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Francis EK, Antonopoulos A, Westman ME, McKay-Demeler J, Laing R, Šlapeta J. A mixed amplicon metabarcoding and sequencing approach for surveillance of drug resistance to levamisole and benzimidazole in Haemonchus spp. Int J Parasitol 2024; 54:55-64. [PMID: 37536387 DOI: 10.1016/j.ijpara.2023.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023]
Abstract
Anthelmintic-resistant parasitic nematodes present a significant threat to sustainable livestock production worldwide. The ability to detect the emergence of anthelmintic resistance at an early stage, and therefore determine which drugs remain most effective, is crucial for minimising production losses. Despite many years of research into the molecular basis of anthelmintic resistance, no molecular-based tools are commercially available for the diagnosis of resistance as it emerges in field settings. We describe a mixed deep amplicon sequencing approach to determine the frequency of the levamisole (LEV)-resistant single nucleotide polymorphism (SNP) within arc-8 exon 4 (S168T) in Haemonchus spp., coupled with benzimidazole (BZ)-resistant SNPs within β-tubulin isotype-1 and the internal transcribed spacer-2 (ITS-2) nemabiome. This constitutes the first known multi-drug and multi-species molecular diagnostic developed for helminths of veterinary importance. Of the ovine, bovine, caprine and camelid Australian field isolates we tested, S168T was detected in the majority of Haemonchus spp. populations from sheep and goats, but rarely at a frequency greater than 16%; an arbitrary threshold we set based on whole genome sequencing (WGS) of LEV-resistant Haemonchus contortus GWBII. Overall, BZ resistance was far more prevalent in Haemonchus spp. than LEV resistance, confirming that LEV is still an effective anthelmintic class for small ruminants in New South Wales, Australia. The mixed amplicon metabarcoding approach described herein paves the way towards the use of large scale sequencing as a surveillance technology in the field, the results of which can be translated into evidence-based recommendations for the livestock sector.
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Affiliation(s)
- Emily Kate Francis
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia
| | - Alistair Antonopoulos
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, G61 1QH Scotland, United Kingdom; Kreavet, Kruibeke, Belgium
| | - Mark Edward Westman
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, New South Wales 2568, Australia
| | - Janina McKay-Demeler
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, New South Wales 2568, Australia
| | - Roz Laing
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, G61 1QH Scotland, United Kingdom
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, New South Wales 2006, Australia; The University of Sydney Institute for Infectious Diseases, New South Wales 2006, Australia.
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Chien YS, Chen FJ, Wu HC, Lin CH, Chang WC, Perera D, Yang JY, Lee MS, Liao YC. Cost-effective complete genome sequencing using the MinION platform for identification of recombinant enteroviruses. Microbiol Spectr 2023; 11:e0250723. [PMID: 37831475 PMCID: PMC10715163 DOI: 10.1128/spectrum.02507-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/30/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE By employing a cost-effective approach for complete genome sequencing, the study has enabled the identification of novel enterovirus strains and shed light on the genetic exchange events during outbreaks. The success rate of genome sequencing and the scalability of the protocol demonstrate its practical utility for routine enterovirus surveillance. Moreover, the study's findings of recombinant strains of EVA71 and CVA2 contributing to epidemics in Malaysia and Taiwan emphasize the need for accurate detection and characterization of enteroviruses. The investigation of the whole genome and upstream ORF sequences has provided insights into the evolution and spread of enterovirus subgenogroups. These findings have important implications for the prevention, control, and surveillance of enteroviruses, ultimately contributing to the understanding and management of enterovirus-related illnesses.
