Myoviridae phage PDX kills enteroaggregative Escherichia coli without human microbiome dysbiosis

Abstract

<b>Introduction.</b> Bacteriophage therapy can be developed to target emerging diarrhoeal pathogens, but doing so in the absence of microbiome disruption, which occurs with antibiotic treatment, has not been established.<b>Aim.</b> Identify a therapeutic bacteriophage that kills diarrhoeagenic enteroaggregative <i>Escherichia coli</i> (EAEC) while leaving the human microbiome intact.<b>Methodology.</b> Phages from wastewater in Portland, OR, USA were screened for bacteriolytic activity by overlay assay. One isolated phage, <i>PDX</i>, was classified by electron microscopy and genome sequencing. A mouse model of infection determined whether the phage was therapeutic against EAEC. 16S metagenomic analysis of anaerobic cultures determined whether a normal human microbiome was altered by treatment.<b>Results.</b> <i>Escherichia</i> virus <i>PDX</i>, a member of the strictly lytic family <i>Myoviridae</i>, killed a case-associated EAEC isolate from a child in rural Tennessee in a dose-dependent manner, and killed EAEC isolates from Columbian children. A single dose of <i>PDX</i> (multiplicity of infection: 100) 1 day post-infection reduced EAEC recovered from mouse faeces. <i>PDX</i> also killed EAEC when cultured anaerobically in the presence of human faecal bacteria. While the addition of EAEC reduced the β-diversity of the human microbiota, that of the cultures with either faeces alone, faeces with EAEC and <i>PDX</i>, or with just <i>PDX</i> phage was not different statistically.<b>Conclusion.</b> <i>PDX</i> killed EAEC isolate EN1E-0007 <i>in vivo</i> and <i>in vitro</i>, while not altering the diversity of normal human microbiota in anaerobic culture, and thus could be part of an effective therapy for children in developing countries and those suffering from EAEC-mediated traveller's diarrhoea without causing dysbiosis.