Results 81 to 90 of about 5,264 (155)

Improving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens like Burkholderia pseudomallei

Journal of Clinical Microbiology
Genomic surveillance of pathogens is essential to trace infections and analyze resistance markers. Core genome multilocus sequence typing (cgMLST) facilitates genomic surveillance by simplified analysis and standardization.
Sarah Weigl, Johanna Dabernig-Heinz, Fabian Granitz, Michaela Lipp, Laura Ostermann, Dag Harmsen, Thanh Trung Trinh, Ivo Steinmetz, Gabriel E. Wagner, Sabine Lichtenegger   +9 more
doaj   +1 more source

Genomic pitfalls in hospital surveillance: unexpected Enterobacter cloacae clustering without epidemiological link highlights the need for cautious core genome MLST analysis interpretation

Antimicrobial Resistance and Infection Control
Whole-genome sequencing has become a key tool for identifying bacterial cross-transmission in healthcare settings. Among the methods used, core-genome Multi-Locus Sequence Typing (cgMLST) is considered as the reference method owing to its standardization.
Maxime Danjean, Guilhem Royer, Christophe Rodriguez, Paul-Louis Woerther, Jean-Winoc Decousser   +4 more
doaj   +1 more source

cgMLST analysis of 26 Tuscany carriage isolates and 37 invasive meningococcal isolates collected in Italy.

, 2019
cgMLST analysis of 26 Tuscany carriage isolates and 37 invasive meningococcal isolates collected in Italy.
Alessandro Miglietta (6188276), Arianna Neri (804214), Fabio Voller (6188291), Eleonora Riccobono (141474), Paola Stefanelli (804219), Luigina Ambrosio (6744098), Paola Vacca (377695), Cecilia Fazio (804216), Gian Maria Rossolini (141530)   +8 more
core   +1 more source

An inter-laboratory study characterizes the impact of bioinformatic approaches on genome-based cluster detection for foodborne bacterial pathogens

Frontiers in Microbiology
Accurate assignment of whole-genome sequences to clusters in foodborne outbreak investigations remains challenging. Variability in bioinformatics tools and quality metrics significantly impacts clustering outcomes.
Leonie F. Forth, Burkhard Malorny, Markus Bönn, Erik Brinks, Grégoire Denay, Carlus Deneke, Hosny El-Adawy, Jennie Fischer, Jannika Fuchs, Ekkehard Hiller, Nancy Bretschneider, Sylvia Kleta, Stefanie Lüth, Tilman Schultze, Henning Petersen, Michaela Projahn, Christian Schäfers, Kerstin Stingl, Andreas J. Stroehlein, Laura Uelze, Kathrin Szabo, Anne Wöhlke, Jörg Linde   +22 more
doaj   +1 more source

Development and validation of a core genome multilocus sequence typing scheme for Citrobacter freundii: application in outbreak investigations and comparative analysis across the Citrobacter genus

Journal of Clinical Microbiology
Citrobacter freundii is a nosocomial pathogen increasingly associated with multidrug resistance and hospital outbreaks. Despite its growing clinical relevance, no standardized core genome multilocus sequence typing (cgMLST) scheme has been available for ...
Bärbel Kieninger, Gabriel E. Wagner, Anca Rath, Anja Eichner, Jürgen Fritsch, Aila Caplunik-Pratsch, Jasmine Alikhani, Parham Heydarzadeh-Ghamsary, Adriana Cabal-Rosel, Werner Ruppitsch, Dag Harmsen, Mohammed R. Abdulla, Lena Ulm, Karsten Becker, Wulf Schneider-Brachert, Christian Kohler   +15 more
doaj   +1 more source

Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing

Antimicrobial Resistance and Infection Control
Background We analyzed an outbreak of Bacillus cereus group (Bcg) at a single-center neonatal intensive care unit level IV by conducting comprehensive sampling of both patients and the environment.
Hauke Tönnies, Axel Heep, Jörg Herrmann, Matthias Lange, Alexander Mellmann, Axel Hamprecht   +5 more
doaj   +1 more source

Validation and implementation of whole-genome sequencing-based analytical methods for molecular surveillance and relatedness analysis of Mycobacterium tuberculosis complex isolates at a national reference laboratory

Heliyon
Whole genome sequencing-based methodologies have become extremely relevant for the molecular surveillance of human pathogens and are being increasingly introduced into national reference laboratory services.
Diana Espadinha, Emma Roycroft, Peter R. Flanagan, Simone Mok, Eleanor McNamara, Thomas R. Rogers, Margaret M. Fitzgibbon   +6 more
doaj   +1 more source

Construction and application of PhyloCode databases from bacterial cgMLST allele sequences v1

This protocol describes how to construct a PhyloCode database from bacterial cgMLST allele sequences and how to convert categorical cgMLST allele profiles into phylogenetically informed continuous values.
Masahiro Suzuki
core   +1 more source

Neighbor–joining (NJ) tree based on core genome multi–locus sequence typing (cgMLST) analysis.

, 2019
The NJ tree is based on allele differences in 1957 core genes found in 126 ESBL–producing E. coli isolates included in the cgMLST analysis. Isolate ID, ST, and ESBL type are written in red for the clinical isolates (n = 45), and in black for the ...
Jana Jass (677208), Faisal Ahmad Khan (7832540), Anna Fagerström (3594854), Paula Mölling (471622), Martin Sundqvist (367060), Bo Söderquist (466146)   +5 more
core   +1 more source

The Clonal Spread and Persistence of Campylobacter in Danish Broiler Farms and Its Association with Human Infections

Pathogens
Campylobacter is the most common cause of bacterial foodborne illness in the EU, primarily linked to poultry. To better understand its transmission dynamics, we applied whole-genome sequencing (WGS) to Campylobacter isolates collected at slaughterhouses ...
Katrine Grimstrup Joensen, Gitte Sørensen, Pernille Gymoese, Louise Gade Dahl, Eva Møller Nielsen   +4 more
doaj   +1 more source