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Le CT, Price EP, Sarovich DS, Nguyen TTA, Powell D, Vu-Khac H, Kurtböke Dİ, Knibb W, Chen SC, Katouli M. Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam. Microb Genom 2022; 8. [PMID: 35786440 PMCID: PMC9455698 DOI: 10.1099/mgen.0.000845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.
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Affiliation(s)
- Cuong T. Le
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Institute for Aquaculture, Nha Trang University, Nha Trang, Vietnam
| | - Erin P. Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Derek S. Sarovich
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Thu T. A. Nguyen
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Daniel Powell
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Hung Vu-Khac
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - D. İpek Kurtböke
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Wayne Knibb
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
| | - Mohammad Katouli
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- *Correspondence: Mohammad Katouli,
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Sow SO, Steele AD, Mwenda JM, Armah GE, Neuzil KM. Reaching every child with rotavirus vaccine: Report from the 10th African rotavirus symposium held in Bamako, Mali. Vaccine 2017; 35:5511-5518. [PMID: 28893479 PMCID: PMC6278848 DOI: 10.1016/j.vaccine.2017.08.084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 01/25/2023]
Abstract
The Center for Vaccine Development - Mali (CVD - Mali), the World Health Organization's regional office in Africa (WHO/AFRO), and the CVD at the University of Maryland School of Medicine hosted the 10th African Rotavirus Symposium in Bamako, Mali on 1-2 June 2016. The symposium is coordinated by WHO/AFRO, the Regional Rotavirus Reference Laboratories, and the African Rotavirus Network (ARN), with support from the Bill & Melinda Gates Foundation. The event brings together leading rotavirus researchers, scientists, and policy-makers from across Africa and the world. Over 150 participants, from 31 countries, including 27 in Africa, joined forces to address the theme "Reaching Every Child in Africa with Rotavirus Vaccines." This symposium, the first in francophone Africa, occurred at an unprecedented time when 33 African countries had introduced rotavirus vaccines into their national immunization programs. The symposium concluded with a Call to Action to introduce rotavirus vaccines in the 21 remaining African countries, to increase access in countries with existing vaccination programs, and to continue surveillance and research on rotavirus and other diarrheal diseases.
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Affiliation(s)
- Samba O Sow
- Centre pour le Développement des Vaccins, Bamako, Mali
| | - A Duncan Steele
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Jason M Mwenda
- World Health Organization Regional Office for Africa, Brazzaville, People's Republic of Congo
| | - George E Armah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
| | - Kathleen M Neuzil
- Center for Vaccine Development and Institute for Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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Vergnaud G, Girault G, Thierry S, Pourcel C, Madani N, Blouin Y. Comparison of French and Worldwide Bacillus anthracis Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clade. PLoS One 2016; 11:e0146216. [PMID: 26901621 PMCID: PMC4763433 DOI: 10.1371/journal.pone.0146216] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
Background Bacillus anthracis, the highly dangerous zoonotic bacterial pathogen species is currently composed of three genetic groups, called A, B and C. Group A is represented worldwide whereas group B is present essentially in Western Europe and Southern Africa. Only three strains from group C have been reported. This knowledge is derived from the genotyping of more than 2000 strains collected worldwide. Strains from both group A and group B are present in France. Previous investigations showed that the majority of sporadic French strains belong to the so-called A.Br.011/009 group A clade and define a very remarkable polytomy with six branches. Here we explore the significance of this polytomy by comparing the French B. anthracis lineages to worldwide lineages. We take advantage of whole genome sequence data previously determined for 122 French strains and 45 strains of various origins. Results A total of 6690 SNPs was identified among the available dataset and used to draw the phylogeny. The phylogeny of the French B group strains which belongs to B.Br.CNEVA indicates an expansion from the south-east part of France (the Alps) towards the south-west (Massif-Central and Pyrenees). The relatively small group A strains belonging to A.Br.001/002 results from at least two independent introductions. Strikingly, the data clearly demonstrates that the currently predominant B. anthracis lineage in North America, called WNA for Western North American, is derived from one branch of the A.Br.011/009 polytomy predominant in France. Conclusions/Significance The present work extends the range of observed substitution rate heterogeneity within B. anthracis, in agreement with its ecology and in contrast with some other pathogens. The population structure of the six branches A.Br.011/009 polytomy identified in France, diversity of branch length, and comparison with the WNA lineage, suggests that WNA is of post-Columbian and west European origin, with France as a likely source. Furthermore, it is tempting to speculate that the polytomy’s most recent common ancestor -MRCA- dates back to the Hundred Years' war between France and England started in the mid-fourteenth century. These events were associated in France with deadly epidemics and major economic and social changes.
