ArticleBMC infectious diseases2013
Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak.
Article in BMC infectious diseases, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing.Molecular diagnosis & therapy · 2021Review
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- Metagenome Analysis as a Tool to Study Bacterial Infection Associated with Acute Surgical Abdomen.Journal of clinical medicine · 2018Article
- Distinct evolutionary patterns of Neisseria meningitidis serogroup B disease outbreaks at two universities in the USA.Microbial genomics · 2018Article
- Article
- Comprehensive Diagnosis of Bacterial Infection Associated with Acute Cholecystitis Using Metagenomic Approach.Frontiers in microbiology · 2017Article
- Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014.BMC microbiology · 2016Article
- Genome Sequencing and Comparative Genomics Analysis Revealed Pathogenic Potential inFrontiers in microbiology · 2016Article
- It Is Not All about Single Nucleotide Polymorphisms: Comparison of Mobile Genetic Elements and Deletions in Listeria monocytogenes Genomes Links Cases of Hospital-Acquired Listeriosis to the Environmental Source.Journal of clinical microbiology · 2015Article
- Computational algorithms to predict Gene Ontology annotations.BMC bioinformatics · 2015Article
- Current and emerging Legionella diagnostics for laboratory and outbreak investigations.Clinical microbiology reviews · 2015Review
- KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes.BMC genomics · 2014Article
- Clinical detection and characterization of bacterial pathogens in the genomics era.Genome medicine · 2014Article
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9 authors.
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Abstract
backgroundNext generation sequencing (NGS) is being increasingly used for the detection and characterization of pathogens during outbreaks. This technology allows rapid sequencing of pathogen full genomes, useful not only for accurate genotyping and molecular epidemiology, but also for identification of drug resistance and virulence traits.
methodsIn this study, an approach based on whole genome sequencing by NGS, comparative genomics, and gene function prediction was set up and retrospectively applied for the investigation of two N. meningitidis serogroup C isolates collected from a cluster of meningococcal disease, characterized by a high fatality rate.
resultsAccording to conventional molecular typing methods, all the isolates had the same typing results and were classified as outbreak isolates within the same N. meningitidis sequence type ST-11, while full genome sequencing demonstrated subtle genetic differences between the isolates. Looking for these specific regions by means of 9 PCR and cycle sequencing assays in other 7 isolates allowed distinguishing outbreak cases from unrelated cases. Comparative genomics and gene function prediction analyses between outbreak isolates and a set of reference N. meningitidis genomes led to the identification of differences in gene content that could be relevant for pathogenesis. Most genetic changes occurred in the capsule locus and were consistent with recombination and horizontal acquisition of a set of genes involved in capsule biosynthesis.
conclusionsThis study showed the added value given by whole genome sequencing by NGS over conventional sequence-based typing methods in the investigation of an outbreak. Routine application of this technology in clinical microbiology will significantly improve methods for molecular epidemiology and surveillance of infectious disease and provide a bulk of data useful to improve our understanding of pathogens biology.
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