Multilocus sequence typing by blast from de novo assemblies against PubMLST
نویسندگان
چکیده
منابع مشابه
Multilocus sequence typing of Cryptosporidium hominis from northern India
BACKGROUND & OBJECTIVES Human cryptosporidiosis is endemic worldwide, and at least eight species have been reported in humans; the most common being Cryptosporidium hominis and C. parvum. Detailed understanding of the epidemiology of Cryptosporidium is increasingly facilitated using standardized universal technique for species differentiation and subtyping. In this study micro- and minisatellit...
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Mycobacterium xenopi is an opportunistic mycobacterial pathogen of increasing clinical importance. Surveillance of M. xenopi is hampered by the absence of tools for genotyping and molecular epidemiology. In this study, we describe the development and evaluation of an effective multilocus sequence typing strategy for M. xenopi.
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OBJECTIVES Incompatibility group N (IncN) plasmids have been associated with the dissemination of antimicrobial resistance and are a major vehicle for the spread of bla(VIM-1) in humans and bla(CTX-M-1) in animals. A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid categorization of IncN plasmids. METHODS Twelve fully sequenced IncN plasmids available at GenBank were ...
متن کاملMultilocus Sequence Typing Tool for Cyclospora cayetanensis
Because the lack of typing tools for Cyclospora cayetanensis has hampered outbreak investigations, we sequenced its genome and developed a genotyping tool. We observed 2 to 10 geographically segregated sequence types at each of 5 selected loci. This new tool could be useful for case linkage and infection/contamination source tracking.
متن کاملMultilocus sequence typing system for Campylobacter jejuni.
The gram-negative bacterium Campylobacter jejuni has extensive reservoirs in livestock and the environment and is a frequent cause of gastroenteritis in humans. To date, the lack of (i) methods suitable for population genetic analysis and (ii) a universally accepted nomenclature has hindered studies of the epidemiology and population biology of this organism. Here, a multilocus sequence typing ...
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ژورنال
عنوان ژورنال: The Journal of Open Source Software
سال: 2016
ISSN: 2475-9066
DOI: 10.21105/joss.00118