Characterization of bacteriophages infecting multidrug-resistant uropathogenic Escherichia coli strains

Abstract

Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infections, and strains that are resistant to antibiotics are a major problem in treating these infections. Phage therapy is a promising alternative approach that can be used to treat infections caused by polyresistant bacterial strains. In the present study, 16 bacteriophages isolated from sewage and surface water were investigated. Phage host specificity was tested on a collection of 77 UPEC strains. The phages infected 2-44 strains, and 80% of the strains were infected by at least one phage. The susceptible E. coli strains belonged predominantly to the B2 phylogenetic group, including strains of two clones, CC131 and CC73, that have a worldwide distribution. All of the phages belonged to class Caudoviricetes and were identified as members of the families Straboviridae, Autographiviridae, and Drexlerviridae and the genera Kagunavirus, Justusliebigvirus, and Murrayvirus. A phage cocktail composed of six phages - four members of the family Straboviridae and two members of the family Autographiviridae - was prepared, and its antibacterial activity was tested in liquid medium. Complete suppression of bacterial growth was observed after 5-22 hours of cultivation, followed by partial regrowth. At 24 hours postinfection, the cocktail suppressed bacterial growth to 43-92% of control values. Similar results were obtained when testing the activity of the phage cocktail in LB and in artificial urine medium. The results indicate that our phage cocktail has potential to inhibit bacterial growth during infection, and they will therefore be preserved in the national phage bank, serving as valuable resources for therapeutic applications.

Keywords: Escherichia coli; UPEC; UTI; bacteriophages; phage therapy.

Fig. 1

Host specificity of phages against a panel of UPEC strains. (A) Sensitivity of 77 UPEC strains to the isolated phages. Legend: strong (4), moderate (3), weak (2), lysis from without (1). (B) Host spectrum of isolated phages according to phylogenetic groups; strains with EOP > 0.01% were counted

Fig. 2

Genome comparison of the new phages with the reference genomes. Comparisons were made in EasyFig

Fig. 3

Bacterial growth curves in the presence of phage cocktail in LB and AU media. Growth inhibition was observed as a decrease in optical density compared to control without phages. Three different MOIs were used: 1 (triangle), 10 (square), 100 (diamond), and none in control (circle). Results are presented as the mean of three measurements replicated in three independent experiments

Fig. 3

Bacterial growth curves in the presence of phage cocktail in LB and AU media. Growth inhibition was observed as a decrease in optical density compared to control without phages. Three different MOIs were used: 1 (triangle), 10 (square), 100 (diamond), and none in control (circle). Results are presented as the mean of three measurements replicated in three independent experiments

Fig. 4

Overall bacterial growth inhibition in the presence of phage cocktail in LB and AU media. Growth inhibition was observed as an area of optical density in cocktail samples divided by an area of optical density in control samples without phages. Three different MOIs were used: 1 (white), 10 (grey), and 100 (black)