Municipal Wastewater in Ottawa, Canada contains a reservoir of bacteriophages with clinically relevant Escherichia coli and Klebsiella pneumoniae Hosts

Abstract

The recent rise of antimicrobial resistant bacteria in health care and environmental settings has been detrimental to the feasibility of antibiotic treatments for patients and agricultural applications. Along with this escalating issue, a resurgence of bacteriophage research has occurred, and phage therapy is proving to be a powerful case-specific alternative. However, a centralized source of phages that are accessible, abundant, and characterized as candidates for potential use in therapeutic applications remains to be fully established. This study aims to identify the range of bacteriophages available in municipal wastewater from Ottawa, Ontario that can infect and lyse Escherichia coli O1:K1:H7 and Klebsiella pneumoniae K3 hosts. Building-level sewer shed, influent, and primary sludge samples were screened for the presence of these phages which were then isolated through several rounds of plaque purification, sequenced by Nanopore technology, and annotated. Ten phages belonging to the genus Kayfunavirus, Vectrevirus, Kuravirus, or Sugarlandvirus were identified and bio-banked from different types of wastewater at several time points. These phages are 96-99% identical to phages isolated in Germany, Switzerland, and Spain, but contain divergent structural and metabolic genes. This work contributes to the ever-growing database of sequenced phages, provided with a physical archive of the organisms, and helps uncover the extent of phage biodiversity at different levels of wastewater treatment facilities that are readily available for screening in phage therapy applications.