ArticleMolecular biology and evolution2019
Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers, 1 of them a synthesis that pooled it.
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Who cites it
108 citing papers in PubMed, 1 synthesis or guideline pooled it, 161 citations in OpenAlex.
- Using molecular methods to delineate norovirus outbreaks: a systematic review.Archives of virology · 2024Pooled it
- Comparing subsampling strategies for efficient pairwise analysis of large pathogen genomic and spatial datasets: An application to Mycobacterium tuberculosis transmission.PLoS computational biology · 2026Article
- Nationwide spread of multidrug resistant Klebsiella pneumoniae across US communities.Nature communications · 2026Article
- Whole-genome sequencing reveals high-risk ESBL and carbapenemase-producing Enterobacterales on maternity ward surfaces in Cameroon.Scientific reports · 2026Article
- Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.Nature microbiology · 2026Article
- Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing.Microbial genomics · 2026Article
- Long-term spatiotemporal evolution of drug-resistant Mycobacterium tuberculosis in China.Nature communications · 2026Article
- Whole-genome sequencing suggests recent transmission of rifampicin-resistant tuberculosis in Botswana.BMC infectious diseases · 2026Article
- Detecting healthcare-associated transmission and antifungal resistance inJournal of clinical microbiology · 2026Article
- Genome sequencing for prevention of health-care-associated bacterial infections.Nature reviews. Microbiology · 2026Review
- Aerosol-based exposure to opportunistic pathogens originating from hospital sink drains.American journal of infection control · 2026Article
- Article
- Whole-genome sequencing reveals genetic diversity and transmission dynamics ofMicrobial genomics · 2026Article
- Genomic epidemiology of theFrontiers in microbiology · 2026Article
- Genomic characterization ofFrontiers in veterinary science · 2026Article
- Transmission dynamics and attributable burden of tuberculosis among young and middle-aged adults in urban Shanghai: a genomic epidemiology study.Frontiers in public health · 2026Article
- Molecular insights into antimicrobial resistance in human bacterial pathogens: mechanisms, resistance genes, and translational diagnostic applications.Frontiers in microbiology · 2026Review
- Beyond traditional outbreak investigation: Using genomic data for enhanced detection of COVID-19 disease clusters in Utah.PloS one · 2026Article
- Exploring the Utility of MALDI-TOF Mass Spectrometry and Antimicrobial Resistance in Hospital Outbreak Detection.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2026Article
- High-risk lineages shape the resistome and virulome of multidrug-resistantFrontiers in cellular and infection microbiology · 2026Article
48 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 6 institutions in 4 countries.
Funding
Abstract
Whole-genome sequencing (WGS) is increasingly used to aid the understanding of pathogen transmission. A first step in analyzing WGS data is usually to define "transmission clusters," sets of cases that are potentially linked by direct transmission. This is often done by including two cases in the same cluster if they are separated by fewer single-nucleotide polymorphisms (SNPs) than a specified threshold. However, there is little agreement as to what an appropriate threshold should be. We propose a probabilistic alternative, suggesting that the key inferential target for transmission clusters is the number of transmissions separating cases. We characterize this by combining the number of SNP differences and the length of time over which those differences have accumulated, using information about case timing, molecular clock, and transmission processes. Our framework has the advantage of allowing for variable mutation rates across the genome and can incorporate other epidemiological data. We use two tuberculosis studies to illustrate the impact of our approach: with British Columbia data by using spatial divisions; with Republic of Moldova data by incorporating antibiotic resistance. Simulation results indicate that our transmission-based method is better in identifying direct transmissions than a SNP threshold, with dissimilarity between clusterings of on average 0.27 bits compared with 0.37 bits for the SNP-threshold method and 0.84 bits for randomly permuted data. These results show that it is likely to outperform the SNP-threshold method where clock rates are variable and sample collection times are spread out. We implement the method in the R package transcluster.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.