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Comparison of whole genome sequencing typing tools for the typing of Belgian Legionella pneumophila outbreaks isolates.
Eur J Clin Microbiol Infect Dis
December 2024
Department of Microbiology and Infection Control, National Reference Centre for Legionella Pneumophila, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090, Brussels, Belgium.
Whole genome sequencing (WGS) marks a turning point for outbreak investigations for microorganisms related to public health matters, like Legionella pneumophila (Lp). Here, we evaluated the available Lp WGS typing tools for isolates of previously documented Belgian outbreaks, as well as small groups of related and non-related isolates. One reference strain and 77 clinical and environmental isolates were evaluated.
View Article and Find Full Text PDFValidation and implementation of whole-genome sequencing-based analytical methods for molecular surveillance and relatedness analysis of complex isolates at a national reference laboratory.
Heliyon
November 2024
Irish Mycobacteria Reference Laboratory (IMRL), St. James' Hospital, Dublin, Ireland.
Whole genome sequencing-based methodologies have become extremely relevant for the molecular surveillance of human pathogens and are being increasingly introduced into national reference laboratory services. In this study, we describe the validation and implementation of core-genome Multi-Locus Sequence Typing (cgMLST) and whole genome single-nucleotide polymorphism (wgSNP) analysis at the Irish Mycobacteria Reference Laboratory, as a replacement for Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing. Concordance of clustering, discriminatory power, and ease-of-use of both WGS analytical methods were evaluated.
View Article and Find Full Text PDFRapid inference of antibiotic susceptibility phenotype of uropathogens using metagenomic sequencing with neighbor typing.
Microbiol Spectr
November 2024
The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.
Unlabelled: Timely diagnostic tools are needed to improve antibiotic treatment. Pairing metagenomic sequencing with genomic neighbor typing algorithms may support rapid clinically actionable results. We created resistance-associated sequence elements (RASE) databases for and .
View Article and Find Full Text PDFMulticenter evaluation of Fourier transform infrared (FTIR) spectroscopy as a first-line typing tool for carbapenemase-producing in clinical settings.
J Clin Microbiol
November 2024
Servicio de Microbiología y Enfermedades Infecciosas, Institute of Health Research Gregorio Marañón (IiSGM), Hospital General Universitario Gregorio Marañón, Madrid, Spain.
Early use of infection control methods is critical for preventing the spread of antimicrobial resistance. Whole-genome sequencing (WGS) is considered the gold standard for investigating outbreaks; however, the turnaround time is usually too long for clinical decision-making and the method is also costly. The aim of this study was to evaluate the performance of Fourier transform infrared (FTIR) and artificial intelligence tools as a first-line typing tool for typing carbapenemase-producing (CPK) in the hospital setting.
View Article and Find Full Text PDFGenomic surveillance of multidrug-resistant organisms based on long-read sequencing.
Genome Med
November 2024
Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
Article Synopsis
- Multidrug-resistant organisms (MDRO) are a major public health concern, and understanding their genomic characteristics is vital for monitoring and controlling infections.
- This study focuses on the use of long-read whole-genome sequencing (WGS) to analyze the molecular profiles of 356 MDRO isolates, including various bacteria such as Klebsiella pneumoniae and methicillin-resistant Staphylococcus aureus (MRSA).
- Results showed that long-read sequencing provides comparable molecular data to short-read sequencing, with high consistency in multi-locus sequence typing (wgMLST) profiles, though some differences were noted in Pseudomonas aeruginosa.
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