin
- Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan. .,Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan. .,School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei, 11031, Taiwan.
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Wagner DD, Carleton HA, Trees E, Katz LS. Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks. PeerJ 2021; 9:e12446. [PMID: 34900416 PMCID: PMC8627651 DOI: 10.7717/peerj.12446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/18/2021] [Indexed: 11/25/2022] Open
Abstract
Background Whole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks. Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upon WGS data quality. Methods Raw, unprocessed WGS reads from Escherichia coli, Salmonella enterica, and Shigella sonnei outbreak clusters were characterized for four quality metrics: PHRED score, read length, library insert size, and ambiguous nucleotide composition. PHRED scores were strongly correlated with improved SNPs analysis results in E. coli and S. enterica clusters. Results Assembly quality showed only moderate correlations with PHRED scores and library insert size, and then only for Salmonella. To improve SNP analyses and assemblies, we compared seven read-healing pipelines to improve these four quality metrics and to see how well they improved SNP analysis and genome assembly. The most effective read healing pipelines for SNPs analysis incorporated quality-based trimming, fixed-width trimming, or both. The Lyve-SET SNPs pipeline showed a more marked improvement than the CFSAN SNP Pipeline, but the latter performed better on raw, unhealed reads. For genome assembly, SPAdes enabled significant improvements in healed E. coli reads only, while Skesa yielded no significant improvements on healed reads. Conclusions PHRED scores will continue to be a crucial quality metric albeit not of equal impact across all types of analyses for all enteric bacteria. While trimming-based read healing performed well for SNPs analyses, different read healing approaches are likely needed for genome assembly or other, emerging WGS analysis methodologies.
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Affiliation(s)
- Darlene D Wagner
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America.,Eagle Medical Services, LLC, Atlanta, GA, United States of America
| | - Heather A Carleton
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Eija Trees
- Association of Public Health Laboratories, Silver Spring, MD, United States of America
| | - Lee S Katz
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America.,Center for Food Safety, University of Georgia, Griffin, GA, United States of America
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7
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Evaluation of a high-throughput, cost-effective Illumina library preparation kit. Sci Rep 2021; 11:15925. [PMID: 34354114 PMCID: PMC8342411 DOI: 10.1038/s41598-021-94911-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
Library preparation for high-throughput sequencing applications is a critical step in producing representative, unbiased sequencing data. The iGenomX Riptide High Throughput Rapid Library Prep Kit purports to provide high-quality sequencing data with lower costs compared to other Illumina library kits. To test these claims, we compared sequence data quality of Riptide libraries to libraries constructed with KAPA Hyper and NEBNext Ultra. Across several single-source genome samples, mapping performance and de novo assembly of Riptide libraries were similar to conventional libraries prepared with the same DNA. Poor performance of some libraries resulted in low sequencing depth. In particular, degraded DNA samples may be challenging to sequence with Riptide. There was little cross-well plate contamination with the overwhelming majority of reads belong to the proper source genomes. The sequencing of metagenome samples using different Riptide primer sets resulted in variable taxonomic assignment of reads. Increased adoption of the Riptide kit will decrease library preparation costs. However, this method might not be suitable for degraded DNA.
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8
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Lau KA, Gonçalves da Silva A, Theis T, Gray J, Ballard SA, Rawlinson WD. Proficiency testing for bacterial whole genome sequencing in assuring the quality of microbiology diagnostics in clinical and public health laboratories. Pathology 2021; 53:902-911. [PMID: 34274166 DOI: 10.1016/j.pathol.2021.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/16/2021] [Accepted: 03/29/2021] [Indexed: 10/20/2022]
Abstract
The adoption of whole genome sequencing (WGS) data over the past decade for pathogen surveillance, and decision-making for infectious diseases has rapidly transformed the landscape of clinical microbiology and public health. However, for successful transition to routine use of these techniques, it is crucial to ensure the WGS data generated meet defined quality standards for pathogen identification, typing, antimicrobial resistance detection and surveillance. Further, the ongoing development of these standards will ensure that the bioinformatic processes are capable of accurately identifying and characterising organisms of interest, and thereby facilitate the integration of WGS into routine clinical and public health laboratory setting. A pilot proficiency testing (PT) program for WGS of infectious agents was developed to facilitate widely applicable standardisation and benchmarking standards for WGS across a range of laboratories. The PT participating laboratories were required to generate WGS data from two bacterial isolates, and submit the raw data for independent bioinformatics analysis, as well as analyse the data with their own processes and answer relevant questions about the data. Overall, laboratories used a diverse range of bioinformatics tools and could generate and analyse high-quality data, either meeting or exceeding the minimum requirements. This pilot has provided valuable insight into the current state of genomics in clinical microbiology and public health laboratories across Australia. It will provide a baseline guide for the standardisation of WGS and enable the development of a PT program that allows an ongoing performance benchmark for accreditation of WGS-based test processes.
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Affiliation(s)
| | - Anders Gonçalves da Silva
- Communicable Diseases Genomics Network (CDGN), Public Health Laboratory Network (PHLN), Australia; Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), The University of Melbourne at The Peter Doherty Institute for Immunity and Infection, Melbourne, Vic, Australia
| | | | - Joanna Gray
- RCPAQAP Biosecurity, St Leonards, NSW, Australia
| | - Susan A Ballard
- Communicable Diseases Genomics Network (CDGN), Public Health Laboratory Network (PHLN), Australia; Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), The University of Melbourne at The Peter Doherty Institute for Immunity and Infection, Melbourne, Vic, Australia
| | - William D Rawlinson
- Serology and Virology Division (SAViD) SEALS Microbiology, NSW Health Pathology, SOMS, BABS, Women's and Children's, University of NSW, Australia
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9
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Evaluating coverage bias in next-generation sequencing of Escherichia coli. PLoS One 2021; 16:e0253440. [PMID: 34166413 PMCID: PMC8224930 DOI: 10.1371/journal.pone.0253440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 06/05/2021] [Indexed: 01/18/2023] Open
Abstract
Whole-genome sequencing is essential to many facets of infectious disease research. However, technical limitations such as bias in coverage and tagmentation, and difficulties characterising genomic regions with extreme GC content have created significant obstacles in its use. Illumina has claimed that the recently released DNA Prep library preparation kit, formerly known as Nextera Flex, overcomes some of these limitations. This study aimed to assess bias in coverage, tagmentation, GC content, average fragment size distribution, and de novo assembly quality using both the Nextera XT and DNA Prep kits from Illumina. When performing whole-genome sequencing on Escherichia coli and where coverage bias is the main concern, the DNA Prep kit may provide higher quality results; though de novo assembly quality, tagmentation bias and GC content related bias are unlikely to improve. Based on these results, laboratories with existing workflows based on Nextera XT would see minor benefits in transitioning to the DNA Prep kit if they were primarily studying organisms with neutral GC content.
