A high resolution four-locus multiplex single nucleotide repeat (SNR) genotyping system in Bacillus anthracis

Kenefic, Leo J.; Beaudry, Jodi A.; Trim, Carla B.; Huynh, Lynn; Zanecki, Shaylan; Matthews, Molly; Schupp, James M.; Ert, Matthew Van; Keim, Paul

doi:10.1016/j.mimet.2007.11.014

Cited by 38 publications

(36 citation statements)

References 7 publications

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“…SNR analysis was performed as described previously, with minor changes (13,16). Multiplex PCRs were performed in a final volume of 20 l containing 1ϫ AmpliTaq Gold PCR buffer, 0.5 U of AmpliTaq Gold DNA polymerase (Applied Biosystems), 3 mM MgCl 2 , dNTPs at 0.2 mM each, and the appropriate concentrations of forward and reverse SNRA primers as reported in Table 2.…”

Section: Methodsmentioning

confidence: 99%

“…Studies of genetic diversity of B. anthracis have relied on multiple-locus variable-number tandem repeat analysis (MLVA) (10,14,17), single-nucleotide polymorphisms (SNP) (15,17) and single-nucleotide repeat analysis (SNRA) (12,13,16). Keim et al described a hierarchical approach called PHRANA (progressive hierarchical resolving assays using nucleic acids) that uses markers that are progressively less stable but have increasing resolving power for typing B. anthracis (SNP, MLVA, and SNRA) (11).…”

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confidence: 99%

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Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

Stratilo

Bader

2012

Appl Environ Microbiol

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ABSTRACTEnvironmental samples were collected from carcass sites during and after anthrax outbreaks in 2000 and 2001 in the bison (Bison bison) population within Wood Buffalo National Park and the Hook Lake Region north of Wood Buffalo National Park.Bacillus anthracisspores were isolated from these samples and confirmed using phenotypic characterization and real-time PCR. ConfirmedB. anthracisisolates were typed using multiple-locus variable-number tandem repeat analysis (MLVA15) and single-nucleotide-repeat analysis (SNRA).B. anthracisisolates split into two clades based on MLVA15, while SNRA allowed some isolates between carcass sites to be distinguished from each other. SNRA polymorphisms were also present within a single carcass site. Some isolates from different carcass sites having the same SNRA type had divergent MLVA types; this finding leads to questions about hierarchical typing methods and the robustness of the fine-scale typing ofBacillus anthracis.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

Stratilo

Bader

2012

Appl Environ Microbiol

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“…Their use can differentiate strains within the same outbreak or epidemic. A recent study has suggested the use of a panel of four SNR markers that may be discriminated with an advanced method of analysis of DNA fragments (Kenefic et al, 2008).…”

Section: Molecular Characterisationmentioning

confidence: 99%

Anthrax

Fasanella¹

2012

Zoonosis

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“…анализ структурных и регуляторных генов, фак-торов патогенности (pagA, lef, cya, capA, capB, capC, capD, capE, abrB, acpA, acpB, atxA, pagR), по дан- [3].…”

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Biological Properties and Molecular-Genetic Characteristics of Bacillus Anthracis Strains, Isolated During the Outbreak of Anthrax in the Yamalo-Nenets Autonomous District in 2016

Куличенко¹,

Еременко²,

Рязанова³

et al. 2017

Problemy Osobo Opasnykh Infektsii

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год отмечен крупнейшей эпизоотией сибир-ской язвы среди северных оленей в ямало-ненецком автономном округе (янао), повлекшей за собой за-болевание 36 человек с одним летальным исходом. в ходе эпидемиологического расследования выде-лены штаммы возбудителя сибирской язвы в пробах цель работы -определение фенотипических свойств и генетических особенностей штаммов Bacillus anthracis, выделенных во время вспышки сибирской язвы на ямале в 2016 г. материалы и методы. исследовали штаммы сибиреязвенного микроба по основным, дополнительным идентифи-кационным тестам и методами canSNP-, MLVA-генотипирования и полногеномного секвенирования. результаты и выводы. выявлена идентичность фенотипических свойств, генотипов и профилей пол-ногеномного секвенирования штаммов вне зависимости от источника выделения. подтвержден общий источник заражения людей. определены филогенетические взаимоотношения исследованных штам-мов и их место в глобальной популяции B. anthracis. впервые изучена вариабельность набора генов, связанных с патогенностью, и показана эффективность использования предложенного алгоритма гене-тического типирования.Ключевые слова: сибирская язва, штаммы Bacillus anthracis, фенотипические свойства, генетиче-ское типирование. Objective of the study was to identify phenotypic properties and genetic peculiarities of Bacillus anthracis strains, isolated during the outbreak of anthrax in the territory of Yamal in 2016. Materials and methods. Investigated were the strains of anthrax agent, applying basic and subsequent identification tests and canSNP-, MLVA-genotyping methods and whole genome sequencing. Results and conclusions. The results showed the identity of the phenotypic properties, canSNP-and MLVA25-genotypes, and profiles of whole genome-sequencing, regardless of the source of the strains isolation. Confirmed was a common source of human infection. Defined were phylogenetic interrelations of the tested strains and their position in global B. anthracis population. For the first time ever explored was variability of the gene pattern, associated with pathogenicity, and demonstrated -the efficiency of the proposed algorithm for genetic typing.

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A high resolution four-locus multiplex single nucleotide repeat (SNR) genotyping system in Bacillus anthracis

Cited by 38 publications

References 7 publications

Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

Anthrax

Biological Properties and Molecular-Genetic Characteristics of Bacillus Anthracis Strains, Isolated During the Outbreak of Anthrax in the Yamalo-Nenets Autonomous District in 2016

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