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Affiliation(s)
- Yeh-Sheng Chien
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Chieh-Hua Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Wen-Chiung Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - David Perera
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Jyh-Yuan Yang
- Research and Diagnosis Center, Centers for Disease Control, Taipei, Taiwan
| | - Min-Shi Lee
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
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Linde J, Brangsch H, Hölzer M, Thomas C, Elschner MC, Melzer F, Tomaso H. Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis. BMC Genomics 2023; 24:258. [PMID: 37173617 PMCID: PMC10182678 DOI: 10.1186/s12864-023-09343-z] [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: 03/02/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Bacterial epidemiology needs to understand the spread and dissemination of strains in a One Health context. This is important for highly pathogenic bacteria such as Bacillus anthracis, Brucella species, and Francisella tularensis. Whole genome sequencing (WGS) has paved the way for genetic marker detection and high-resolution genotyping. While such tasks are established for Illumina short-read sequencing, Oxford Nanopore Technology (ONT) long-read sequencing has yet to be evaluated for such highly pathogenic bacteria with little genomic variations between strains. In this study, three independent sequencing runs were performed using Illumina, ONT flow cell version 9.4.1, and 10.4 for six strains of each of Ba. anthracis, Br. suis and F. tularensis. Data from ONT sequencing alone, Illumina sequencing alone and two hybrid assembly approaches were compared. RESULTS As previously shown, ONT produces ultra-long reads, while Illumina produces short reads with higher sequencing accuracy. Flow cell version 10.4 improved sequencing accuracy over version 9.4.1. The correct (sub-)species were inferred from all tested technologies, individually. Moreover, the sets of genetic markers for virulence, were almost identical for the respective species. The long reads of ONT allowed to assemble not only chromosomes of all species to near closure, but also virulence plasmids of Ba. anthracis. Assemblies based on nanopore data alone, Illumina data alone, and both hybrid assemblies correctly detected canonical (sub-)clades for Ba. anthracis and F. tularensis as well as multilocus sequence types for Br. suis. For F. tularensis, high-resolution genotyping using core-genome MLST (cgMLST) and core-genome Single-Nucleotide-Polymorphism (cgSNP) typing produced highly comparable results between data from Illumina and both ONT flow cell versions. For Ba. anthracis, only data from flow cell version 10.4 produced similar results to Illumina for both high-resolution typing methods. However, for Br. suis, high-resolution genotyping yielded larger differences comparing Illumina data to data from both ONT flow cell versions. CONCLUSIONS In summary, combining data from ONT and Illumina for high-resolution genotyping might be feasible for F. tularensis and Ba. anthracis, but not yet for Br. suis. The ongoing improvement of nanopore technology and subsequent data analysis may facilitate high-resolution genotyping for all bacteria with highly stable genomes in future.
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Affiliation(s)
- Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany.
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Christine Thomas
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Mandy C Elschner
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
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Makhoul M, Chawla HS, Wittkop B, Stahl A, Voss-Fels KP, Zetzsche H, Snowdon RJ, Obermeier C. Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:942461. [PMID: 36420025 PMCID: PMC9676936 DOI: 10.3389/fpls.2022.942461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/03/2022] [Indexed: 05/26/2023]
Abstract
The gene VERNALIZATION1 (VRN1) is a key controller of vernalization requirement in wheat. The genome of hexaploid wheat (Triticum aestivum) harbors three homoeologous VRN1 loci on chromosomes 5A, 5B, and 5D. Structural sequence variants including small and large deletions and insertions and single nucleotide polymorphisms (SNPs) in the three homoeologous VRN1 genes not only play an important role in the control of vernalization requirement, but also have been reported to be associated with other yield related traits of wheat. Here we used single-molecule sequencing of barcoded long-amplicons to assay the full-length sequences (∼13 kbp plus 700 bp from the promoter sequence) of the three homoeologous VRN1 genes in a panel of 192 predominantly European winter wheat cultivars. Long read sequences revealed previously undetected duplications, insertions and single-nucleotide polymorphisms in the three homoeologous VRN1 genes. All the polymorphisms were confirmed by Sanger sequencing. Sequence analysis showed the predominance of the winter alleles vrn-A1, vrn-B1, and vrn-D1 across the investigated cultivars. Associations of SNPs and structural variations within the three VRN1 genes with 20 economically relevant traits including yield, nodal root-angle index and quality related traits were evaluated at the levels of alleles, haplotypes, and copy number variants. Cultivars carrying structural variants within VRN1 genes showed lower grain yield, protein yield and biomass compared to those with intact genes. Cultivars carrying a single vrn-A1 copy and a unique haplotype with a high number of SNPs were found to have elevated grain yield, kernels per spike and kernels per m2 along with lower grain sedimentation values. In addition, we detected a novel SNP polymorphism within the G-quadruplex region of the promoter of vrn-A1 that was associated with deeper roots in winter wheat. Our findings show that multiplex, single-molecule long-amplicon sequencing is a useful tool for detecting variants in target genes within large plant populations, and can be used to simultaneously assay sequence variants among target multiple gene homoeologs in polyploid crops. Numerous novel VRN1 haplotypes and alleles were identified that showed significantly associations to economically important traits. These polymorphisms were converted into PCR or KASP assays for use in marker-assisted breeding.
