Purpose: The genomic diversity of a large population of JJPX01.0061 isolated from surface waters across the VES was investigated using whole genome sequencing (WGS) approaches.
Methods: More than 70 environmental JJPX01.0061 isolates spanning seven years from the VES were subjected to whole genome shotgun sequencing, assembled, and aligned using a reference-based mapping approach to a closed Newport genome (CFSAN024225). A maximum likelihood tree was then constructed based on total SNP variation and evaluated in light of geographic variation based on the location from which each isolate was collected.
Results: Genomic diversity within this PFGE subtype clustered the strains into four distinct clade separated by a range of only 5 to more than 100 SNPs. Two clades (C and D) sorted isolates uniquely based on specific creeks and were identical (C, 0 SNPs intraclade variation) or nearly identical (D, 1 SNPs). Two additional clades (A and B) were polyphyletic with respect to creek location suggesting two independent introductions of JJPX01.0061 variants into each of these locales. Finally, clade B, comprised largely of Newports from 2007, was separated from more recent Newport groupings by at least 100 SNPs suggesting that substantial microevolutionary change has accrued within this lineage, a find consistent with its establishment and prolonged environmental persistence.
Significance: Genetic diversification of JJPX01.0061supports its long-term and endemic persistence within this regional microcosm. Occasional reintroduction of distinct genomic variants into common creek environments is also seen pointing to a potential role for geese or other water fowl species in the local mixing of isolates.