Search Results - "Microbial genomics"

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification by Schwengers, Oliver, Jelonek, Lukas, Dieckmann, Marius Alfred, Beyvers, Sebastian, Blom, Jochen, Goesmann, Alexander

“…Command-line annotation software tools have continuously gained popularity compared to centralized online services due to the worldwide increase of sequenced…”
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ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes by Florensa, Alfred Ferrer, Kaas, Rolf Sommer, Clausen, Philip Thomas Lanken Conradsen, Aytan-Aktug, Derya, Aarestrup, Frank M.

“…Antimicrobial resistance (AMR) is one of the most important health threats globally. The ability to accurately identify resistant bacterial isolates and the…”
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MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies by Robertson, James, Nash, John H. E.

“…Large-scale bacterial population genetics studies are now routine due to cost-effective Illumina short-read sequencing. However, analysing plasmid content…”
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Completing bacterial genome assemblies with multiplex MinION sequencing by Wick, Ryan R., Judd, Louise M., Gorrie, Claire L., Holt, Kathryn E.

“…Illumina sequencing platforms have enabled widespread bacterial whole genome sequencing. While Illumina data is appropriate for many analyses, its short read…”
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Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii by Hamidian, Mohammad, Nigro, Steven J.

“…Acinetobacter baumannii is a nosocomial pathogen that has emerged as a global threat because of high levels of resistance to many antibiotics, particularly…”
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ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping by Beghain, Johann, Bridier-Nahmias, Antoine, Le Nagard, Hervé, Denamur, Erick, Clermont, Olivier

“…The genus Escherichia is composed of Escherichia albertii , E. fergusonii , five cryptic Escherichia clades and E. coli sensu stricto. Furthermore, the E. coli…”
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Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex by Lam, Margaret M. C., Wick, Ryan R., Judd, Louise M., Holt, Kathryn E., Wyres, Kelly L.

“…The outer polysaccharide capsule and lipopolysaccharide (LPS) antigens are key targets for novel control strategies targeting Klebsiella pneumoniae and related…”
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SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments by Page, Andrew J., Taylor, Ben, Delaney, Aidan J., Soares, Jorge, Seemann, Torsten, Keane, Jacqueline A., Harris, Simon R.

“…Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting…”
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ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads by Hunt, Martin, Mather, Alison E, Sánchez-Busó, Leonor, Page, Andrew J, Parkhill, Julian, Keane, Jacqueline A, Harris, Simon R

“…Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the…”
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Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses by Pérez-Cobas, Ana Elena, Gomez-Valero, Laura, Buchrieser, Carmen

“…Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics…”
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Microreact: visualizing and sharing data for genomic epidemiology and phylogeography by Argimón, Silvia, Abudahab, Khalil, Goater, Richard J. E., Fedosejev, Artemij, Bhai, Jyothish, Glasner, Corinna, Feil, Edward J., Holden, Matthew T. G., Yeats, Corin A., Grundmann, Hajo, Spratt, Brian G., Aanensen, David M.

“…Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple…”
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chewBBACA: A complete suite for gene-by-gene schema creation and strain identification by Silva, Mickael, Machado, Miguel P., Silva, Diogo N., Rossi, Mirko, Moran-Gilad, Jacob, Santos, Sergio, Ramirez, Mario, Carriço, João André

“…Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source…”
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Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive by Wyres, Kelly L., Cahill, Sarah M., Holt, Kathryn E., Hall, Ruth M., Kenyon, Johanna J.

“…Multiply antibiotic-resistant Acinetobacter baumannii infections are a global public health concern and accurate tracking of the spread of specific lineages is…”
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Identification of Klebsiella capsule synthesis loci from whole genome data by Wyres, Kelly L., Wick, Ryan R., Gorrie, Claire, Jenney, Adam, Follador, Rainer, Thomson, Nicholas R., Holt, Kathryn E.

“…Klebsiella pneumoniae is a growing cause of healthcare-associated infections for which multi-drug resistance is a concern. Its polysaccharide capsule is a…”
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Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations by Lam, Margaret M. C., Wick, Ryan R., Wyres, Kelly L., Gorrie, Claire L., Judd, Louise M., Jenney, Adam W. J., Brisse, Sylvain, Holt, Kathryn E.

“…Mobile genetic elements (MGEs) that frequently transfer within and between bacterial species play a critical role in bacterial evolution, and often carry key…”
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Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores by Schwengers, Oliver, Barth, Patrick, Falgenhauer, Linda, Hain, Torsten, Chakraborty, Trinad, Goesmann, Alexander

“…Plasmids are extrachromosomal genetic elements that replicate independently of the chromosome and play a vital role in the environmental adaptation of…”
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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes by De Maio, Nicola, Shaw, Liam P., Hubbard, Alasdair, George, Sophie, Sanderson, Nicholas D., Swann, Jeremy, Wick, Ryan, AbuOun, Manal, Stubberfield, Emma, Hoosdally, Sarah J., Crook, Derrick W., Peto, Timothy E. A., Sheppard, Anna E., Bailey, Mark J., Read, Daniel S., Anjum, Muna F., Walker, A. Sarah, Stoesser, Nicole

“…Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly…”
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Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history by Coscolla, Mireia, Gagneux, Sebastien, Menardo, Fabrizio, Loiseau, Chloé, Ruiz-Rodriguez, Paula, Borrell, Sonia, Otchere, Isaac Darko, Asante-Poku, Adwoa, Asare, Prince, Sánchez-Busó, Leonor, Gehre, Florian, Sanoussi, C. N’Dira, Antonio, Martin, Affolabi, Dissou, Fyfe, Janet, Beckert, Patrick, Niemann, Stefan, Alabi, Abraham S., Grobusch, Martin P., Kobbe, Robin, Parkhill, Julian, Beisel, Christian, Fenner, Lukas, Böttger, Erik C., Meehan, Conor J., Harris, Simon R., de Jong, Bouke C., Yeboah-Manu, Dorothy, Brites, Daniela

“…Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC). The MTBC comprises several human-adapted lineages known as M…”
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Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction by Sanderson, Nicholas D., Kapel, Natalia, Rodger, Gillian, Webster, Hermione, Lipworth, Samuel, Street, Teresa L., Peto, Timothy, Crook, Derrick, Stoesser, Nicole

“…Complete, accurate, cost-effective, and high-throughput reconstruction of bacterial genomes for large-scale genomic epidemiological studies is currently only…”
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On the limits of 16S rRNA gene-based metagenome prediction and functional profiling by Matchado, Monica Steffi, Rühlemann, Malte, Reitmeier, Sandra, Kacprowski, Tim, Frost, Fabian, Haller, Dirk, Baumbach, Jan, List, Markus

“…Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the…”
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