Myoviridae phage PDX kills enteroaggregative Escherichia coli without human microbiome dysbiosis

Abstract

Introduction 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. Aim Identify a therapeutic bacteriophage that kills diarrhoeagenic enteroaggregative Escherichia coli (EAEC) while leaving the human microbiome intact. Methodology Phages from wastewater in Portland, OR, USA were screened for bacteriolytic activity by overlay assay. One isolated phage, PDX , 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. Results Escherichia virus PDX , a member of the strictly lytic family Myoviridae , 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 PDX (multiplicity of infection: 100) 1 day post-infection reduced EAEC recovered from mouse faeces. PDX 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 PDX , or with just PDX phage was not different statistically. Conclusion PDX killed EAEC isolate EN1E-0007 in vivo and in vitro , 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.

Isolation and Characterization of Bacteriophages That Infect Citrobacter rodentium, a Model Pathogen for Intestinal Diseases

“…The overuse and misuse of antibiotics in the treatment of diarrhea have led to an alarming increase of AMR in diarrheagenic bacteria [ 1 , 2 , 3 ]. Phage therapy has been effective at reducing E. coli burden in the murine gut with antibiotic pretreatment [ 5 , 6 , 7 , 8 ]. Although C. rodentium is widely used as an exemplary in vivo model system for gastrointestinal bacterial diseases [ 9 , 86 ], there are no reports using this species for phage therapy development.…”

“…Mouse models for the study of EPEC diseases have had limited utility, because gastrointestinal microbiota defends well against human E. coli infections [ 4 ]. Consequently, most mouse models of E. coli gastrointestinal diseases require substantial antibiotic pre-treatment to reduce resident bacteria [ 5 , 6 , 7 , 8 ]. The preferred surrogate for EPEC diseases is the mouse-restricted pathogen Citrobacter rodentium [ 9 ].…”

Phage Therapy in Gastrointestinal Diseases

“…Therefore, it is important to consider phages as a key component of the microbiome in further analysis of FMT [ 38 ]. A recent study has shown that phageome alone may be sufficient to eliminate C. difficile infection and restore a healthy microbial structure [ 39 ]. The evaluation was performed in five patients with symptomatic CD with chronic relapse.…”

“…In all cases, FFT restored normal stool habits and removed C. difficile symptoms for at least 6 months. These results highlight that bacteriophages alone modulate the bacterial community restoring homeostasis [ 39 ].…”

“…Furthermore, the acquisition of metagenomic information about the intestinal phages is essential for the development of future specific phage therapies for pathogens in the intestine. In a recent study the bacteriome and virome of the same stool samples from 101 healthy adults have been metagenomically analyzed to understand host-bacteria-phage associations in the intestine [ 39 ]. In total, 114 prophages were successfully identified.…”