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On the ability to extract MLVA profiles of Vibrio cholerae isolates from WGS data generated with Oxford Nanopore Technologies.
BMC Res Notes
January 2025
Center for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research (IREC), Université catholique de Louvain (UCLouvain), Brussels, Belgium.
Objective: Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used to subtype pathogens causing foodborne and waterborne disease outbreaks. The MLVAType shiny application was previously designed to extract MLVA profiles of Vibrio cholerae isolates from whole-genome sequencing (WGS) data, and provide backward compatibility with traditional MLVA typing methods. The previous development and validation work was conducted using short (pair-end 300 and 150 nt long) reads from Illumina MiSeq and Hiseq sequencing.
View Article and Find Full Text PDFOutbreak of perichondritis associated with ear piercings and a contaminated water system.
Epidemiol Infect
January 2025
Health Protection Operations, South West, UK Health Security Agency, Bristol, UK.
In September 2023, the UK Health Security Agency's (UKHSA) South West Health Protection Team received notification of patients with perichondritis. All five cases had attended the same cosmetic piercing studio and a multi-disciplinary outbreak control investigation was subsequently initiated. An additional five cases attending the same studio were found.
View Article and Find Full Text PDFDefects in the Mitochondrial Genome of Dogs with Recurrent Tumours.
Int J Mol Sci
December 2024
Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 St., 20-950 Lublin, Poland.
This study presents a comprehensive analysis of mitochondrial DNA (mtDNA) variations in dogs diagnosed with primary and recurrent tumours, employing Oxford Nanopore Technologies (ONT) for sequencing. Our investigation focused on mtDNA extracted from blood and tumour tissues of three dogs, aiming to pinpoint polymorphisms, mutations, and heteroplasmy levels that could influence mitochondrial function in cancer pathogenesis. Notably, we observed the presence of mutations in the D-loop region, especially in the VNTR region, which may be crucial for mitochondrial replication, transcription, and genome stability, suggesting its potential role in cancer progression.
View Article and Find Full Text PDFA Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation.
Mol Biol Evol
December 2024
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
Pangenomes can facilitate a deeper understanding of genome complexity. Using de novo phased long-read assemblies of eight representative goat breeds, we constructed a graph-based pangenome of goats (Capra hircus) and discovered 113-Mb autosomal novel sequences. Combining this multi-assembly pangenome with low-coverage PacBio HiFi sequences, we constructed a long-read structural variations (SVs) database containing 59,325 SV deletions, 84,910 SV insertions, and 24,954 other complex SV alleles.
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.
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