ArticleThe Journal of infectious diseases2015
Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing.
Article in The Journal of infectious diseases, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 2 of them syntheses that pooled it.
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Who cites it
51 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark.The Lancet. Microbe · 2021Pooled it
- Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review.BMC medicine · 2016Pooled it
- Antimicrobial Resistance in Neisseria gonorrhoeae: Proceedings of the STAR Sexually Transmitted Infection-Clinical Trial Group Programmatic Meeting.Sexually transmitted diseases · 2019Trial
- Gene conversion and duplication contribute to genetic variation in an outbreak ofMicrobial genomics · 2025Article
- Drug Resistance and Epidemiological Success of Modern Mycobacterium tuberculosis Lineages in Western India.The Journal of infectious diseases · 2025Article
- Rapid identification of lactic acid bacteria at species/subspecies level via ensemble learning of Ramanomes.Frontiers in microbiology · 2024Article
- Article
- Insight into pathogenomics and phylogeography of hypervirulent and highly-lethal Mycobacterium tuberculosis strain cluster.BMC infectious diseases · 2023Article
- Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data.Journal of clinical microbiology · 2023Article
- Single Nucleotide Polymorphism-Based Real-Time PCR Screening Assay for Rapid Tracking of Bacterial Infection Clusters To Complement Whole-Genome Sequencing Efforts during Outbreak Investigations.Microbiology spectrum · 2022Article
- Practical approach to detection and surveillance of emerging highly resistant Mycobacterium tuberculosis Beijing 1071-32-cluster.Scientific reports · 2021Article
- Microbial source tracking using metagenomics and other new technologies.Journal of microbiology (Seoul, Korea) · 2021Review
- Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis.Molecular biology and evolution · 2021Article
- Mutation ofFrontiers in public health · 2021Article
- Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination.Applied and environmental microbiology · 2020Article
- Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana.Frontiers in medicine · 2020Article
- Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservationJournal of genetics · 2020Review
- Tuberculosis in migrants - screening, surveillance and ethics.Pneumonia (Nathan Qld.) · 2020Review
- Trends of Two Epidemic Multidrug-Resistant Strains ofThe American journal of tropical medicine and hygiene · 2019Article
- Development and application of affordable SNP typing approaches to genotype Mycobacterium tuberculosis complex strains in low and high burden countries.Scientific reports · 2019Article
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17 authors.
Funding
Abstract
backgroundWhole-genome sequencing (WGS) is increasingly used in molecular-epidemiological investigations of bacterial pathogens, despite cost- and time-intensive analyses. We combined strain-specific single-nucleotide polymorphism (SNP) typing and targeted WGS to investigate a tuberculosis cluster spanning 21 years in Bern, Switzerland.
methodsOn the basis of genome sequences of 3 historical outbreak Mycobacterium tuberculosis isolates, we developed a strain-specific SNP-typing assay to identify further cases. We screened 1642 patient isolates and performed WGS on all identified cluster isolates. We extracted SNPs to construct genomic networks. Clinical and social data were retrospectively collected.
resultsWe identified 68 patients associated with the outbreak strain. Most received a tuberculosis diagnosis in 1991-1995, but cases were observed until 2011. Two thirds were homeless and/or substance abusers. Targeted WGS revealed 133 variable SNP positions among outbreak isolates. Genomic network analyses suggested a single origin of the outbreak, with subsequent division into 3 subclusters. Isolates from patients with confirmed epidemiological links differed by 0-11 SNPs.
conclusionsStrain-specific SNP genotyping allowed rapid and inexpensive identification of M. tuberculosis outbreak isolates in a population-based strain collection. Subsequent targeted WGS provided detailed insights into transmission dynamics. This combined approach could be applied to track bacterial pathogens in real time and at high resolution.
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