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10
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Nahar A, Baker AL, Nichols DS, Bowman JP, Britz ML. Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-Antarctic Rhodococcus and Williamsia Species. Microorganisms 2021; 9:microorganisms9061253. [PMID: 34207615 PMCID: PMC8227252 DOI: 10.3390/microorganisms9061253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Bacteria containing mycolic acids in their cell envelope are often recalcitrant to cell lysis, so extracting DNA of sufficient quality for third-generation sequencing and high-fidelity genome assembly requires optimization, even when using commercial kits with protocols for hard-to-lyse bacteria. We benchmarked three spin-column-based kits against a classical DNA extraction method employing lysozyme, proteinase K and SDS for six lysozyme-resistant, sub-Antarctic strains of Corynebaceriales. Prior cultivation in broths containing glycine at highly growth-inhibitory concentrations (4.0–4.5%) improved cell lysis using both classical and kit methods. The classical method produced DNA with average fragment sizes of 27–59 Kbp and tight fragment size ranges, meeting quality standards for genome sequencing, assembly and phylogenomic analyses. By 16S rRNA gene sequencing, we classified two strains as Williamsia and four strains as Rhodococcus species. Pairwise comparison of average nucleotide identity (ANI) and alignment fraction (AF), plus genome clustering analysis, confirmed Rhodococcus sp. 1163 and 1168 and Williamsia sp. 1135 and 1138 as novel species. Phylogenetic, lipidomic and biochemical analyses classified psychrotrophic strains 1139 and 1159 as R. qingshengii and R. erythropolis, respectively, using ANI similarity of >98% and AF >60% for species delineation. On this basis, some members of the R. erythropolis genome cluster groups, including strains currently named as R. enclensis, R. baikonurensis, R. opacus and R. rhodochrous, would be reclassified either as R. erythropolis or R. qingshengii.
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Affiliation(s)
- Akhikun Nahar
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
- Correspondence: (A.N.); (M.L.B.)
| | - Anthony L. Baker
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
| | - David S. Nichols
- Central Science Laboratory, Division of Research, University of Tasmania, Hobart, TAS 7005, Australia;
| | - John P. Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
| | - Margaret L. Britz
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7005, Australia; (A.L.B.); (J.P.B.)
- Correspondence: (A.N.); (M.L.B.)
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11
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Ransom EM, Potter RF, Dantas G, Burnham CAD. Genomic Prediction of Antimicrobial Resistance: Ready or Not, Here It Comes! Clin Chem 2021; 66:1278-1289. [PMID: 32918462 DOI: 10.1093/clinchem/hvaa172] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/01/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) technologies are being used to predict antimicrobial resistance. The field is evolving rapidly and transitioning out of the research setting into clinical use. Clinical laboratories are evaluating the accuracy and utility of genomic resistance prediction, including methods for NGS, downstream bioinformatic pipeline components, and the clinical settings in which this type of testing should be offered. CONTENT We describe genomic sequencing as it pertains to predicting antimicrobial resistance in clinical isolates and samples. We elaborate on current methodologies and workflows to perform this testing and summarize the current state of genomic resistance prediction in clinical settings. To highlight this aspect, we include 3 medically relevant microorganism exemplars: Mycobacterium tuberculosis, Staphylococcus aureus, and Neisseria gonorrhoeae. Last, we discuss the future of genomic-based resistance detection in clinical microbiology laboratories. SUMMARY Antimicrobial resistance prediction by genomic approaches is in its infancy for routine patient care. Genomic approaches have already added value to the current diagnostic testing landscape in specific circumstances and will play an increasingly important role in diagnostic microbiology. Future advancements will shorten turnaround time, reduce costs, and improve our analysis and interpretation of clinically actionable results.
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Affiliation(s)
- Eric M Ransom
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Robert F Potter
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Gautam Dantas
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO.,Departments of Pediatrics and Medicine, Washington University School of Medicine, St. Louis, MO
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12
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Haendiges J, Jinneman K, Gonzalez-Escalona N. Choice of library preparation affects sequence quality, genome assembly, and precise in silico prediction of virulence genes in shiga toxin-producing Escherichia coli. PLoS One 2021; 16:e0242294. [PMID: 33761524 PMCID: PMC7990515 DOI: 10.1371/journal.pone.0242294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/04/2021] [Indexed: 11/24/2022] Open
Abstract
Whole genome sequencing (WGS) provides essential public health information and is used worldwide for pathogen surveillance, epidemiology, and source tracking. Foodborne pathogens are often sequenced using rapid library preparation chemistries based on transposon technology; however, this method may miss random segments of genomes that can be important for accurate downstream analyses. As new technologies become available, it may become possible to achieve better overall coverage. Here we compare the sequence quality obtained using libraries prepared from the Nextera XT and Nextera DNA Prep (Illumina, San Diego, CA) chemistries for 31 Shiga toxin-producing Escherichia coli (STEC) O121:H19 strains, which had been isolated from flour during a 2016 outbreak. The Nextera DNA Prep gave superior performance metrics including sequence quality, assembly quality, uniformity of genome coverage, and virulence gene identification, among other metrics. Comprehensive detection of virulence genes is essential for making educated assessments of STECs virulence potential. The phylogenetic SNP analysis did not show any differences in the variants detected by either library preparation method which allows isolates prepared from either library method to be analysed together. Our comprehensive comparison of these chemistries should assist researchers wishing to improve their sequencing workflow for STECs and other genomic risk assessments.
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Affiliation(s)
- Julie Haendiges
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
- * E-mail: (JH); (NGE)
| | - Karen Jinneman
- Office of Regulatory Affairs, Food and Drug Administration, Bothell, Washington, United States of America
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, United States of America
- * E-mail: (JH); (NGE)
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13
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Modlin SJ, Robinhold C, Morrissey C, Mitchell SN, Ramirez-Busby SM, Shmaya T, Valafar F. Exact mapping of Illumina blind spots in the Mycobacterium tuberculosis genome reveals platform-wide and workflow-specific biases. Microb Genom 2021; 7. [PMID: 33502304 PMCID: PMC8190613 DOI: 10.1099/mgen.0.000465] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Whole-genome sequencing (WGS) is fundamental to Mycobacterium tuberculosis basic research and many clinical applications. Coverage across Illumina-sequenced M. tuberculosis genomes is known to vary with sequence context, but this bias is poorly characterized. Here, through a novel application of phylogenomics that distinguishes genuine coverage bias from deletions, we discern Illumina ‘blind spots’ in the M. tuberculosis reference genome for seven sequencing workflows. We find blind spots to be widespread, affecting 529 genes, and provide their exact coordinates, enabling salvage of unaffected regions. Fifty-seven pe/ppe genes (the primary families assumed to exhibit Illumina bias) lack blind spots entirely, while the remaining pe/ppe genes account for 55.1 % of blind spots. Surprisingly, we find coverage bias persists in homopolymers as short as 6 bp, shorter tracts than previously reported. While G+C-rich regions challenge all Illumina sequencing workflows, a modified Nextera library preparation that amplifies DNA with a high-fidelity polymerase markedly attenuates coverage bias in G+C-rich and homopolymeric sequences, expanding the ‘Illumina-sequenceable’ genome. Through these findings, and by defining workflow-specific exclusion criteria, we spotlight effective strategies for handling bias in M. tuberculosis Illumina WGS. This empirical analysis framework may be used to systematically evaluate coverage bias in other species using existing sequencing data.
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Affiliation(s)
- Samuel J Modlin
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Cassidy Robinhold
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Christopher Morrissey
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Scott N Mitchell
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Sarah M Ramirez-Busby
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Tal Shmaya
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Faramarz Valafar
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, School of Public Health, San Diego State University, San Diego, CA 92182, USA
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14
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Tegally H, San JE, Giandhari J, de Oliveira T. Unlocking the efficiency of genomics laboratories with robotic liquid-handling. BMC Genomics 2020; 21:729. [PMID: 33081689 PMCID: PMC7576741 DOI: 10.1186/s12864-020-07137-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/11/2020] [Indexed: 02/08/2023] Open
Abstract
In research and clinical genomics laboratories today, sample preparation is the bottleneck of experiments, particularly when it comes to high-throughput next generation sequencing (NGS). More genomics laboratories are now considering liquid-handling automation to make the sequencing workflow more efficient and cost effective. The question remains as to its suitability and return on investment. A number of points need to be carefully considered before introducing robots into biological laboratories. Here, we describe the state-of-the-art technology of both sophisticated and do-it-yourself (DIY) robotic liquid-handlers and provide a practical review of the motivation, implications and requirements of laboratory automation for genome sequencing experiments.
