Escherichia Species Diversity Across Pristine and Impacted Catchments: Evidence for Avian Sources of Escherichia marmotae in Aotearoa/New Zealand

A total of 1347 Escherichia isolates from water, soil, sediment, biofilm, and faecal samples (n = 413) across five pristine (native forest) and five impacted (pastoral or urban) sites were subtyped into E. coli phylotypes and non-E. coli Escherichia spp. (Escherichia marmotae, Escherichia ruysiae and Escherichia whittamii). Impacted sites showed a higher prevalence of E. coli, particularly the ruminant-associated phylotype B1, across water, biofilm, sediment, and mammalian faeces. In contrast, E. marmotae (189 isolates) were more common in pristine sites and avian faeces, with a prevalence of 28.7%. Metabarcoding of the hypervariable gene gnd further revealed that Escherichia population diversity was greatest in aquatic environments (water, sediment, biofilm). Escherichia population diversity was also associated with elevated freshwater E. coli concentrations, increased prevalence of pathogenic E. coli virulence factors (stx1, stx2 and eae), and higher livestock numbers. In contrast, diversity measures for Escherichia populations were lowest in avian faeces and soil samples, and samples obtained from pristine sites with fewer faecal sources. These findings highlight the ecological role of birds as reservoirs of E. marmotae and their contribution to microbial diversity in New Zealand's freshwater ecosystems.