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Affiliation(s)
- Manar Makhoul
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Harmeet S. Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Kai Peter Voss-Fels
- Institute for Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Holger Zetzsche
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
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Lin JJ, Tien CF, Kuo YP, Lin EJ, Tsai WH, Chen MY, Tsai PJ, Su YW, Pathak N, Yang JM, Yu CY, Chuang ZS, Wu HC, Tsai WT, Dai SS, Liao HC, Chai KM, Su YS, Chuang TH, Liu SJ, Chen HW, Dou HY, Chen FJ, Chen CT, Liao CL, Yu GY. Furin and TMPRSS2 Resistant Spike Induces Robust Humoral and Cellular Immunity Against SARS-CoV-2 Lethal Infection. Front Immunol 2022; 13:872047. [PMID: 35585971 PMCID: PMC9108258 DOI: 10.3389/fimmu.2022.872047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/24/2022] [Indexed: 12/23/2022] Open
Abstract
An effective COVID-19 vaccine against broad SARS-CoV-2 variants is still an unmet need. In the study, the vesicular stomatitis virus (VSV)-based vector was used to express the SARS-CoV-2 Spike protein to identify better vaccine designs. The replication-competent of the recombinant VSV-spike virus with C-terminal 19 amino acid truncation (SΔ19 Rep) was generated. A single dose of SΔ19 Rep intranasal vaccination is sufficient to induce protective immunity against SARS-CoV-2 infection in hamsters. All the clones isolated from the SΔ19 Rep virus contained R682G mutation located at the Furin cleavage site. An additional S813Y mutation close to the TMPRSS2 cleavage site was identified in some clones. The enzymatic processing of S protein was blocked by these mutations. The vaccination of the R682G-S813Y virus produced a high antibody response against S protein and a robust S protein-specific CD8+ T cell response. The vaccinated animals were protected from the lethal SARS-CoV-2 (delta variant) challenge. The S antigen with resistance to enzymatic processes by Furin and TMPRSS2 will provide better immunogenicity for vaccine design.