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Affiliation(s)
- Houriiyah Tegally
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa.
| | - James Emmanuel San
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa
| | - Jennifer Giandhari
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa
| | - Tulio de Oliveira
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, K-RITH Tower Building, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa.
- Department of Global Health, University of Washington, 908 Jefferson Street, 13th Floor, Seattle, WA, 98104, USA.
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15
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Uelze L, Borowiak M, Bönn M, Brinks E, Deneke C, Hankeln T, Kleta S, Murr L, Stingl K, Szabo K, Tausch SH, Wöhlke A, Malorny B. German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing. Front Microbiol 2020; 11:573972. [PMID: 33013811 PMCID: PMC7516015 DOI: 10.3389/fmicb.2020.573972] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/14/2020] [Indexed: 12/05/2022] Open
Abstract
We compared the consistency, accuracy and reproducibility of next-generation short read sequencing between ten laboratories involved in food safety (research institutes, state laboratories, universities and companies) from Germany and Austria. Participants were asked to sequence six DNA samples of three bacterial species (Campylobacter jejuni, Listeria monocytogenes and Salmonella enterica) in duplicate, according to their routine in-house sequencing protocol. Four different types of Illumina sequencing platforms (MiSeq, NextSeq, iSeq, NovaSeq) and one Ion Torrent sequencing instrument (S5) were involved in the study. Sequence quality parameters were determined for all data sets and centrally compared between laboratories. SNP and cgMLST calling were performed to assess the reproducibility of sequence data collected for individual samples. Overall, we found Illumina short read data to be more accurate (higher base calling accuracy, fewer miss-assemblies) and consistent (little variability between independent sequencing runs within a laboratory) than Ion Torrent sequence data, with little variation between the different Illumina instruments. Two laboratories with Illumina instruments submitted sequence data with lower quality, probably due to the use of a library preparation kit, which shows difficulty in sequencing low GC genome regions. Differences in data quality were more evident after assembling short reads into genome assemblies, with Ion Torrent assemblies featuring a great number of allele differences to Illumina assemblies. Clonality of samples was confirmed through SNP calling, which proved to be a more suitable method for an integrated data analysis of Illumina and Ion Torrent data sets in this study.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Markus Bönn
- Landesamt für Verbraucherschutz Sachsen-Anhalt (LAV), Halle (Saale), Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut (MRI), Kiel, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, AG Molecular Genetics and Genome Analysis, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Sylvia Kleta
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Larissa Murr
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - Kerstin Stingl
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Kathrin Szabo
- Department 5, Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Anne Wöhlke
- Food and Veterinary Institute, Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Braunschweig, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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16
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Uelze L, Borowiak M, Deneke C, Szabó I, Fischer J, Tausch SH, Malorny B. Reply to Li et al., "GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently Affect Salmonella Serotype Prediction Using SeqSero2". Appl Environ Microbiol 2020; 86:e01260-20. [PMID: 32680857 PMCID: PMC7480391 DOI: 10.1128/aem.01260-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Laura Uelze
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Maria Borowiak
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Carlus Deneke
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - István Szabó
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Jennie Fischer
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Simon H Tausch
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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17
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Dohál M, Porvazník I, Pršo K, Rasmussen EM, Solovič I, Mokrý J. Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and sequencing data analysis. Tuberculosis (Edinb) 2020; 123:101946. [PMID: 32741530 DOI: 10.1016/j.tube.2020.101946] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022]
Abstract
The numbers of patients with tuberculosis (TB) caused by resistant strains are still alarming. Therefore, it is necessary to determine resistance more quickly and precisely, than it is with the currently used phenotypic and genotypic methods. In recent years, technological advances have been made and the whole-genome sequencing (WGS) method has been introduced as a part of routine diagnostics in clinical laboratories. Comparing a wide range of mycobacterial genomic variations with a reference genome leads to a consistent evaluation of molecular-epidemiology and resistance of Mycobacterium tuberculosis (M. tuberculosis) to a wide range of anti-TB drugs. The quality of the obtained sequencing data is closely related to the type of sample and the method used for DNA extraction and sequencing library preparation. Moreover, the correct interpretation of results is also influenced by a bioinformatic data processing. A large number of bioinformatics pipelines are currently available, the sensitivity of which varies due to the different sizes of databases containing relevant mutations. This review focuses on the individual steps included in the sequencing workflow and factors that may affect the interpretation of final results.
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Affiliation(s)
- Matúš Dohál
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia.
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia; Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Kristián Pršo
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
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18
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Guimaraes AMS, Zimpel CK. Mycobacterium bovis: From Genotyping to Genome Sequencing. Microorganisms 2020; 8:E667. [PMID: 32375210 PMCID: PMC7285088 DOI: 10.3390/microorganisms8050667] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium bovis is the main pathogen of bovine, zoonotic, and wildlife tuberculosis. Despite the existence of programs for bovine tuberculosis (bTB) control in many regions, the disease remains a challenge for the veterinary and public health sectors, especially in developing countries and in high-income nations with wildlife reservoirs. Current bTB control programs are mostly based on test-and-slaughter, movement restrictions, and post-mortem inspection measures. In certain settings, contact tracing and surveillance has benefited from M. bovis genotyping techniques. More recently, whole-genome sequencing (WGS) has become the preferential technique to inform outbreak response through contact tracing and source identification for many infectious diseases. As the cost per genome decreases, the application of WGS to bTB control programs is inevitable moving forward. However, there are technical challenges in data analyses and interpretation that hinder the implementation of M. bovis WGS as a molecular epidemiology tool. Therefore, the aim of this review is to describe M. bovis genotyping techniques and discuss current standards and challenges of the use of M. bovis WGS for transmission investigation, surveillance, and global lineages distribution. We compiled a series of associated research gaps to be explored with the ultimate goal of implementing M. bovis WGS in a standardized manner in bTB control programs.
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Affiliation(s)
- Ana M. S. Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, University of São Paulo, São Paulo 01246-904, Brazil;
| | - Cristina K. Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, University of São Paulo, São Paulo 01246-904, Brazil;
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, São Paulo 01246-904, Brazil
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19
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Sato MP, Ogura Y, Nakamura K, Nishida R, Gotoh Y, Hayashi M, Hisatsune J, Sugai M, Takehiko I, Hayashi T. Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes. DNA Res 2020; 26:391-398. [PMID: 31364694 PMCID: PMC6796507 DOI: 10.1093/dnares/dsz017] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/17/2019] [Indexed: 01/23/2023] Open
Abstract
In bacterial genome and metagenome sequencing, Illumina sequencers are most frequently used due to their high throughput capacity, and multiple library preparation kits have been developed for Illumina platforms. Here, we systematically analysed and compared the sequencing bias generated by currently available library preparation kits for Illumina sequencing. Our analyses revealed that a strong sequencing bias is introduced in low-GC regions by the Nextera XT kit. The level of bias introduced is dependent on the level of GC content; stronger bias is generated as the GC content decreases. Other analysed kits did not introduce this strong sequencing bias. The GC content-associated sequencing bias introduced by Nextera XT was more remarkable in metagenome sequencing of a mock bacterial community and seriously affected estimation of the relative abundance of low-GC species. The results of our analyses highlight the importance of selecting proper library preparation kits according to the purposes and targets of sequencing, particularly in metagenome sequencing, where a wide range of microbial species with various degrees of GC content is present. Our data also indicate that special attention should be paid to which library preparation kit was used when analysing and interpreting publicly available metagenomic data.
