Typing methods based on whole genome sequencing data

L Uelze, J Grützke, M Borowiak, JA Hammerl… - One Health …, 2020 - Springer
Whole genome sequencing (WGS) of foodborne pathogens has become an effective
method for investigating the information contained in the genome sequence of bacterial …

Bioinformatics in bioscience and bioengineering: recent advances, applications, and perspectives

K Uesaka, H Oka, R Kato, K Kanie, T Kojima… - Journal of bioscience …, 2022 - Elsevier
Recent advances have led to the emergence of highly comprehensive and analytical
approaches, such as omics analysis and high-resolution, time-resolved bioimaging analysis …

Population genomics meets the taxonomy of cyanobacteria

P Dvořák, E Jahodářová, A Stanojković, S Skoupý… - Algal Research, 2023 - Elsevier
The emergence of cyanobacterial species (speciation) is driven by mutation, selection, gene
flow, and geographical and ecological isolation. Population genomics explores the process …

Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial …

B Bogaerts, A Van den Bossche… - Journal of Clinical …, 2024 - Am Soc Microbiol
Whole-genome sequencing has become the method of choice for bacterial outbreak
investigation, with most clinical and public health laboratories currently routinely using short …

Invasion and diversity in Pseudomonas aeruginosa urinary tract infections

JN Newman, RV Floyd… - Journal of medical …, 2022 - microbiologyresearch.org
Introduction. P. aeruginosa is an opportunistic Gram-negative pathogen frequently isolated
in urinary tract infections (UTI) affecting elderly and catheterized patients and associated …

Mycobacterium bovis: From Genotyping to Genome Sequencing

AMS Guimaraes, CK Zimpel - Microorganisms, 2020 - mdpi.com
Mycobacterium bovis is the main pathogen of bovine, zoonotic, and wildlife tuberculosis.
Despite the existence of programs for bovine tuberculosis (bTB) control in many regions, the …

A bioinformatics whole-genome sequencing workflow for clinical mycobacterium tuberculosis complex isolate analysis, validated using a reference collection …

B Bogaerts, T Delcourt, K Soetaert… - Journal of Clinical …, 2021 - Am Soc Microbiol
The use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has
increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular …

Genome Comparison Identifies Different Bacillus Species in a Bast Fibre-Retting Bacterial Consortium and Provides Insights into Pectin Degrading Genes

S Datta, D Saha, L Chattopadhyay, B Majumdar - Scientific reports, 2020 - nature.com
Retting of bast fibres requires removal of pectin, hemicellulose and other non-cellulosic
materials from plant stem tissues by a complex microbial community. A microbial retting …

In Silico Evaluation of Variant Calling Methods for Bacterial Whole-Genome Sequencing Assays

YM Seah, MK Stewart, D Hoogestraat… - Journal of Clinical …, 2023 - Am Soc Microbiol
Identification and analysis of clinically relevant strains of bacteria increasingly relies on
whole-genome sequencing. The downstream bioinformatics steps necessary for calling …

Isolation and characterization of Staphylococcus argenteus strains from retail foods and slaughterhouses in Japan

Y Wakabayashi, K Takemoto, S Iwasaki… - International journal of …, 2022 - Elsevier
Staphylococcus argenteus has been recently established as a novel species of
Staphylococcus aureus complex. It is known to cause various human diseases, such as skin …