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Affiliation(s)
- Jhe-Jhih Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Chih-Feng Tien
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Yi-Ping Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - En-Ju Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Wei-Hsiang Tsai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Ming-Yu Chen
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Pei-Ju Tsai
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Wen Su
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Nikhil Pathak
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Jinn-Moon Yang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Chia-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Zih-Shiuan Chuang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Wan-Ting Tsai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Shih-Syong Dai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Hung-Chun Liao
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Kit Man Chai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Siang Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Shih-Jen Liu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsin-Wei Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Chiung-Tong Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chin-Len Liao
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Guann-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- *Correspondence: Guann-Yi Yu,
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Systems-Based Approach for Optimization of Assembly-Free Bacterial MLST Mapping. Life (Basel) 2022; 12:life12050670. [PMID: 35629339 PMCID: PMC9147691 DOI: 10.3390/life12050670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
Epidemiological surveillance of bacterial pathogens requires real-time data analysis with a fast turnaround, while aiming at generating two main outcomes: (1) species-level identification and (2) variant mapping at different levels of genotypic resolution for population-based tracking and surveillance, in addition to predicting traits such as antimicrobial resistance (AMR). Multi-locus sequence typing (MLST) aids this process by identifying sequence types (ST) based on seven ubiquitous genome-scattered loci. In this paper, we selected one assembly-dependent and one assembly-free method for ST mapping and applied them with the default settings and ST schemes they are distributed with, and systematically assessed their accuracy and scalability across a wide array of phylogenetically divergent Public Health-relevant bacterial pathogens with available MLST databases. Our data show that the optimal k-mer length for stringMLST is species-specific and that genome-intrinsic and -extrinsic features can affect the performance and accuracy of the program. Although suitable parameters could be identified for most organisms, there were instances where this program may not be directly deployable in its current format. Next, we integrated stringMLST into our freely available and scalable hierarchical-based population genomics platform, ProkEvo, and further demonstrated how the implementation facilitates automated, reproducible bacterial population analysis.
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Liao YC, Wu HC, Liou CH, Lauderdale TLY, Huang IW, Lai JF, Chen FJ. Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer. Front Microbiol 2022; 13:875347. [PMID: 35422786 PMCID: PMC9002326 DOI: 10.3389/fmicb.2022.875347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/09/2022] [Indexed: 11/26/2022] Open
Abstract
Molecular typing is an essential tool that has been extensively applied in laboratories as well as in clinical settings. Next-generation sequencing technologies promise high-throughput and cost-effective molecular applications; however, the accessibility of these technologies is limited due to the high capital cost. Oxford Nanopore Technologies (ONT) offers a MinION device with the advantages of real-time data analysis, rapid library preparation, and low cost per test. However, the advantages of the MinION device are often overshadowed by its lower raw accuracy. Herein, we present a concise multilocus sequence typing protocol of Staphylococcus aureus using multiplex polymerase chain reaction and Rapid Barcoding Kit for barcoding and MinION device for sequencing. Moreover, to clarify the effects of carryover DNA on tasks that require high sequence accuracy, we used the MinION flow cell in successive runs of washing and reusing. Our results revealed that the MinION flow cell could achieve accurate typing of a total of 467 samples with 3,269 kilobase-long genes within a total of 5 runs. This thus demonstrates the effectiveness of a portable nanopore MinION sequencer in providing accurate, rapid, and routine molecular typing.
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Affiliation(s)
- Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Ci-Hong Liou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Tsai-Ling Yang Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - I-Wen Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Jui-Fen Lai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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8