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Affiliation(s)
- Mitsuhiko P Sato
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Ruriko Nishida
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan.,Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Masahiro Hayashi
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu, Gifu, Japan.,Center for Conservation of Microbial Genetic Resource, Gifu University, Gifu, Gifu, Japan
| | - Junzo Hisatsune
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Hiroshima, Japan.,Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoyuki Sugai
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Hiroshima, Japan.,Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Itoh Takehiko
- Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
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20
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Murphy TW, Hsieh YP, Zhu B, Naler LB, Lu C. Microfluidic Platform for Next-Generation Sequencing Library Preparation with Low-Input Samples. Anal Chem 2020; 92:2519-2526. [PMID: 31894965 DOI: 10.1021/acs.analchem.9b04086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Advances in next-generation sequencing (NGS) have made available a wealth of information that had previously been inaccessible to researchers and clinicians. NGS has been applied to understand genomic, transcriptomic, and epigenomic changes and gained traction as a significant tool capable of accelerating diagnosis, prognosis, and biomarker discovery. However, these NGS assays have yet to be practical methods for patient stratification or diagnosis because of the gap between the tiny quantities of biomaterials provided by a clinical sample and the large DNA input required by most of these assays. Current library preparation methodologies typically require large input amounts of DNA and a long and complicated manual process. Here, we present a microfluidic droplet-based system for NGS library preparation, capable of reducing the number of pipetting steps significantly, reducing reagent consumption by 10×, and automating much of the process, while supporting an extremely low DNA input requirement (10 pg per library). This semiautomated technology will allow for low-input preparations of 8 libraries simultaneously while reducing batch-to-batch variation and operator hands-on time.
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Affiliation(s)
- Travis W Murphy
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Yuan-Pang Hsieh
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Bohan Zhu
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Lynette B Naler
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Chang Lu
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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21
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Pasquali F, Do Valle I, Palma F, Remondini D, Manfreda G, Castellani G, Hendriksen RS, De Cesare A. Application of different DNA extraction procedures, library preparation protocols and sequencing platforms: impact on sequencing results. Heliyon 2019; 5:e02745. [PMID: 31720479 PMCID: PMC6838873 DOI: 10.1016/j.heliyon.2019.e02745] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 04/01/2019] [Accepted: 10/25/2019] [Indexed: 01/22/2023] Open
Abstract
In this study three DNA extraction procedures, two library preparation protocols and two sequencing platforms were applied to analyse six bacterial cultures and their corresponding DNA obtained as part of a proficiency test. The impact of each variable on sequencing results was assessed using the following parameters: reads quality, assembly and alignment statistics; number of single nucleotide polymorphisms (SNPs), detected applying assembly- and alignment-based strategies; antimicrobial resistance genes (ARGs), identified on de novo assemblies of all sequenced genomes. The investigated nucleic acid extraction procedures, library preparation kits and sequencing platforms do not significantly affect de novo assembly statistics and number of SNPs and ARGs. The only exception was observed for two duplicates, which were associated to one PCR-based library preparation kit. Results from this comparative study can support researchers in the choice toward the available pre-sequencing and sequencing options, and might suggest further comparisons to be performed.
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Affiliation(s)
- F Pasquali
- Department of Food and Agricultural Sciences, Alma Mater Studiorum-University of Bologna, via del Florio 2, Ozzano dell'Emilia, 40064 Italy
| | - I Do Valle
- Department of Physics, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115-5000, USA
| | - F Palma
- Department of Food and Agricultural Sciences, Alma Mater Studiorum-University of Bologna, via del Florio 2, Ozzano dell'Emilia, 40064 Italy
| | - D Remondini
- Department of Physics and Astronomy, Alma Mater Studiorum-University of Bologna, viale Berti Pichat 6/2, 40127, Bologna, Italy
| | - G Manfreda
- Department of Food and Agricultural Sciences, Alma Mater Studiorum-University of Bologna, via del Florio 2, Ozzano dell'Emilia, 40064 Italy
| | - G Castellani
- Department of Physics and Astronomy, Alma Mater Studiorum-University of Bologna, viale Berti Pichat 6/2, 40127, Bologna, Italy
| | - R S Hendriksen
- Technical University of Denmark, Kemitorvet, Kgs. Lyngby, 2800, Denmark
| | - A De Cesare
- Department of Food and Agricultural Sciences, Alma Mater Studiorum-University of Bologna, via del Florio 2, Ozzano dell'Emilia, 40064 Italy
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22
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Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies. Tuberculosis (Edinb) 2019; 119:101865. [PMID: 31563810 DOI: 10.1016/j.tube.2019.101865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 09/19/2019] [Accepted: 09/22/2019] [Indexed: 11/22/2022]
Abstract
This study describes the analysis of DNA from heat-killed (boilate) isolates of Mycobacterium tuberculosis from two UK outbreaks where DNA was of sub-optimal quality for the standard methodologies routinely used in microbial genomics. An Illumina library construction method developed for sequencing ancient DNA was successfully used to obtain whole genome sequences, allowing analysis of the outbreak by gene-by-gene MLST, SNP mapping and phylogenetic analysis. All cases were spoligotyped to the same Haarlem H1 sub-lineage. This is the first described application of ancient DNA library construction protocols to allow whole genome sequencing of a clinical tuberculosis outbreak. Using this method it is possible to obtain epidemiologically meaningful data even when DNA is of insufficient quality for standard methods.
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23
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Seth-Smith HMB, Bonfiglio F, Cuénod A, Reist J, Egli A, Wüthrich D. Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation. Front Public Health 2019; 7:241. [PMID: 31508405 PMCID: PMC6719548 DOI: 10.3389/fpubh.2019.00241] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022] Open
Abstract
Whole genome sequencing (WGS) has become the new gold standard for bacterial outbreak investigation, due to the high resolution available for typing. While sequencing is currently predominantly performed on Illumina devices, the preceding library preparation can be performed using various protocols. Enzymatic fragmentation library preparation protocols are fast, have minimal hands-on time, and work with small quantities of DNA. The aim of our study was to compare three library preparation protocols for molecular typing: Nextera XT (Illumina); Nextera Flex (Illumina); and QIAseq FX (Qiagen). We selected 12 ATCC strains from human Gram-positive and Gram-negative pathogens with %G+C-content ranging from 27% (Fusobacterium nucleatum) to 73% (Micrococcus luteus), each having a high quality complete genome assembly available, to allow in-depth analysis of the resulting Illumina sequence data quality. Additionally, we selected isolates from previously analyzed cases of vancomycin-resistant Enterococcus faecium (VRE) (n = 7) and a local outbreak of Klebsiella aerogenes (n = 5). The number of protocol steps and time required were compared, in order to test the suitability for routine laboratory work. Data analyses were performed with standard tools commonly used in outbreak situations: Ridom SeqSphere+ for cgMLST; CLC genomics workbench for SNP analysis; and open source programs. Nextera Flex and QIAseq FX were found to be less sensitive than Nextera XT to variable %G+C-content, resulting in an almost uniform distribution of read-depth. Therefore, low coverage regions are reduced to a minimum resulting in a more complete representation of the genome. Thus, with these two protocols, more alleles were detected in the cgMLST analysis, producing a higher resolution of closely related isolates. Furthermore, they result in a more complete representation of accessory genes. In particular, the high data quality and relative simplicity of the workflow of Nextera Flex stood out in this comparison. This thorough comparison within an ISO/IEC 17025 accredited environment will be of interest to those aiming to optimize their clinical microbiological genome sequencing.
