bioinformatics
BacteriologyA Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore SequencingAmplicon 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...
CommentaryComputer Vision and Artificial Intelligence Are Emerging Diagnostic Tools for the Clinical MicrobiologistArtificial 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...
BacteriologyReduced In Vitro Susceptibility of Streptococcus pyogenes to β-Lactam Antibiotics Associated with Mutations in the pbp2x Gene Is Geographically WidespreadRecently, 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...
BacteriologyPilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of OutbreaksGenomic 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...
BacteriologyWhole-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.
MinireviewReal-Time Analysis and Visualization of Pathogen Sequence DataThe 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.