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Logan R, Fleischmann Z, Annis S, Wehe AW, Tilly JL, Woods DC, Khrapko K. 3GOLD: optimized Levenshtein distance for clustering third-generation sequencing data. BMC Bioinformatics 2022; 23:95. [PMID: 35307007 PMCID: PMC8934446 DOI: 10.1186/s12859-022-04637-7] [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: 05/14/2021] [Accepted: 03/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Third-generation sequencing offers some advantages over next-generation sequencing predecessors, but with the caveat of harboring a much higher error rate. Clustering-related sequences is an essential task in modern biology. To accurately cluster sequences rich in errors, error type and frequency need to be accounted for. Levenshtein distance is a well-established mathematical algorithm for measuring the edit distance between words and can specifically weight insertions, deletions and substitutions. However, there are drawbacks to using Levenshtein distance in a biological context and hence has rarely been used for this purpose. We present novel modifications to the Levenshtein distance algorithm to optimize it for clustering error-rich biological sequencing data. RESULTS We successfully introduced a bidirectional frameshift allowance with end-user determined accommodation caps combined with weighted error discrimination. Furthermore, our modifications dramatically improved the computational speed of Levenstein distance. For simulated ONT MinION and PacBio Sequel datasets, the average clustering sensitivity for 3GOLD was 41.45% (S.D. 10.39) higher than Sequence-Levenstein distance, 52.14% (S.D. 9.43) higher than Levenshtein distance, 55.93% (S.D. 8.67) higher than Starcode, 42.68% (S.D. 8.09) higher than CD-HIT-EST and 61.49% (S.D. 7.81) higher than DNACLUST. For biological ONT MinION data, 3GOLD clustering sensitivity was 27.99% higher than Sequence-Levenstein distance, 52.76% higher than Levenshtein distance, 56.39% higher than Starcode, 48% higher than CD-HIT-EST and 70.4% higher than DNACLUST. CONCLUSION Our modifications to Levenshtein distance have improved its speed and accuracy compared to the classic Levenshtein distance, Sequence-Levenshtein distance and other commonly used clustering approaches on simulated and biological third-generation sequenced datasets. Our clustering approach is appropriate for datasets of unknown cluster centroids, such as those generated with unique molecular identifiers as well as known centroids such as barcoded datasets. A strength of our approach is high accuracy in resolving small clusters and mitigating the number of singletons.
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Affiliation(s)
- Robert Logan
- College of Science, Department of Biology, Northeastern University, 330 Huntington Ave, Boston, MA, 02115, USA.,Department of Biology, Eastern Nazarene College, 23 E Elm Ave, Quincy, MA, 02170, USA
| | - Zoe Fleischmann
- College of Science, Department of Biology, Northeastern University, 330 Huntington Ave, Boston, MA, 02115, USA
| | - Sofia Annis
- College of Science, Department of Biology, Northeastern University, 330 Huntington Ave, Boston, MA, 02115, USA
| | - Amy Wangsness Wehe
- Health and Natural Sciences Division, Mathematics Department, Fitchburg State University, Fitchburg, MA, 01420-2697, USA
| | - Jonathan L Tilly
- College of Science, Department of Biology, Northeastern University, 330 Huntington Ave, Boston, MA, 02115, USA
| | - Dori C Woods
- College of Science, Department of Biology, Northeastern University, 330 Huntington Ave, Boston, MA, 02115, USA
| | - Konstantin Khrapko
- College of Science, Department of Biology, Northeastern University, 330 Huntington Ave, Boston, MA, 02115, USA.
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9
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Liao YC, Chen FJ, Chuang MC, Wu HC, Ji WC, Yu GY, Huang TS. High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination. Int J Mol Sci 2022; 23:3257. [PMID: 35328676 PMCID: PMC8954144 DOI: 10.3390/ijms23063257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 12/10/2022] Open
Abstract
For tiling of the SARS-CoV-2 genome, the ARTIC Network provided a V4 protocol using 99 pairs of primers for amplicon production and is currently the widely used amplicon-based approach. However, this technique has regions of low sequence coverage and is labour-, time-, and cost-intensive. Moreover, it requires 14 pairs of primers in two separate PCRs to obtain spike gene sequences. To overcome these disadvantages, we proposed a single PCR to efficiently detect spike gene mutations. We proposed a bioinformatic protocol that can process FASTQ reads into spike gene consensus sequences to accurately call spike protein variants from sequenced samples or to fairly express the cases of missing amplicons. We evaluated the in silico detection rate of primer sets that yield amplicon sizes of 400, 1200, and 2500 bp for spike gene sequencing of SARS-CoV-2 to be 59.49, 76.19, and 92.20%, respectively. The in silico detection rate of our proposed single PCR primers was 97.07%. We demonstrated the robustness of our analytical protocol against 3000 Oxford Nanopore sequencing runs of distinct datasets, thus ensuring high-integrity sequencing of spike genes for variant SARS-CoV-2 determination. Our protocol works well with the data yielded from versatile primer designs, making it easy to determine spike protein variants.
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Affiliation(s)
- Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, No. 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan
| | - Feng-Jui Chen
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, No. 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan; (F.-J.C.); (H.-C.W.); (G.-Y.Y.)
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| | - Min-Chieh Chuang
- Department of Chemistry, Tunghai University, Taichung 40704, Taiwan; (M.-C.C.); (W.-C.J.)
| | - Han-Chieh Wu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, No. 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan; (F.-J.C.); (H.-C.W.); (G.-Y.Y.)
| | - Wan-Chen Ji
- Department of Chemistry, Tunghai University, Taichung 40704, Taiwan; (M.-C.C.); (W.-C.J.)
| | - Guann-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, No. 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan; (F.-J.C.); (H.-C.W.); (G.-Y.Y.)
| | - Tsi-Shu Huang
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan;
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Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections. Microorganisms 2021; 9:microorganisms9040707. [PMID: 33808095 PMCID: PMC8065434 DOI: 10.3390/microorganisms9040707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/27/2021] [Accepted: 03/28/2021] [Indexed: 01/28/2023] Open
Abstract
Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.
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11
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Wu X, Luo H, Xu F, Ge C, Li S, Deng X, Wiedmann M, Baker RC, Stevenson A, Zhang G, Tang S. Evaluation of Salmonella Serotype Prediction With Multiplex Nanopore Sequencing. Front Microbiol 2021; 12:637771. [PMID: 33776971 PMCID: PMC7987803 DOI: 10.3389/fmicb.2021.637771] [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] [Received: 12/04/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
The use of whole genome sequencing (WGS) data generated by the long-read sequencing platform Oxford Nanopore Technologies (ONT) has been shown to provide reliable results for Salmonella serotype prediction in a previous study. To further meet the needs of industry for accurate, rapid, and cost-efficient Salmonella confirmation and serotype classification, we evaluated the serotype prediction accuracy of using WGS data from multiplex ONT sequencing with three, four, five, seven, or ten Salmonella isolates (each isolate represented one Salmonella serotype) pooled in one R9.4.1 flow cell. Each multiplexing strategy was repeated with five flow cells, and the loaded samples were sequenced simultaneously in a GridION sequencer for 48 h. In silico serotype prediction was performed using both SeqSero2 (for raw reads and genome assemblies) and SISTR (for genome assemblies) software suites. An average of 10.63 Gbp of clean sequencing data was obtained per flow cell. We found that the unevenness of data yield among each multiplexed isolate was a major barrier for shortening sequencing time. Using genome assemblies, both SeqSero2 and SISTR accurately predicted all the multiplexed isolates under each multiplexing strategy when depth of genome coverage ≥50× for each isolate. We identified that cross-sample barcode assignment was a major cause of prediction errors when raw sequencing data were used for prediction. This study also demonstrated that, (i) sequence data generated by ONT multiplex sequencing can be used to simultaneously predict serotype for three to ten Salmonella isolates, (ii) with three to ten Salmonella isolates multiplexed, genome coverage at ≥50× per isolate was obtained within an average of 6 h of ONT multiplex sequencing, and (iii) with five isolates multiplexed, the cost per isolate might be reduced to 23% of that incurred with single ONT sequencing. This study is a starting point for future validation of multiplex ONT WGS as a cost-efficient and rapid Salmonella confirmation and serotype classification tool for the food industry.
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Affiliation(s)
- Xingwen Wu
- Mars Global Food Safety Center, Beijing, China
| | - Hao Luo
- Mars Global Food Safety Center, Beijing, China
| | - Feng Xu
- Mars Global Food Safety Center, Beijing, China
| | - Chongtao Ge
- Mars Global Food Safety Center, Beijing, China
| | - Shaoting Li
- Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Xiangyu Deng
- Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | | | | | | | - Silin Tang
- Mars Global Food Safety Center, Beijing, China
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