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Affiliation(s)
- Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,DBM Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ferdinando Bonfiglio
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Personalized Health Basel, University of Basel, Basel, Switzerland
| | - Aline Cuénod
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Josiane Reist
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Daniel Wüthrich
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,DBM Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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24
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Lizarazo E, Couto N, Vincenti-Gonzalez M, Raangs EC, Velasco Z, Bethencourt S, Jaenisch T, Friedrich AW, Tami A, Rossen JW. Applied shotgun metagenomics approach for the genetic characterization of dengue viruses. J Biotechnol 2019; 306S:100009. [PMID: 34112375 DOI: 10.1016/j.btecx.2019.100009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 12/19/2022]
Abstract
Dengue virus (DENV), an arthropod-borne virus, has rapidly spread in recent years. DENV diagnosis is performed through virus serology, isolation or molecular detection, while genotyping is usually done through Sanger sequencing of the envelope gene. This study aimed to optimize the use of shotgun metagenomics and subsequent bioinformatics analysis to detect and type DENV directly from clinical samples without targeted amplification. Additionally, presence of DENV quasispecies (intra-host variation) was revealed by detecting single nucleotide variants. Viral RNA was isolated with or without DNase-I treatment from 17 DENV (1-4) positive blood samples. cDNA libraries were generated using either a combination of the NEBNext® RNA to synthesize cDNA followed by Nextera XT DNA library preparation, or the TruSeq RNA V2 (TS) library preparation kit. Libraries were sequenced using both the MiSeq and NextSeq. Bioinformatic analysis showed complete ORFs for all samples by all approaches, but longer contigs and higher sequencing depths were obtained with the TS kit. No differences were observed between MiSeq and NextSeq sequencing. Detection of multiple DENV serotypes in a single sample was feasible. Finally, results were obtained within three days with associated reagents costs between €130-170/sample. Therefore, shotgun metagenomics is suitable for identification and typing of DENV in a clinical setting.
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Affiliation(s)
- Erley Lizarazo
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Maria Vincenti-Gonzalez
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Erwin C Raangs
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Zoraida Velasco
- Universidad de Carabobo, Facultad Experimental de Ciencias y Tecnología, Departamento de Biología, Valencia, Venezuela
| | - Sarah Bethencourt
- Universidad de Carabobo, Facultad de Ciencias de la Salud. Departamento de Ciencias Fisiológicas, Unidad de Investigación en Inmunología, Valencia, Venezuela
| | - Thomas Jaenisch
- University of Heidelberg, Heidelberg University Hospital, Department of Infectious Diseases, Section of Clinical Tropical Medicine, Heidelberg, Germany
| | - Alexander W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Adriana Tami
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands; Universidad de Carabobo, Facultad de Ciencias de la Salud, Departamento de Parasitología, Valencia, Venezuela
| | - John W Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.
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25
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van der Werf MJ, Ködmön C. Whole-Genome Sequencing as Tool for Investigating International Tuberculosis Outbreaks: A Systematic Review. Front Public Health 2019; 7:87. [PMID: 31058125 PMCID: PMC6478655 DOI: 10.3389/fpubh.2019.00087] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022] Open
Abstract
Background: Whole-genome sequencing (WGS) can support the investigation of tuberculosis (TB) outbreaks. The technique has been applied to estimate the timing and directionality of transmission and to exclude cases from an investigation. This review assesses how WGS was applied in international outbreak investigations and discusses the advantages and challenges of the application of WGS. Methods: Databases were searched for reports on international TB outbreak investigations. Information was extracted on: Why was WGS applied?; How was WGS applied?; Organizational issues; WGS methodology; What was learned/what were the implications of the WGS investigation?; and challenges and lessons learned. Results: Three studies reporting on international outbreak investigations were identified. Retrospective WGS sequencing was performed in all studies and prospective typing in two to study TB transmission. In one study, WGS data were produced centrally (i.e., in one laboratory) and analysis was done centrally. In two studies, WGS data production was done in a decentralized manner, and analysis was centralized in one laboratory. Three groups of professionals were involved in the international outbreak investigation: public health authorities, laboratory experts, and clinicians. The reported WGS methodology applied differed between the studies in some aspects, e.g., sequencing platform; quality measures, percentage of the reference genome covered, and the mean genomic coverage; analysis, use of a reference genome or de novo assembly; and software used for alignment and analysis. In all three studies, in-house scripts were used for variance calling, and the single nucleotide polymorphism (SNP) approach was used for analysis. All outbreak investigation reports stated that WGS refuted suspected transmission events and provided supporting evidence for epidemiological data. Several challenges were reported of which most were not related to WGS. The only challenge related to WGS was the timeframe of getting WGS data if WGS is not routinely performed. Conclusions: WGS was considered a useful addition in international TB outbreak investigations. Further standardization of the WGS methodology and good structures for international collaboration and coordination are needed to take full advantage of this new technology. Whether the use of WGS results in earlier detection of cases and thus limits transmission still needs to be determined.
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Affiliation(s)
| | - Csaba Ködmön
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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26
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McTaggart LR, Copeland JK, Surendra A, Wang PW, Husain S, Coburn B, Guttman DS, Kus JV. Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis. Front Microbiol 2019; 10:512. [PMID: 30930884 PMCID: PMC6428700 DOI: 10.3389/fmicb.2019.00512] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Invasive fungal infections are an increasingly important cause of human morbidity and mortality. We generated a next-generation sequencing (NGS)-based method designed to detect a wide range of fungi and applied it to analysis of the fungal microbiome (mycobiome) of the lung during fungal infection. Internal transcribed spacer 1 (ITS1) amplicon sequencing and a custom analysis pipeline detected 96% of species from three mock communities comprised of potential fungal lung pathogens with good recapitulation of the expected species distributions (Pearson correlation coefficients r = 0.63, p = 0.004; r = 0.71, p < 0.001; r = 0.62, p = 0.002). We used this pipeline to analyze mycobiomes of bronchoalveolar lavage (BAL) specimens classified as culture-negative (n = 50) or culture-positive (n = 39) for Blastomyces dermatitidis/gilchristii, the causative agent of North America blastomycosis. Detected in 91.4% of the culture-positive samples, Blastomyces dominated (>50% relative abundance) the mycobiome in 68.6% of these culture-positive samples but was absent in culture-negative samples. To overcome any bias in relative abundance due to between-sample variation in fungal biomass, an abundance-weighting calculation was used to normalize the data by accounting for sample-specific PCR cycle number and PCR product concentration data utilized during sample preparation. After normalization, there was a statistically significant greater overall abundance of ITS1 amplicon in the Blastomyces-culture-positive samples versus culture-negative samples. Moreover, the normalization revealed a greater biomass of yeast and environmental fungi in several Blastomyces-culture-positive samples than in the culture-negative samples. Successful detection of Coccidioides, Scedosporium, Phaeoacremonium, and Aspergillus in 6 additional culture-positive BALs by ITS1 amplicon sequencing demonstrates the ability of this method to detect a broad range of fungi from clinical specimens, suggesting that it may be a potentially useful adjunct to traditional fungal microbiological testing for the diagnosis of respiratory mycoses.
