Zhu, H. X. | Search bioRxiv

bioRxiv2024

Discovery and characterisation of new phage targeting uropathogenic Escherichia coli

Antimicrobial resistance (AMR) is increasing at an escalating rate with few new therapeutic options in the pipeline. Urinary tract infections (UTIs) are one of the most prevalent bacterial infections globally and are particularly prone to becoming recurrent and antibiotic resistant. The aim of this study was to discover and characterise new bacterial viruses (phage) against uropathogenic Escherichia coli (UPEC), which is the leading cause of UTIs. Six phages from the Autographiviridae family and Guernseyvirinae sub-family were isolated from wastewater and sequenced. The length of the isolated phage genomes was between 39,471 bp and 45,233 bp, with a GC content between 45.0% and 51.0%, and 57 to 84 predicted coding sequences (CDS) per genome. These phages were found to infect between 25 - 75% of the twelve UPEC strains tested. Using sequence comparison and predicted structural alignments, we show a similarity between the C-terminal domain of the tail fiber proteins of two phage that correlates with their host range. In vitro characterisation of phage cocktails against a single bacterial strain did not perform better than the best-performing phage, but did show synergistic improvement against a mixed UPEC strain population. Lastly, we measured the effectiveness of treatment with phage with different lytic kinetics in a sequential treatment and found it was improved over single phage treatment.

microbiology↗

bioRxiv2022

IbpAB small heat shock proteins are not host factors for bacteriophage {varphi}X174 replication

Bacteriophages exploit host proteins for successful infection. Small heat shock proteins are a universally conserved family of stress-induced molecular chaperones that prevent irreversible aggregation of proteins. Two small heat shock proteins, IbpA and IbpB, are a class of holding modulators or "holdases", which bind partially folded proteins and await ATP-driven folding chaperones for refolding. Bacteriophage {phi}X174 is a small, icosahedral, and non-tailed virus belonging to the Microviridae. During {phi}X174 infection of Escherichia coli C122, IbpA and IbpB were previously found to be the most highly upregulated host proteins, with expression levels comparable to {phi}X174 proteins. In this work, to understand the role of IbpA and IbpB during {phi}X174 infection, we used a hybrid approach of CRISPR interference and genomic knockouts to disrupt the ibpA and ibpB genes. We show that these two proteins do not appear to be necessary for efficient {phi}X174 replication, and moreover, their absence has no effect on {phi}X174 fecundity. ImportanceThe small heat shock proteins (sHsps) are universally conserved family of stress-induced molecular chaperones that prevent irreversible protein aggregation. In E. coli, the IbpA/B sHsps work together, and separately, to bind partially folded proteins and await ATP-driven folding chaperones for refolding. These proteins are highly upregulated during protein overexpression and bacteriophage infection, but their collective role in bacteriophage infection has not been investigated. Here, we show that the ibpA/B genes are dispensable for bacteriophage {phi}X174 infection, and are likely not essential host factors despite their abundance during diverse phage infections. Instead, this work points towards their role as cell wall integrity sensors, similar to the phage shock protein system, in addition to their canonical role as holdases of cytoplasmic protein.

microbiology↗