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Genomic Surveillance for Antimicrobial Resistance in Mannheimia haemolytica Using Nanopore Single Molecule Sequencing Technology

https://doi.org/10.1101/395087
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MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
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Nanopore sequencing and assembly of a human genome with ultra-long reads
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Characterization of bla CMY Plasmids and Their Possible Role in Source Attribution of Salmonella enterica Serotype Typhimurium Infections
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The Sequence Alignment/Map format and SAMtools
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QUAST: quality assessment tool for genome assemblies
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Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data
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Activity of non-fluorinated quinolones (NFQs) against quinolone-resistant Escherichia coli and Streptococcus pneumoniae
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The development of the BSAC standardized method of disc diffusion testing
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tet(L)-mediated tetracycline resistance in bovine Mannheimia and Pasteurella isolates
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Identification of acquired antimicrobial resistance genes
inferredcites →https://doi.org/10.1093/jac/dks496openalex-snapshot
Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing
inferredcites →https://doi.org/10.1093/jac/dkt180openalex-snapshot
Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data
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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
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The Pfam protein families database: towards a more sustainable future
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HMMER web server: 2015 update
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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
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Completing bacterial genome assemblies with multiplex MinION sequencing
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Circos: An information aesthetic for comparative genomics
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Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene
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Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
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Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
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The Comprehensive Antibiotic Resistance Database
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Molecular Epidemiology of Ceftiofur-Resistant Escherichia coli Isolates from Dairy Calves
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Complete Genome Sequence of Mannheimia haemolytica Strain Mh10517, Isolated from Sheep in South Africa
inferredcites →https://doi.org/10.1128/genomea.00188-13openalex-snapshot
Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle
inferredcites →https://doi.org/10.1128/genomea.00318-13openalex-snapshot
Complete Genome Sequence of Mannheimia haemolytica Strain 42548 from a Case of Bovine Respiratory Disease
inferredcites →https://doi.org/10.1128/genomea.00417-15openalex-snapshot
Complete Closed Genome Sequences of a Mannheimia haemolytica Serotype A1 Leukotoxin Deletion Mutant and Its Wild-Type Parent Strain
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Comparison of Meropenem MICs and Susceptibilities for Carbapenemase-Producing Klebsiella pneumoniae Isolates by Various Testing Methods
inferredcites →https://doi.org/10.1128/jcm.01069-17openalex-snapshot
Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates
inferredcites →https://doi.org/10.1128/jcm.02452-13openalex-snapshot
Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples
inferredcites →https://doi.org/10.1128/jcm.03117-13openalex-snapshot
Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing
inferredcites →https://doi.org/10.1128/jcm.03617-13openalex-snapshot
Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli
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Mechanisms of Antibiotic Resistance
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MEASUREMENT OF IN SITU ACTIVITIES OF NONPHOTOSYNTHETIC MICROORGANISMS IN AQUATIC AND TERRESTRIAL HABITATS
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Antimicrobial multidrug resistance and coresistance patterns of Mannheimia haemolytica isolated from bovine respiratory disease cases—a three-year (2009–2011) retrospective analysis
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BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/s12864-016-3316-8openalex-snapshot
Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes
inferredcites →https://doi.org/10.1186/s13059-015-0677-2openalex-snapshot
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
inferredcites →https://doi.org/10.1186/s13059-016-1103-0openalex-snapshot
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
inferredcites →https://doi.org/10.1371/journal.pcbi.1005595openalex-snapshot
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
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GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands
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Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.3311/ppee.10015openalex-snapshot
Beyond Homopolymer Errors: a Systematic Investigation of Nanopore-based DNA Sequencing Characteristics Using HLA-DQA2
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Metagenomics: The Next Culture-Independent Game Changer
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A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies
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Isolation, Characterization, and Antibacterial Activity of Hard-to-Culture Actinobacteria from Cave Moonmilk Deposits
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