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Affiliation(s)
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | | | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Shahid Husain
- Division of Infectious Diseases, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julianne V Kus
- Public Health Ontario, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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27
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Vecera M, Sana J, Oppelt J, Tichy B, Alena K, Lipina R, Smrcka M, Jancalek R, Hermanova M, Kren L, Slaby O. Testing of library preparation methods for transcriptome sequencing of real life glioblastoma and brain tissue specimens: A comparative study with special focus on long non-coding RNAs. PLoS One 2019; 14:e0211978. [PMID: 30742682 PMCID: PMC6370216 DOI: 10.1371/journal.pone.0211978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/24/2019] [Indexed: 11/19/2022] Open
Abstract
Current progress in the field of next-generation transcriptome sequencing have contributed significantly to the study of various malignancies including glioblastoma multiforme (GBM). Differential sequencing of transcriptomes of patients and non-tumor controls has a potential to reveal novel transcripts with significant role in GBM. One such candidate group of molecules are long non-coding RNAs (lncRNAs) which have been proved to be involved in processes such as carcinogenesis, epigenetic modifications and resistance to various therapeutic approaches. To maximize the value of transcriptome sequencing, a proper protocol for library preparation from tissue-derived RNA needs to be found which would produce high quality transcriptome sequencing data and increase the number of detected lncRNAs. It is important to mention that success of library preparation is determined by the quality of input RNA, which is in case of real-life tissue specimens very often altered in comparison to high quality RNA commonly used by manufacturers for development of library preparation chemistry. In the present study, we used GBM and non-tumor brain tissue specimens and compared three different commercial library preparation kits, namely NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific), SENSE Total RNA-Seq Library Prep Kit (Lexogen) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Libraries generated using SENSE kit were characterized by the most normal distribution of normalized average GC content, the least amount of over-represented sequences and the percentage of ribosomal RNA reads (0.3–1.5%) and highest numbers of uniquely mapped reads and reads aligning to coding regions. However, NEBNext kit performed better having relatively low duplication rates, even transcript coverage and the highest number of hits in Ensembl database for every biotype of our interest including lncRNAs. Our results indicate that out of three approaches the NEBNext library preparation kit was most suitable for the study of lncRNAs via transcriptome sequencing. This was further confirmed by highly consistent data reached in an independent validation on an expanded cohort.
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Affiliation(s)
- Marek Vecera
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jiri Sana
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Boris Tichy
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Kopkova Alena
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Radim Lipina
- Department of Neurosurgery, University Hospital Ostrava, Ostrava, Czech Republic
| | - Martin Smrcka
- Department of Neurosurgery, University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Radim Jancalek
- Department of Neurosurgery, St. Anne’s University Hospital and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marketa Hermanova
- 1st Department of Pathological Anatomy, St. Anne’s University Hospital and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Leos Kren
- Department of Pathology, University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ondrej Slaby
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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28
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Tal S, Ben Izhak M, Wachtel C, Wiseman A, Braun T, Yechezkel E, Golan E, Hadas R, Turjeman A, Banet-Noach C, Bronstein M, Lublin A, Berman E, Raviv Z, Pirak M, Klement E, Louzoun Y. Evaluating methods for Avian avulavirus-1 whole genome sequencing. Gene 2019; 721S:100004. [PMID: 32550541 PMCID: PMC7285907 DOI: 10.1016/j.gene.2019.100004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/03/2019] [Indexed: 11/18/2022]
Abstract
Background Avian avulavirus-1 (AAvV-1, previously Newcastle Disease Virus) is responsible for poultry and wild birds' disease outbreaks. Numerous whole genome sequencing methods were reported for this virus. These methods included cloning, specific primers amplification, shotgun PCR approaches, Sequence Independent Single Primer Amplification and next generation sequencing platform kits. Methods Three methods were used to sequence 173 Israeli Avian avulavirus-1 field isolates and one vaccine strain (VH). The sequencing was performed on Proton and Ion Torrent Personal Genome Machine and to a lesser extent, Illumina MiSeq and NextSeq sequencers. Target specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) products sequenced via the Ion torrent sequencer had a high error rate and truncated genomes. All the next generation sequencing platform sequencing kits generated high sequence accuracy and near-complete genomic size. Results A high level of mutations was observed in the intergenic regions between the avian avulavirus-1 genes. Within genes, multiple regions are more mutated than the Fusion region currently used for typing. Conclusions Our findings suggest that the whole genome sequencing by the Ion torrent sequencing kit is sufficient. However, when higher fidelity is desired, the Illumina NextSeq and Proton torrent sequencing kits were found to be preferable.
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Affiliation(s)
- Saar Tal
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Meirav Ben Izhak
- Life Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel
| | | | - Anat Wiseman
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Tzipi Braun
- Life Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel
| | - Elinor Yechezkel
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Einav Golan
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Ruth Hadas
- Kimron Veterinary Institute, Division of Avian Diseases, Israel
| | - Adi Turjeman
- The Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | | | - Michal Bronstein
- The Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Avishai Lublin
- Kimron Veterinary Institute, Division of Avian Diseases, Israel
| | - Elyakum Berman
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Ziv Raviv
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Michael Pirak
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Eyal Klement
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Yoram Louzoun
- Department of Mathematics and Gonda Brain Research Center, Bar Ilan University, Israel
- Corresponding author at: Math Department and Gonda Brain Research Center, Bar Ilan University, Ramat Gan 52900, Israel.
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29
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DEBrowser: interactive differential expression analysis and visualization tool for count data. BMC Genomics 2019; 20:6. [PMID: 30611200 PMCID: PMC6321710 DOI: 10.1186/s12864-018-5362-x] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/11/2018] [Indexed: 01/09/2023] Open
Abstract
Background Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immunoprecipitation sequencing (CLIP-Seq) or RNA immunoprecipitation (RIP-Seq) sequencing, DNA accessibility by assay for transposase-accessible chromatin (ATAC-Seq), DNase or MNase sequencing libraries. The processing of these sequencing techniques involves library-specific approaches. However, in all cases, once the sequencing libraries are processed, the result is a count table specifying the estimated number of reads originating from each genomic locus. Differential analysis to determine which loci have different cellular activity under different conditions starts with the count table and iterates through a cycle of data assessment, preparation and analysis. Such complex analysis often relies on multiple programs and is therefore a challenge for those without programming skills. Results We developed DEBrowser as an R bioconductor project to interactively visualize every step of the differential analysis, without programming. The application provides a rich and interactive web based graphical user interface built on R’s shiny infrastructure. DEBrowser allows users to visualize data with various types of graphs that can be explored further by selecting and re-plotting any desired subset of data. Using the visualization approaches provided, users can determine and correct technical variations such as batch effects and sequencing depth that affect differential analysis. We show DEBrowser’s ease of use by reproducing the analysis of two previously published data sets. Conclusions DEBrowser is a flexible, intuitive, web-based analysis platform that enables an iterative and interactive analysis of count data without any requirement of programming knowledge. Electronic supplementary material The online version of this article (10.1186/s12864-018-5362-x) contains supplementary material, which is available to authorized users.
