ArticleJournal of clinical microbiology2011
Inadequacies of minimum spanning trees in molecular epidemiology.
Article in Journal of clinical microbiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed.
- Observer-Based Source Localization in Tree Infection Networks via Laplace Transforms.Bulletin of mathematical biology · 2026Article
- Contact precautions prevent cross-contamination of extended-spectrum beta-lactamase-producing Enterobacterales in an intensive care unit: a prospective observational study.Annals of intensive care · 2025Article
- Multi-cluster outbreak ofEpidemiology and infection · 2025Article
- Identification and epidemiological analysis of a putative novel hantavirus in Australian flying foxes.Virus genes · 2025Article
- Analyses of the Genetic Diversity and Population Structures ofJournal of fungi (Basel, Switzerland) · 2024Article
- Outbreak ofEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2024Article
- Investigation of an international water polo tournament in Czechia as a potential source for early introduction of the SARS-CoV-2 Omicron variant into Belgium, Switzerland and Germany, November 2021.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2023Article
- Genotyping and biofilm formation of Mycoplasma hyopneumoniae and their association with virulence.Veterinary research · 2022Article
- Molecular epidemiology of community- and hospital-associated Clostridioides difficile infections in Jönköping, Sweden, October 2017 - March 2018.APMIS : acta pathologica, microbiologica, et immunologica Scandinavica · 2022Article
- Outbreak ofEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2022Article
- Identification of a canine coronavirus in Australian racing Greyhounds.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2022Article
- Exploring genetic diversity, population structure, and phylogeography inStudies in mycology · 2021Article
- Trends in the molecular epidemiology and population genetics of emergingStudies in mycology · 2021Article
- Investigations on spreading of PRRSV among swine herds by improved minimum spanning network analysis.Scientific reports · 2020Article
- Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Outbreak of gastroenteritis highlighting the diagnostic and epidemiological challenges of enteroinvasiveEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2020Article
- Outbreak of unusual HEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2019Article
- Degree and centrality-based approaches in network-based variable selection: Insights from the Singapore Longitudinal Aging Study.PloS one · 2019Article
- Antimicrobial Resistance, Virulence Factors, and Genetic Profiles of Vibrio parahaemolyticus from Seafood.Applied and environmental microbiology · 2018Article
- Microevolution of Streptococcus agalactiae ST-261 from Australia Indicates Dissemination via Imported Tilapia and Ongoing Adaptation to Marine Hosts or Environment.Applied and environmental microbiology · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Minimum spanning trees (MSTs) are frequently used in molecular epidemiology research to estimate relationships among individual strains or isolates. Nevertheless, there are significant caveats to MST algorithms that have been largely ignored in molecular epidemiology studies and that have the potential to confound or alter the interpretation of the results of those analyses. Specifically, (i) presenting a single, arbitrarily selected MST illustrates only one of potentially many equally optimal solutions, and (ii) statistical metrics are not used to assess the credibility of MST estimations. Here, we survey published MSTs previously used to infer microbial population structure in order to determine the effect of these factors. We propose a technique to estimate the number of alternative MSTs for a data set and find that multiple MSTs exist for each case in our survey. By implementing a bootstrapping metric to evaluate the reliability of alternative MST solutions, we discover that they encompass a wide range of credibility values. On the basis of these observations, we conclude that current approaches to studying population structure using MSTs are inadequate. We instead propose a systematic approach to MST estimation that bases analyses on the optimal computation of an input distance matrix, provides information about the number and configurations of alternative MSTs, and allows identification of the most credible MST or MSTs by using a bootstrapping metric. It is our hope this algorithm will become the new "gold standard" approach for analyzing MSTs for molecular epidemiology so that this generally useful computational approach can be used informatively and to its full potential.
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