ArticleGenome biology2019
Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 22 citations in OpenAlex.
- Low-level contamination confounds population genomic analysis.G3 (Bethesda, Md.) · 2026Article
- Impact of sequencing read quality on whole-genome sequencing outcomes for foodborne pathogens using a BacWORK standardized analysis workflow.Bioinformatics advances · 2026Article
- Genomic insights intoFrontiers in microbiology · 2026Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- An inter-laboratory study characterizes the impact of bioinformatic approaches on genome-based cluster detection for foodborne bacterial pathogens.Frontiers in microbiology · 2025Article
- Harmonization of supervised machine learning practices for efficient source attribution of Listeria monocytogenes based on genomic data.BMC genomics · 2023Article
- Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.International journal of molecular sciences · 2022Review
- A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches.Scientific data · 2022Article
- Contamination detection in genomic data: more is not enough.Genome biology · 2022Review
- Multidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases.Microbiology spectrum · 2021Article
- Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.Microbial genomics · 2021Article
- Article
- Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.Virus evolution · 2021Article
- The Population Genetics, Virulence, and Public Health Concerns ofFrontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogenetics, and multi-locus sequencing typing, have not been quantified. By developing and analyzing 720 Listeria monocytogenes, Salmonella enterica, and Escherichia coli short-read datasets, we demonstrate that within-species contamination causes errors that confound clustering analyses, while between-species contamination generally does not. Contaminant reads mapping to references or becoming incorporated into chimeric sequences during assembly are the sources of those errors. Contamination sufficient to influence clustering analyses is present in public sequence databases.
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