Core Genome Multi-locus Sequence Typing Analyses of Leptospira spp. Using the Bacterial Isolate Genome Sequence Database.
Sign Up to like & getrecommendations! Published in 2020 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-0459-5_2
Abstract: With the advent of whole-genome sequencing (WGS), comparative analysis has led to the use of core genome MLST (cgMLST) schemes for the high-resolution reproducible typing of bacterial isolates. In cgMLST, hundreds of loci are used… read more here.
Keywords: genome multi; database; core genome; genome ... See more keywords
Fusarium in the age of genomics
Sign Up to like & getrecommendations! Published in 2017 at "Tropical Plant Pathology"
DOI: 10.1007/s40858-017-0128-6
Abstract: Fusarium is a large genus that includes animal and plant pathogenic species as well as saprophytes. Moreover, specimens from this genus are used in biocontrol as well as for industrial applications. We integrated various disciplines… read more here.
Keywords: supernumerary chromosomes; fusarium age; core chromosomes; supernumerary genome ... See more keywords
Core genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow.
Sign Up to like & getrecommendations! Published in 2020 at "Diagnostic microbiology and infectious disease"
DOI: 10.1016/j.diagmicrobio.2020.114996
Abstract: Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates… read more here.
Keywords: microbiology; pneumoniae isolates; pneumoniae; core genome ... See more keywords
Will the emergence of core genome MLST end the role of in silico MLST?
Sign Up to like & getrecommendations! Published in 2018 at "Food microbiology"
DOI: 10.1016/j.fm.2017.09.003
Abstract: The technological advancement of molecular epidemiological analysis using next-generation sequencing (NGS) for foodborne pathogens has a groundbreaking impact over the past three years. In particular, the emergence of cg (core genome) multilocus sequence typing(MLST) has… read more here.
Keywords: mlst; silico mlst; role; core genome ... See more keywords
Proteins from the core genome of Corynebacterium ulcerans respond for pathogenicity and reveal promising vaccine targets for diphtheria.
Sign Up to like & getrecommendations! Published in 2021 at "Microbial pathogenesis"
DOI: 10.1016/j.micpath.2021.105263
Abstract: Corynebacterium ulcerans is an emerging pathogen able to transmit the acute infection diphtheria to humans. Although there is a well-established vaccine based on the toxin produced by Corynebacterium diphtheriae, another species of this genus known… read more here.
Keywords: vaccine targets; corynebacterium ulcerans; corynebacterium; core genome ... See more keywords
HierCC: a multi-level clustering scheme for population assignments based on core genome MLST
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab234
Abstract: Summary Motivation Routine infectious disease surveillance is increasingly based on large-scale whole-genome sequencing databases. Real-time surveillance would benefit from immediate assignments of each genome assembly to hierarchical population structures. Here we present pHierCC, a pipeline… read more here.
Keywords: clustering scheme; multi level; core genome; population ... See more keywords
Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany
Sign Up to like & getrecommendations! Published in 2023 at "Microbial Genomics"
DOI: 10.1099/mgen.0.000937
Abstract: The increase of Vancomycin-resistant Enterococcus faecium (VREfm) in recent years has been partially attributed to the rise of specific clonal lineages, which have been identified throughout Germany. To date, there is no gold standard for… read more here.
Keywords: core genome; analysis; cgmlst; snp ... See more keywords
Tracking the distribution, genetic diversity, and lineage of Brucella melitensis recovered from humans and animals in Egypt based on core-genome SNP analysis and in silico MLVA-16.
Sign Up to like & getrecommendations! Published in 2022 at "Transboundary and emerging diseases"
DOI: 10.1111/tbed.14768
Abstract: Brucellosis is one of the most common neglected zoonotic diseases globally, with a public health significance and a high economic loss in the livestock industry caused by the bacteria of the genus Brucella. In this… read more here.
Keywords: silico mlva; brucella; core genome; mlva ... See more keywords
Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Clinical Microbiology"
DOI: 10.1128/jcm.01145-17
Abstract: ABSTRACT Mycoplasma gallisepticum is the most virulent and economically important Mycoplasma species for poultry worldwide. Currently, M. gallisepticum strain differentiation based on sequence analysis of 5 loci remains insufficient for accurate outbreak investigation. Recently, whole-genome… read more here.
Keywords: sequence; gallisepticum; mycoplasma gallisepticum; core genome ... See more keywords
Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Clinical Microbiology"
DOI: 10.1128/jcm.01987-17
Abstract: ABSTRACT Clostridium difficile, recently renamed Clostridioides difficile, is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome… read more here.
Keywords: clostridium difficile; difficile; core genome; genome multilocus ... See more keywords
The core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis
Sign Up to like & getrecommendations! Published in 2020 at "BMC Genomics"
DOI: 10.1186/s12864-020-06817-2
Abstract: Mycoplasma anserisalpingitidis is a waterfowl pathogen that mainly infects geese, can cause significant economic losses and is present worldwide. With the advance of whole genome sequencing technologies, new methods are available for the researchers; one… read more here.
Keywords: genome multi; core genome; schema; genome ... See more keywords