Whole genome sequence analysis and characterization of lytic bacteriophages against antimicrobial-resistant diarrheagenic Escherichia coli strains isolated from various sources in Addis Ababa, Ethiopia

Abstract

Abstract The emergence of antibiotic resistance in E. coli strains has sparked a fervent investigation of alternative therapies such as the use of lytic bacteriophages. Phage whole genome sequencing is a novel method for learning more about proteins and other biomolecules encoded by phages, particularly phage lytic enzymes that are crucial to the lysis of bacterial cells. Seven potential lytic E. coli phages; EH-B-A (A1), EP-M-A, EP-B-K (E2), EI-SP-GF, ET-SD-TH, and ST-TK isolated from activated dairy farm sludges, Rivers, and hospital liquid waste were described. For sequencing, an Illumina NextSeq 550 sequencer was used. The virus nucleotide collection (nr/nt) (taxid:10239) was used to evaluate the whole genome sequences. Phylogenetic analysis was done using MEGA11 software. Genome sequencing revealed that each bacteriophage contains a linear double-stranded DNA genome. Phage isolates were taxonomically identified as 4 (57%) Myoviridae and 3 (43%) Siphoviridae phages. Phage genome length varied from 24264 to 143,710 bp, and their GC contents ranged from 43 to 54%. 33–218 CDSs (coding sequences) in total were predicted, with 19–77% of CDSs encoding functional proteins. All phages lacked tRNA in their genomes, except for EI-SP-GF, which possessed five tRNAs. Based on phylogenetic tree analysis, the phage isolates were related to Enterobacteria and E. coli phage sequences in the database. Screening did not show any genes encoding for a CRISPR-like system, virulence, antibiotic resistance, or lysogeny. Because of their stringent lytic nature, these phage isolates may be applied in the future to treat E. coli infections. This study may provide some primary data for the development of phage control techniques and advance our understanding of the genetic composition of E. coli phages.