Novel Escherichia coli-Infecting Bacteriophages Isolated from Uganda That Target Human Clinical Isolates

Abstract

Background: The antimicrobial resistance catastrophe is a growing global health threat and predicted to be worse in developing countries. Phages for Global Health (PGH) is training scientists in these regions to isolate relevant therapeutic phages for pathogenic bacteria within their locality, and thus contributing to making phage technology universally available.

Materials and methods: During the inaugural PGH workshop in East Africa, samples from Ugandan municipal sewage facilities were collected and two novel Escherichia coli lytic phages were isolated and characterized.

Results: The phages, UP19 (capsid diameter ∼100 nm, contractile tail ∼120/20 nm) and UP30 (capsid diameter ∼70 nm, noncontractile tail of ∼170/20 nm), lysed ∼82% and ∼36% of the 11 clinical isolates examined, respectively. The genomes of UP19 (171.402 kb, 282 CDS) and UP30 (49.834 kb, 75 CDS) closely match the genera Dhakavirus and Tunavirus, respectively.

Conclusion: The phages isolated have therapeutic potential for further development against E. coli infections.

Keywords: Escherichia coli phage; Phages for Global Health; antimicrobial resistance; phage therapy.

FIG. 1.

Morphologies of the two newly isolated Escherichia coli phages (A) UP19 and (B) UP30 from Uganda during the PGH workshop held at Makerere University in 2017. PGH, Phages for Global Health. Both phages belonged to Class Caudoviricetes with UP19 isolated directly from a sewage sample and phage UP30, isolated from an overnight enrichment procedure with the liquid culture of host, PA5. Phage dimension was based on measuring at least 10 particles (standard deviation, 0.47) on ImageJ. Bar ∼100 nm.

FIG. 2.

Genome maps of E. coli phages (Ai) UP19 and (Aii) UP30 isolated in Uganda during the inaugural PGH workshop in 2017 and alignments of (Bi) UP19 and (Bii) UP30 to type phages showing regions of gene similarities. Genomes were annotated with PHROGS database and visualized using Proksee. The phages were isolated from sewage samples collected in Kampala municipal area. Genomes were annotated with PHROGS database and alignments conducted using Clinker. Accession numbers of phages used in the alignment are shown in Supplementary Table S2. The data for this study have been deposited in the ENA PRJEB61472.

FIG. 3.

Images of VIRIDIC generated heatmap showing intergenomic similarity values and alignment indicators for phage UP19 (A) and UP30 (B) isolates from in this study and other closely related phages. Based on the ICTV established thresholds for the demarcation of viruses into species (95%) and into genera (∼70%) we could infer both phages UP19 and UP30 as novel species based on the intergenomic similarities shown on the heatmaps. International Committee on Taxonomy of Viruses.