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Affiliation(s)
- Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
- * E-mail:
| | - Guillaume Girault
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Simon Thierry
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Nora Madani
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Yann Blouin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
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4
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Aloui C, Sut C, Cognasse F, Granados V, Hassine M, Chakroun T, Garraud O, Laradi S. Development of a highly resolutive method, using a double quadruplex tetra-primer-ARMS-PCR coupled with capillary electrophoresis to study CD40LG polymorphisms. Mol Cell Probes 2015; 29:335-342. [PMID: 26577033 DOI: 10.1016/j.mcp.2015.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/06/2015] [Accepted: 11/06/2015] [Indexed: 12/18/2022]
Abstract
Polymorphisms in the CD40 ligand gene (CD40LG) are associated with various immunological disorders such as tumors, autoimmune and infectious diseases. The aim of this study was to develop a highly optimized double quadruplex tetra-primer amplification refractory mutation system PCR (double quadruplex T-ARMS-PCR) coupled with capillary electrophoresis to allow genotyping of eight relevant candidate CD40LG SNPs and to establish haplotypes. After conducting the double quadruplex T-ARMS-PCR, the genotypes obtained through agarose electrophoresis were compared with those obtained through capillary electrophoresis. This strategy was applied to analyze the genetic patterns of CD40LG in two distinct cohorts of blood donors (211 French and 274 Tunisian). The T-ARMS-PCR method was rapid, inexpensive, reproducible and reliable for SNP determination. Regarding the separation technique, capillary electrophoresis allows traceable and semi-automated analysis while agarose electrophoresis remains a cost-effective technique that does not require specialized or costly equipment. Using these methods, we identified significantly different genetic heterogeneity between the two investigated populations (p ≤ 0.0001) and we also extensively characterized their haplotypes. The obtained genotype distribution and the optimized quadruplex T-ARMS-PCR technique coupled with capillary electrophoresis provides valuable information for studying pathologic inflammation leading to various diseases in which CD40LG might be a candidate gene.
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Affiliation(s)
- Chaker Aloui
- GIMAP-EA3064, University of Lyon, Saint-Etienne, 42270 Saint-Priest-en-Jarez, France; French Blood Establishment, EFS Auvergne-Loire, 42023 Saint-Etienne, France
| | - Caroline Sut
- GIMAP-EA3064, University of Lyon, Saint-Etienne, 42270 Saint-Priest-en-Jarez, France; French Blood Establishment, EFS Auvergne-Loire, 42023 Saint-Etienne, France
| | - Fabrice Cognasse
- GIMAP-EA3064, University of Lyon, Saint-Etienne, 42270 Saint-Priest-en-Jarez, France; French Blood Establishment, EFS Auvergne-Loire, 42023 Saint-Etienne, France
| | - Viviana Granados
- Department of Molecular Genetics, Saint-Etienne University Hospital, 42270 Saint-Priest-en-Jarez, France
| | - Mohsen Hassine
- Blood Bank of Monastir, F. Bourguiba University Hospital, 5000 Monastir, Tunisia
| | - Tahar Chakroun
- Regional Centre of Transfusion of Sousse, F. Hached University Hospital, 4000 Sousse, Tunisia
| | - Olivier Garraud
- GIMAP-EA3064, University of Lyon, Saint-Etienne, 42270 Saint-Priest-en-Jarez, France; National Institut of Blood Transfusion, 75739 Paris, France
| | - Sandrine Laradi
- GIMAP-EA3064, University of Lyon, Saint-Etienne, 42270 Saint-Priest-en-Jarez, France; French Blood Establishment, EFS Auvergne-Loire, 42023 Saint-Etienne, France.
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5
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Derzelle S. Single-nucleotide polymorphism discrimination using high-resolution melting analysis for the genotyping of Bacillus anthracis. Methods Mol Biol 2015; 1247:361-371. [PMID: 25399109 DOI: 10.1007/978-1-4939-2004-4_26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
High-resolution melting (HRM) is a post-PCR technique that determines with high precision the melt profile of PCR products using a new generation of double-stranded DNA-binding dyes and accurate fluorescence data acquisition over small temperature increments. The method can be used to interrogate small sets of single-nucleotide polymorphisms (SNPs). Here, we describe a simple and cost-effective HRM-based method for the screening of 14 phylogenetically informative SNPs within the genome of Bacillus anthracis that subtype the species into 13 major sublineages or subgroups. Fourteen monoplex and seven duplex SNP-discrimination assays have been designed. We detail the parameters most important for the successful application of HRM for B. anthracis genotyping.