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30
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Timme RE, Rand H, Sanchez Leon M, Hoffmann M, Strain E, Allard M, Roberson D, Baugher JD. GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015. Microb Genom 2018; 4. [PMID: 29906258 PMCID: PMC6113870 DOI: 10.1099/mgen.0.000185] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Pathogen monitoring is becoming more precise as sequencing technologies become more affordable and accessible worldwide. This transition is especially apparent in the field of food safety, which has demonstrated how whole-genome sequencing (WGS) can be used on a global scale to protect public health. GenomeTrakr coordinates the WGS performed by public-health agencies and other partners by providing a public database with real-time cluster analysis for foodborne pathogen surveillance. Because WGS is being used to support enforcement decisions, it is essential to have confidence in the quality of the data being used and the downstream data analyses that guide these decisions. Routine proficiency tests, such as the one described here, have an important role in ensuring the validity of both data and procedures. In 2015, the GenomeTrakr proficiency test distributed eight isolates of common foodborne pathogens to participating laboratories, who were required to follow a specific protocol for performing WGS. Resulting sequence data were evaluated for several metrics, including proper labelling, sequence quality and new single nucleotide polymorphisms (SNPs). Illumina MiSeq sequence data collected for the same set of strains across 21 different laboratories exhibited high reproducibility, while revealing a narrow range of technical and biological variance. The numbers of SNPs reported for sequencing runs of the same isolates across multiple laboratories support the robustness of our cluster analysis pipeline in that each individual isolate cultured and resequenced multiple times in multiple places are all easily identifiable as originating from the same source.
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Affiliation(s)
- Ruth E Timme
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Hugh Rand
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Maria Sanchez Leon
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Errol Strain
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Dwayne Roberson
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Joseph D Baugher
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
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31
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Leung KSS, Siu GKH, Tam KKG, To SWC, Rajwani R, Ho PL, Wong SSY, Zhao WW, Ma OCK, Yam WC. Comparative Genomic Analysis of Two Clonally Related Multidrug Resistant Mycobacterium tuberculosis by Single Molecule Real Time Sequencing. Front Cell Infect Microbiol 2017; 7:478. [PMID: 29188195 PMCID: PMC5694780 DOI: 10.3389/fcimb.2017.00478] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/31/2017] [Indexed: 12/02/2022] Open
Abstract
Background: Multidrug-resistant tuberculosis (MDR-TB) is posing a major threat to global TB control. In this study, we focused on two consecutive MDR-TB isolated from the same patient before and after the initiation of anti-TB treatment. To better understand the genomic characteristics of MDR-TB, Single Molecule Real-Time (SMRT) Sequencing and comparative genomic analyses was performed to identify mutations that contributed to the stepwise development of drug resistance and growth fitness in MDR-TB under in vivo challenge of anti-TB drugs. Result: Both pre-treatment and post-treatment strain demonstrated concordant phenotypic and genotypic susceptibility profiles toward rifampicin, pyrazinamide, streptomycin, fluoroquinolones, aminoglycosides, cycloserine, ethionamide, and para-aminosalicylic acid. However, although both strains carried identical missense mutations at rpoB S531L, inhA C-15T, and embB M306V, MYCOTB Sensititre assay showed that the post-treatment strain had 16-, 8-, and 4-fold elevation in the minimum inhibitory concentrations (MICs) toward rifabutin, isoniazid, and ethambutol respectively. The results have indicated the presence of additional resistant-related mutations governing the stepwise development of MDR-TB. Further comparative genomic analyses have identified three additional polymorphisms between the clinical isolates. These include a single nucleotide deletion at nucleotide position 360 of rv0888 in pre-treatment strain, and a missense mutation at rv3303c (lpdA) V44I and a 6-bp inframe deletion at codon 67-68 in rv2071c (cobM) in the post-treatment strain. Multiple sequence alignment showed that these mutations were occurring at highly conserved regions among pathogenic mycobacteria. Using structural-based and sequence-based algorithms, we further predicted that the mutations potentially have deleterious effect on protein function. Conclusion: This is the first study that compared the full genomes of two clonally-related MDR-TB clinical isolates during the course of anti-TB treatment. Our work has demonstrated the robustness of SMRT Sequencing in identifying mutations among MDR-TB clinical isolates. Comparative genome analysis also suggested novel mutations at rv0888, lpdA, and cobM that might explain the difference in antibiotic resistance and growth pattern between the two MDR-TB strains.
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Affiliation(s)
- Kenneth Siu-Sing Leung
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | - Kingsley King-Gee Tam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sabrina Wai-Chi To
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Rahim Rajwani
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | - Pak-Leung Ho
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Samson Sai-Yin Wong
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wei W. Zhao
- KingMed Diagnostics, Science Park, Hong Kong, Hong Kong
| | | | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
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Tyler AD, Randell E, Baikie M, Antonation K, Janella D, Christianson S, Tyrrell GJ, Graham M, Van Domselaar G, Sharma MK. Application of whole genome sequence analysis to the study of Mycobacterium tuberculosis in Nunavut, Canada. PLoS One 2017; 12:e0185656. [PMID: 28982116 PMCID: PMC5628838 DOI: 10.1371/journal.pone.0185656] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022] Open
Abstract
Canada has one of the lowest rates of tuberculosis (TB) in the world, however, among certain sub-populations, disease incidence rates approach those observed in sub-Saharan Africa, and other high incidence regions. In this study, we applied mycobacterial interspersed repetitive unit (MIRU) variable number of tandem repeat (VNTR) and whole genome sequencing (WGS) to the analysis of Mycobacterium tuberculosis isolates obtained from Northern communities in the territory of Nunavut. WGS was carried out using the Illumina MiSeq, with identified variants used to infer phylogenetic relationships and annotated to infer functional implications. Additionally, the sequencing data from these isolates were augmented with publically available WGS to evaluate data from the Nunavut outbreak in the broader Canadian context. In this study, isolates could be classified into four major clusters by MIRU-VNTR analysis. These could be further resolved into sub-clusters using WGS. No evidence for antimicrobial resistance, either genetic or phenotypic, was observed in this cohort. Among most subjects with multiple samples, reactivation/incomplete treatment likely contributed to recurrence. However, isolates from two subjects appeared more likely to have occurred via reinfection, based on the large number of genomic single nucleotide variants detected. Finally, although quite distinct from previously reported Canadian MTB strains, isolates obtained from Nunavut clustered most closely with a cohort of samples originating in the Nunavik region of Northern Quebec. This study demonstrates the benefit of using WGS for discriminatory analysis of MTB in Canada, especially in high incidence regions. It further emphasizes the importance of focusing epidemiological intervention efforts on interrupting transmission chains of endemic TB throughout Northern communities, rather than relying on strategies applied in regions where the majority of TB cases result from importation of foreign strains.
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Affiliation(s)
- Andrea D. Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | | | - Kym Antonation
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Debra Janella
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Sara Christianson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Gregory J. Tyrrell
- The Division of Diagnostic and Applied Microbiology, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- The Provincial Laboratory for Public Health (Microbiology), Edmonton, Alberta, Canada
| | - Morag Graham
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Meenu K. Sharma
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
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Ring JD, Sturk-Andreaggi K, Peck MA, Marshall C. A performance evaluation of Nextera XT and KAPA HyperPlus for rapid Illumina library preparation of long-range mitogenome amplicons. Forensic Sci Int Genet 2017; 29:174-180. [DOI: 10.1016/j.fsigen.2017.04.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/29/2017] [Accepted: 04/03/2017] [Indexed: 12/19/2022]
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McNerney R, Clark TG, Campino S, Rodrigues C, Dolinger D, Smith L, Cabibbe AM, Dheda K, Schito M. Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action. Int J Infect Dis 2017; 56:130-135. [PMID: 27986491 DOI: 10.1016/j.ijid.2016.11.422] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 11/15/2022] Open
Abstract
Whole genome sequencing (WGS) can provide a comprehensive analysis of Mycobacterium tuberculosis mutations that cause resistance to anti-tuberculosis drugs. With the deployment of bench-top sequencers and rapid analytical software, WGS is poised to become a useful tool to guide treatment. However, direct sequencing from clinical specimens to provide a full drug resistance profile remains a serious challenge. This article reviews current practices for extracting M. tuberculosis DNA and possible solutions for sampling sputum. Techniques under consideration include enzymatic digestion, physical disruption, chemical degradation, detergent solubilization, solvent extraction, ligand-coated magnetic beads, silica columns, and oligonucleotide pull-down baits. Selective amplification of genomic bacterial DNA in sputum prior to WGS may provide a solution, and differential lysis to reduce the levels of contaminating human DNA is also being explored. To remove this bottleneck and accelerate access to WGS for patients with suspected drug-resistant tuberculosis, it is suggested that a coordinated and collaborative approach be taken to more rapidly optimize, compare, and validate methodologies for sequencing from patient samples.
