Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

• Published in: Genome Biology Vol. 20; no. 1; p. 286
• Main Authors: Pightling, Arthur W., Pettengill, James B., Wang, Yu, Rand, Hugh, Strain, Errol
• Format: Journal Article
• Language: English
• Published: England BioMed Central 18.12.2019; BMC
• Subjects: Cluster Analysis; Contaminants; Contamination; data collection; Datasets; DNA Contamination; E coli; Escherichia coli; Escherichia coli - genetics; Gene mapping; genome; Genome, Bacterial; Genomes; Influence; Listeria; Listeria monocytogenes; Listeria monocytogenes - genetics; Nucleotide sequence; Phylogenetics; Phylogeny; Salmonella; Salmonella enterica; Salmonella enterica - genetics; Short Report; Single-nucleotide polymorphism; Species; Whole Genome Sequencing; Salmonella enterica; MLST; SNP; Clustering analyses; Whole-genome sequencing; Escherichia coli; Multi-locus sequence typing; Comparative genomics; Listeria monocytogenes; Phylogenetics; Single-nucleotide polymorphism; Contamination
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-019-1914-x

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.