Recommended publications

Antimicrobial resistance and surveillance

• Antimicrobial resistance surveillance in the genomic age
• ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
• Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing
• Identification of acquired antimicrobial resistance genes
• Predicting antimicrobial susceptibility for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data
• SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
• The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST subcommittee
• Using the NCBI AMRFinder tool to determine antimicrobial resistance genotype-phenotype correlations within a collection of NARMS isolates

Bacterial species identification

• Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions
• Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology
• Transforming clinical microbiology with bacterial genome sequencing

Genome assembly

• Do it yourself guide to genome assembly

Horizontal gene transfer

• Identification of plasmids by PCR-based replicon typing
• In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing

Virulence of E. coli

• Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli

Whole genome sequencing

• Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
• Hackflex: low cost Illumina sequencing library construction for high samples counts
• Rapid bacterial genome sequencing: methods and applications in clinical microbiology
• Twenty years of bacterial genome sequencingWGS-based phylogeny and outbreak detection

WGS-based phylogeny and outbreak detection

• A beginner’s guide to phylogenetics
• Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica
• Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations
• Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak
• Solving the problem of comparing whole bacterial genomes across different sequencing platforms
• Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches