Genome Analysis of Bacteriophage (U1G) of <em>Schitoviridae</em>, Host Receptor Prediction using Machine Learning Tools and its Evaluation to Mitigate Colistin Resistant Clinical Isolate of<em> Escherichia Coli</em> <em>In Vitro</em> and <em>In Vivo</em>

Abstract

The objective of the present study is to isolate phages targeting colistin resistant E. coli clinical isolates (U3790 and U1007), sequence and analyze the phage genome and use machine learning tools to predict host cell surface receptor and finally evaluate the efficiency of the phage in vitro and in vivo in a zebrafish model. Phage targeting colistin resistant U3790 could not be isolated possibly due to presence of capsule and intact prophages in genome of U3790 strain. Phage specific for E. coli U1007 was isolated from Ganges River (designated as U1G). The obtained phage was triple purified and enriched. U1G phages had a greater burst size of 195 PFU/cell and a short latent time of 25 min. TEM analysis showed that U1Gphage possessed a capsid of 70 nm in diameter with a shorter tail, which shows that U1G belongs to the family Podoviridae. Genome sequencing and analysis revealed that the size of the phage genome is 73275 bp with no tRNA sequence, antibiotic resistant or virulent genes. PHASTER annotation revealed the presence of phage RNA polymerase gene in the genome, which favors the classification of phage under a new family Schitoviridae. A machine learning (ML) based multi-class classification model using algorithms such as Random Forest, Logistic Regression, and Decision Tree were employed to predict the host receptor targeted by U1G phage and the best performing two algorithms predicted LPS O antigen as the host receptor targeted by the U1G receptor binding protein (RBP), the tail spike protein. The isolated phage was stable from pH 5.0 to 9.0 and upto 45&amp;deg;C. In vitro time kill assay showed an initial 5 log decline in CFU/ml of U1007 at 2 h in the presence of U1G followed by regrowth, Addition of colistin with U1G restricted the growth until 6 h, however it also resulted in a regrowth by 24 h. The phage did not pose any toxicity to zebrafish as evidenced by liver/brain enzyme profiles. In vivo intramuscular infection study showed that U1G and Col + U1G treatment caused a 0.8 log and 1.4 log decline, respectively underscoring its potential for use in phage cocktail therapy.