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Affiliation(s)
- Ruth McNerney
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Camilla Rodrigues
- Department of Microbiology, P.D. Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | | | - Liezel Smith
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa
| | - Andrea M Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, South Africa
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Bespyatykh JA, Shitikov EA, Ilina EN. Proteomics for the Investigation of Mycobacteria. Acta Naturae 2017; 9:15-25. [PMID: 28461970 PMCID: PMC5406656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Indexed: 10/25/2022] Open
Abstract
The physiology of Mycobacterium tuberculosis, the causative agent of tuberculosis, is being studied with intensity. However, despite the genomic and transcriptomic data available today, the pathogenic potential of these bacteria remains poorly understood. Therefore, proteomic approaches seem relevant in studying mycobacteria. This review covers the main stages in the proteomic analysis methods used to study mycobacteria. The main achievements in the area of M. tuberculosis proteomics are described in general. Special attention is paid to the proteomic features of the Beijing family, which is widespread in Russia. Considering that the proteome is a set of all the proteins in the cell, post-translational modifications of mycobacterium proteins are also described.
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Affiliation(s)
- J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow, 119435, Russia
| | - E. A. Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow, 119435, Russia
| | - E. N. Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow, 119435, Russia
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Phelan J, O’Sullivan DM, Machado D, Ramos J, Whale AS, O’Grady J, Dheda K, Campino S, McNerney R, Viveiros M, Huggett JF, Clark TG. The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs. Genome Med 2016; 8:132. [PMID: 28003022 PMCID: PMC5178084 DOI: 10.1186/s13073-016-0385-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/30/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resistance in Mycobacterium tuberculosis to aid treatment decisions. However, there are few little data regarding the precision of such sequencing for assigning resistance profiles. METHODS We investigated two sequencing platforms (Illumina MiSeq, Ion Torrent PGM™) and two rapid analytic pipelines (TBProfiler, Mykrobe predictor) using a well characterised reference strain (H37Rv) and clinical isolates from patients with tuberculosis resistant to up to 13 drugs. Results were compared to phenotypic drug susceptibility testing. To assess analytical robustness individual DNA samples were subjected to repeated sequencing. RESULTS The MiSeq and Ion PGM systems accurately predicted drug-resistance profiles and there was high reproducibility between biological and technical sample replicates. Estimated variant error rates were low (MiSeq 1 per 77 kbp, Ion PGM 1 per 41 kbp) and genomic coverage high (MiSeq 51-fold, Ion PGM 53-fold). MiSeq provided superior coverage in GC-rich regions, which translated into incremental detection of putative genotypic drug-specific resistance, including for resistance to para-aminosalicylic acid and pyrazinamide. The TBProfiler bioinformatics pipeline was concordant with reported phenotypic susceptibility for all drugs tested except pyrazinamide and para-aminosalicylic acid, with an overall concordance of 95.3%. When using the Mykrobe predictor concordance with phenotypic testing was 73.6%. CONCLUSIONS We have demonstrated high comparative reproducibility of two sequencing platforms, and high predictive ability of the TBProfiler mutation library and analytical pipeline, when profiling resistance to first- and second-line anti-tuberculosis drugs. However, platform-specific variability in coverage of some genome regions may have implications for predicting resistance to specific drugs. These findings may have implications for future clinical practice and thus deserve further scrutiny, set within larger studies and using updated mutation libraries.
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Affiliation(s)
- Jody Phelan
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT London, UK
| | | | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Jorge Ramos
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Alexandra S. Whale
- Molecular Biology, LGC Ltd, Queens Road, Teddington, Middlesex TW11 0LY UK
| | - Justin O’Grady
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Keertan Dheda
- Division of Pulmonary Medicine and UCT Lung Institute, Lung Infection and Immunity Unit, University of Cape Town, Groote Schuur Hospital, Observatory, 7925, Cape Town, South Africa
| | - Susana Campino
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT London, UK
| | - Ruth McNerney
- Division of Pulmonary Medicine and UCT Lung Institute, Lung Infection and Immunity Unit, University of Cape Town, Groote Schuur Hospital, Observatory, 7925, Cape Town, South Africa
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisbon, Portugal
| | - Jim F. Huggett
- Molecular Biology, LGC Ltd, Queens Road, Teddington, Middlesex TW11 0LY UK
- School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, GU2 7XH UK
| | - Taane G. Clark
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
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Huptas C, Scherer S, Wenning M. Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly. BMC Res Notes 2016; 9:269. [PMID: 27176120 PMCID: PMC4864918 DOI: 10.1186/s13104-016-2072-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 05/02/2016] [Indexed: 01/09/2023] Open
Abstract
Background Next-generation sequencing (NGS) technology has paved the way for rapid and cost-efficient de novo sequencing of bacterial genomes. In particular, the introduction of PCR-free library preparation procedures (LPPs) lead to major improvements as PCR bias is largely reduced. However, in order to facilitate the assembly of Illumina paired-end sequence data and to enhance assembly performance, an increase of insert sizes to facilitate the repeat bridging and resolution capabilities of current state of the art assembly tools is needed. In addition, information concerning the relationships between genomic GC content, library insert size and sequencing quality as well as the influence of library insert size, read length and sequencing depth on assembly performance would be helpful to specifically target sequencing projects. Results Optimized DNA fragmentation settings and fine-tuned resuspension buffer to bead buffer ratios during fragment size selection were integrated in the Illumina TruSeq® DNA PCR-free LPP in order to produce sequencing libraries varying in average insert size for bacterial genomes within a range of 35.4–73.0 % GC content. The modified protocol consumes only half of the reagents per sample, thus doubling the number of preparations possible with a kit. Examination of different libraries revealed that sequencing quality decreases with increased genomic GC content and with larger insert sizes. The estimation of assembly performance using assembly metrics like corrected NG50 and NGA50 showed that libraries with larger insert sizes can result in substantial assembly improvements as long as appropriate assembly tools are chosen. However, such improvements seem to be limited to genomes with a low to medium GC content. A positive trend between read length and assembly performance was observed while sequencing depth is less important, provided a minimum coverage is reached. Conclusions Based on the optimized protocol developed, sequencing libraries with flexible insert sizes and lower reagent costs can be generated. Furthermore, increased knowledge about the interplay of sequencing quality, insert size, genomic GC content, read length, sequencing depth and the assembler used will help molecular biologists to set up an optimal experimental and analytical framework with respect to Illumina next-generation sequencing of bacterial genomes. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-2072-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher Huptas
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs-und Lebensmittelforschung (ZIEL), Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Siegfried Scherer
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs-und Lebensmittelforschung (ZIEL), Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Mareike Wenning
- Lehrstuhl für Mikrobielle Ökologie, Zentralinstitut für Ernährungs-und Lebensmittelforschung (ZIEL), Wissenschaftszentrum Weihenstephan, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
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