Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs

• DOI: 10.1099/mgen.0.000544
• Publication Date: 2021-03-15T16:16:25Z
• Authors: Timothy J. Dallman; David R. Greig; Saheer E. Gharbia; Claire Jenkins
• Keywords: Lineage (genetic); SNP; Linkage (software)

Sequence similarity of pathogen genomes can infer the relatedness between isolates as fewer genetic differences identified pairs isolates, less time since divergence from a common ancestor. Clustering based on hierarchical single linkage clustering pairwise SNP distances has been employed to detect and investigate outbreaks. Here, we evaluated evidence-base for interpretation phylogenetic clusters Shiga toxin-producing Escherichia coli (STEC) O157:H7. Whole genome sequences 1193 STEC O157:H7 submitted Public Health England July 2015 December 2016 were mapped Sakai reference strain. Hierarchical was performed difference all at descending distance thresholds. Cases with known epidemiological links fell within 5-SNP clusters. Five-SNP community where an link not more likely be temporally and/or geographically related than sporadic cases. Ten-SNP occurred infrequently challenging cases few, dispersed. A cluster threshold 5-SNPs utility detection outbreaks linked both persistent point sources. Deeper analysis revealed that distinction domestic UK imported could inferred sub-lineage level. associated domestically acquired infection fall are predominantly travel caused by contaminated food.