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bioinformatics

  • Open Access
    A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing
    Bacteriology
    A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

    Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations, with the most significant being the inability to resolve mixed amplicons when closely related species are coamplified from a mixed culture. This often leads to either increased turnaround time or...

    Stefan Moritz Neuenschwander, Miguel Angel Terrazos Miani, Heiko Amlang, Carmen Perroulaz, Pascal Bittel, Carlo Casanova, Sara Droz, Jean-Pierre Flandrois, Stephen L. Leib, Franziska Suter-Riniker, Alban Ramette
  • Free
    Computer Vision and Artificial Intelligence Are Emerging Diagnostic Tools for the Clinical Microbiologist
    Commentary
    Computer Vision and Artificial Intelligence Are Emerging Diagnostic Tools for the Clinical Microbiologist

    Artificial intelligence (AI) is increasingly becoming an important component of clinical microbiology informatics. Researchers, microbiologists, laboratorians, and diagnosticians are interested in AI-based testing because these solutions have the potential to improve a test’s turnaround time, quality, and cost. A study by Mathison et al. used computer vision AI (B. A. Mathison, J. L. Kohan, J. F. Walker, R. B. Smith, et al., J Clin...

    Daniel D. Rhoads
  • Reduced <em>In Vitro</em> Susceptibility of <span class="named-content genus-species" id="named-content-1">Streptococcus pyogenes</span> to β-Lactam Antibiotics Associated with Mutations in the <em>pbp2x</em> Gene Is Geographically Widespread
    Bacteriology
    Reduced In Vitro Susceptibility of Streptococcus pyogenes to β-Lactam Antibiotics Associated with Mutations in the pbp2x Gene Is Geographically Widespread

    Recently, two related Streptococcus pyogenes strains with reduced susceptibility to ampicillin, amoxicillin, and cefotaxime, antibiotics commonly used to treat S. pyogenes infections, were reported. The two strains had the same nonsynonymous (amino acid-substituting) mutation in the pbp2x...

    James M. Musser, Stephen B. Beres, Luchang Zhu, Randall J. Olsen, Jaana Vuopio, Hanne-Leena Hyyryläinen, Kirsi Gröndahl-Yli-Hannuksela, Karl G. Kristinsson, Jessica Darenberg, Birgitta Henriques-Normark, Steen Hoffmann, Dominque A. Caugant, Andrew J. Smith, Diane S. J. Lindsay, David M. Boragine, Timothy Palzkill
  • Open Access
    Identification of Infectious Agents in High-Throughput Sequencing Data Sets Is Easily Achievable Using Free, Cloud-Based Bioinformatics Platforms
    Letter to the Editor
    Identification of Infectious Agents in High-Throughput Sequencing Data Sets Is Easily Achievable Using Free, Cloud-Based Bioinformatics Platforms
    Joseph G. Chappell, Timothy Byaruhanga, Theocharis Tsoleridis, Jonathan K. Ball, C. Patrick McClure
  • Open Access
    Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> Genomes and Detection of Outbreaks
    Bacteriology
    Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks

    Genomic surveillance that combines bacterial sequencing and epidemiological information will become the gold standard for outbreak detection, but its clinical translation is hampered by the lack of automated interpretation tools. We performed a prospective pilot study to evaluate the analysis of methicillin-resistant Staphylococcus aureus (MRSA) genomes using the Next...

    Nicholas M. Brown, Beth Blane, Kathy E. Raven, Narender Kumar, Danielle Leek, Eugene Bragin, Paul A. Rhodes, David A. Enoch, Rachel Thaxter, Julian Parkhill, Sharon J. Peacock
  • Open Access
    Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of <span class="named-content genus-species" id="named-content-1">Campylobacter jejuni</span> and <span class="named-content genus-species" id="named-content-2">Salmonella enterica</span>
    Bacteriology
    Whole-Genome Sequencing and Bioinformatic Analysis of Isolates from Foodborne Illness Outbreaks of Campylobacter jejuni and Salmonella enterica

    Whole-genome sequencing (WGS) via next-generation sequencing (NGS) technologies is a powerful tool for determining the relatedness of bacterial isolates in foodborne illness detection and outbreak investigations. WGS has been applied to national outbreaks (for example, Listeria monocytogenes); however, WGS has rarely been used in smaller local outbreaks.

    ...
    Kelly F. Oakeson, Jennifer Marie Wagner, Andreas Rohrwasser, Robyn Atkinson-Dunn
  • Real-Time Analysis and Visualization of Pathogen Sequence Data
    Minireview
    Real-Time Analysis and Visualization of Pathogen Sequence Data

    The rapid development of sequencing technologies has to led to an explosion of pathogen sequence data, which are increasingly collected as part of routine surveillance or clinical diagnostics. In public health, sequence data are used to reconstruct the evolution of pathogens, to anticipate future spread, and to target interventions.

    Richard A. Neher, Trevor Bedford
  • Free
    Bacteriology
    Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole-Genome Sequences
    Amy Mason, Dona Foster, Phelim Bradley, Tanya Golubchik, Michel Doumith, N. Claire Gordon, Bruno Pichon, Zamin Iqbal, Peter Staves, Derrick Crook, A. Sarah Walker, Angela Kearns, Tim Peto
  • Letter to the Editor
    mcr-3 and mcr-4 Variants in Carbapenemase-Producing Clinical Enterobacteriaceae Do Not Confer Phenotypic Polymyxin Resistance
    Jeanette W. P. Teo, Marimuthu Kalisvar, Indumathi Venkatachalam, Oon Tek Ng, Raymond T. P. Lin, Sophie Octavia
  • Minireview
    Towards a Universal Molecular Microbiological Test
    Richard J. N. Allcock, Amy V. Jennison, David Warrilow

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