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Affiliation(s)
- Sylviane Derzelle
- Bacterial Zoonosis Unit, Animal Health Laboratory, University Paris-Est, Anses, 23 Avenue du Général de Gaulle, 94706, Maisons-Alfort Cedex, France,
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6
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A multiplex bead-based suspension array assay for interrogation of phylogenetically informative single nucleotide polymorphisms for Bacillus anthracis. J Microbiol Methods 2013; 95:357-65. [DOI: 10.1016/j.mimet.2013.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/03/2013] [Accepted: 10/06/2013] [Indexed: 11/24/2022]
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7
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Lin X, Wu J, Li H, Wang Z, Lin JM. Determination of mini-short tandem repeat (miniSTR) loci by using the combination of polymerase chain reaction (PCR) and microchip electrophoresis. Talanta 2013; 114:131-7. [DOI: 10.1016/j.talanta.2013.04.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 03/26/2013] [Accepted: 04/04/2013] [Indexed: 11/27/2022]
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8
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Song L, Li W, Li G, Wei D, Ge P, Li G, Zheng F, Sun X. Rapid detection of bacteria in urine samples by the “three-plug-injection” method using capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 935:32-5. [DOI: 10.1016/j.jchromb.2013.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 07/10/2013] [Accepted: 07/16/2013] [Indexed: 11/25/2022]
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9
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Foster JT, Price LB, Beckstrom-Sternberg SM, Pearson T, Brown WD, Kiesling DM, Allen CA, Liu CM, Beckstrom-Sternberg J, Roberto FF, Keim P. Genotyping of Brucella species using clade specific SNPs. BMC Microbiol 2012; 12:110. [PMID: 22712667 PMCID: PMC3747857 DOI: 10.1186/1471-2180-12-110] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 06/04/2012] [Indexed: 01/05/2023] Open
Abstract
Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs) that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340) of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.
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Affiliation(s)
- Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
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10
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Ahmed MU, Dunn L, Ivanova EP. Evaluation of Current Molecular Approaches for Genotyping ofCampylobacter jejuniStrains. Foodborne Pathog Dis 2012; 9:375-85. [DOI: 10.1089/fpd.2011.0988] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Monir U. Ahmed
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
| | - Louise Dunn
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
| | - Elena P. Ivanova
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
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11
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Birdsell DN, Pearson T, Price EP, Hornstra HM, Nera RD, Stone N, Gruendike J, Kaufman EL, Pettus AH, Hurbon AN, Buchhagen JL, Harms NJ, Chanturia G, Gyuranecz M, Wagner DM, Keim PS. Melt analysis of mismatch amplification mutation assays (Melt-MAMA): a functional study of a cost-effective SNP genotyping assay in bacterial models. PLoS One 2012; 7:e32866. [PMID: 22438886 PMCID: PMC3306377 DOI: 10.1371/journal.pone.0032866] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 02/01/2012] [Indexed: 11/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and biologically informative markers extensively used across broad scientific disciplines. Newly identified SNP markers are publicly available at an ever-increasing rate due to advancements in sequencing technologies. Efficient, cost-effective SNP genotyping methods to screen sample populations are in great demand in well-equipped laboratories, but also in developing world situations. Dual Probe TaqMan assays are robust but can be cost-prohibitive and require specialized equipment. The Mismatch Amplification Mutation Assay, coupled with melt analysis (Melt-MAMA), is flexible, efficient and cost-effective. However, Melt-MAMA traditionally suffers from high rates of assay design failures and knowledge gaps on assay robustness and sensitivity. In this study, we identified strategies that improved the success of Melt-MAMA. We examined the performance of 185 Melt-MAMAs across eight different pathogens using various optimization parameters. We evaluated the effects of genome size and %GC content on assay development. When used collectively, specific strategies markedly improved the rate of successful assays at the first design attempt from ∼50% to ∼80%. We observed that Melt-MAMA accurately genotypes across a broad DNA range (∼100 ng to ∼0.1 pg). Genomic size and %GC content influence the rate of successful assay design in an independent manner. Finally, we demonstrated the versatility of these assays by the creation of a duplex Melt-MAMA real-time PCR (two SNPs) and conversion to a size-based genotyping system, which uses agarose gel electrophoresis. Melt-MAMA is comparable to Dual Probe TaqMan assays in terms of design success rate and accuracy. Although sensitivity is less robust than Dual Probe TaqMan assays, Melt-MAMA is superior in terms of cost-effectiveness, speed of development and versatility. We detail the parameters most important for the successful application of Melt-MAMA, which should prove useful to the wider scientific community.
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Affiliation(s)
- Dawn N. Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erin P. Price
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie M. Hornstra
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Roxanne D. Nera
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nathan Stone
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey Gruendike
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Emily L. Kaufman
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Amanda H. Pettus
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Audriana N. Hurbon
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jordan L. Buchhagen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - N. Jane Harms
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Gvantsa Chanturia
- National Center for Disease Control and Public Health and Ilia State University, Tbilisi, Georgia, United States of America
| | - Miklos Gyuranecz
- Veterinary Medical Research Institute, Hungarian Academy of Sciences, Budapest, Hungary
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul S. Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail:
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12
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Li D, Truong TV, Bills TM, Holt BC, VanDerwerken DN, Williams JR, Acharya A, Robison RA, Tolley HD, Lee ML. GC/MS Method for Positive Detection of Bacillus anthracis Endospores. Anal Chem 2012; 84:1637-44. [DOI: 10.1021/ac202606x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dan Li
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Tai V. Truong
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Teri M. Bills
- Department of Microbiology and
Molecular Biology, Brigham Young University, Provo, Utah 84602, United States
| | - Brian C. Holt
- Department of Statistics, Brigham Young University, Provo, Utah 84602, United
States
| | | | - John R. Williams
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Abhilasha Acharya
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Richard A. Robison
- Department of Microbiology and
Molecular Biology, Brigham Young University, Provo, Utah 84602, United States
| | - H. Dennis Tolley
- Department of Statistics, Brigham Young University, Provo, Utah 84602, United
States
| | - Milton L. Lee
- Department
of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
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13
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Ban E, Park SH, Kang MJ, Lee HJ, Song EJ, Yoo YS. Growing trend of CE at the omics level: The frontier of systems biology - An update. Electrophoresis 2011; 33:2-13. [DOI: 10.1002/elps.201100344] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/16/2011] [Accepted: 08/16/2011] [Indexed: 02/03/2023]
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14
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Derzelle S, Laroche S, Le Flèche P, Hauck Y, Thierry S, Vergnaud G, Madani N. Characterization of genetic diversity of Bacillus anthracis in France by using high-resolution melting assays and multilocus variable-number tandem-repeat analysis. J Clin Microbiol 2011; 49:4286-92. [PMID: 21998431 PMCID: PMC3232934 DOI: 10.1128/jcm.05439-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 10/04/2011] [Indexed: 11/20/2022] Open
Abstract
Using high-resolution melting (HRM) analysis, we developed a cost-effective method to genotype a set of 13 phylogenetically informative single-nucleotide polymorphisms (SNPs) within the genome of Bacillus anthracis. SNP discrimination assays were performed in monoplex or duplex and applied to 100 B. anthracis isolates collected in France from 1953 to 2009 and a few reference strains. HRM provided a reliable and cheap alternative to subtype B. anthracis into one of the 12 major sublineages or subgroups. All strains could be correctly positioned on the canonical SNP (canSNP) phylogenetic tree, except the divergent Pasteur vaccine strain ATCC 4229. We detected the cooccurrence of three canSNP subgroups in France. The dominant B.Br.CNEVA sublineage was found to be prevalent in the Alps, the Pyrenees, the Auvergne region, and the Saône-et-Loire department. Strains affiliated with the A.Br.008/009 subgroup were observed throughout most of the country. The minor A.Br.001/002 subgroup was restricted to northeastern France. Multiple-locus variable-number tandem-repeat analysis using 24 markers further resolved French strains into 60 unique profiles and identified some regional patterns. Diversity found within the A.Br.008/009 and B.Br.CNEVA subgroups suggests that these represent old, ecologically established clades in France. Phylogenetic relationships with strains from other parts of the world are discussed.
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Affiliation(s)
- S Derzelle
- Bacterial Zoonosis Unit, Maisons-Alfort Laboratory for Animal Health, ANSES, 23 Avenue du Général de Gaulle, 94706 Maisons Alfort cedex, France.
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