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Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria

Antimicrobial resistance (AMR) is a major problem globally. The main bacterial organisms associated with urinary tract infection (UTI) associated sepsis are E. coli and Klebsiella along with Enterobacter species. These all have AMR strains known as ESBL (Extended Spectrum Beta-Lactamase), which are...

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Autores principales: Haines, Melissa E. K., Hodges, Francesca E., Nale, Janet Y., Mahony, Jennifer, van Sinderen, Douwe, Kaczorowska, Joanna, Alrashid, Bandar, Akter, Mahmuda, Brown, Nathan, Sauvageau, Dominic, Sicheritz-Pontén, Thomas, Thanki, Anisha M., Millard, Andrew D., Galyov, Edouard E., Clokie, Martha R. J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044893/
https://www.ncbi.nlm.nih.gov/pubmed/33868187
http://dx.doi.org/10.3389/fmicb.2021.613529
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author Haines, Melissa E. K.
Hodges, Francesca E.
Nale, Janet Y.
Mahony, Jennifer
van Sinderen, Douwe
Kaczorowska, Joanna
Alrashid, Bandar
Akter, Mahmuda
Brown, Nathan
Sauvageau, Dominic
Sicheritz-Pontén, Thomas
Thanki, Anisha M.
Millard, Andrew D.
Galyov, Edouard E.
Clokie, Martha R. J.
author_facet Haines, Melissa E. K.
Hodges, Francesca E.
Nale, Janet Y.
Mahony, Jennifer
van Sinderen, Douwe
Kaczorowska, Joanna
Alrashid, Bandar
Akter, Mahmuda
Brown, Nathan
Sauvageau, Dominic
Sicheritz-Pontén, Thomas
Thanki, Anisha M.
Millard, Andrew D.
Galyov, Edouard E.
Clokie, Martha R. J.
author_sort Haines, Melissa E. K.
collection PubMed
description Antimicrobial resistance (AMR) is a major problem globally. The main bacterial organisms associated with urinary tract infection (UTI) associated sepsis are E. coli and Klebsiella along with Enterobacter species. These all have AMR strains known as ESBL (Extended Spectrum Beta-Lactamase), which are featured on the WHO priority pathogens list as “critical” for research. Bacteriophages (phages), as viruses that can infect and kill bacteria, could provide an effective tool to tackle these AMR strains. There is currently no “gold standard” for developing a phage cocktail. Here we describe a novel approach to develop an effective phage cocktail against a set of ESBL-producing E. coli and Klebsiella largely isolated from patients in United Kingdom hospitals. By comparing different measures of phage efficacy, we show which are the most robust, and suggest an efficient screening cascade that could be used to develop phage cocktails to target other AMR bacterial species. A target panel of 38 ESBL-producing clinical strains isolated from urine samples was collated and used to test phage efficacy. After an initial screening of 68 phages, six were identified and tested against these 38 strains to determine their clinical coverage and killing efficiency. To achieve this, we assessed four different methods to assess phage virulence across these bacterial isolates. These were the Direct Spot Test (DST), the Efficiency of Plating (EOP) assay, the planktonic killing assay (PKA) and the biofilm assay. The final ESBL cocktail of six phages could effectively kill 23/38 strains (61%), for Klebsiella 13/19 (68%) and for E. coli 10/19 (53%) based on the PKA data. The ESBL E. coli collection had six isolates from the prevalent UTI-associated ST131 sequence type, five of which were targeted effectively by the final cocktail. Of the four methods used to assess phage virulence, the data suggests that PKAs are as effective as the much more time-consuming EOPs and data for the two assays correlates well. This suggests that planktonic killing is a good proxy to determine which phages should be used in a cocktail. This assay when combined with the virulence index also allows “phage synergy” to inform cocktail design.
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spelling pubmed-80448932021-04-15 Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria Haines, Melissa E. K. Hodges, Francesca E. Nale, Janet Y. Mahony, Jennifer van Sinderen, Douwe Kaczorowska, Joanna Alrashid, Bandar Akter, Mahmuda Brown, Nathan Sauvageau, Dominic Sicheritz-Pontén, Thomas Thanki, Anisha M. Millard, Andrew D. Galyov, Edouard E. Clokie, Martha R. J. Front Microbiol Microbiology Antimicrobial resistance (AMR) is a major problem globally. The main bacterial organisms associated with urinary tract infection (UTI) associated sepsis are E. coli and Klebsiella along with Enterobacter species. These all have AMR strains known as ESBL (Extended Spectrum Beta-Lactamase), which are featured on the WHO priority pathogens list as “critical” for research. Bacteriophages (phages), as viruses that can infect and kill bacteria, could provide an effective tool to tackle these AMR strains. There is currently no “gold standard” for developing a phage cocktail. Here we describe a novel approach to develop an effective phage cocktail against a set of ESBL-producing E. coli and Klebsiella largely isolated from patients in United Kingdom hospitals. By comparing different measures of phage efficacy, we show which are the most robust, and suggest an efficient screening cascade that could be used to develop phage cocktails to target other AMR bacterial species. A target panel of 38 ESBL-producing clinical strains isolated from urine samples was collated and used to test phage efficacy. After an initial screening of 68 phages, six were identified and tested against these 38 strains to determine their clinical coverage and killing efficiency. To achieve this, we assessed four different methods to assess phage virulence across these bacterial isolates. These were the Direct Spot Test (DST), the Efficiency of Plating (EOP) assay, the planktonic killing assay (PKA) and the biofilm assay. The final ESBL cocktail of six phages could effectively kill 23/38 strains (61%), for Klebsiella 13/19 (68%) and for E. coli 10/19 (53%) based on the PKA data. The ESBL E. coli collection had six isolates from the prevalent UTI-associated ST131 sequence type, five of which were targeted effectively by the final cocktail. Of the four methods used to assess phage virulence, the data suggests that PKAs are as effective as the much more time-consuming EOPs and data for the two assays correlates well. This suggests that planktonic killing is a good proxy to determine which phages should be used in a cocktail. This assay when combined with the virulence index also allows “phage synergy” to inform cocktail design. Frontiers Media S.A. 2021-03-29 /pmc/articles/PMC8044893/ /pubmed/33868187 http://dx.doi.org/10.3389/fmicb.2021.613529 Text en Copyright © 2021 Haines, Hodges, Nale, Mahony, van Sinderen, Kaczorowska, Alrashid, Akter, Brown, Sauvageau, Sicheritz-Pontén, Thanki, Millard, Galyov and Clokie. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Haines, Melissa E. K.
Hodges, Francesca E.
Nale, Janet Y.
Mahony, Jennifer
van Sinderen, Douwe
Kaczorowska, Joanna
Alrashid, Bandar
Akter, Mahmuda
Brown, Nathan
Sauvageau, Dominic
Sicheritz-Pontén, Thomas
Thanki, Anisha M.
Millard, Andrew D.
Galyov, Edouard E.
Clokie, Martha R. J.
Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria
title Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria
title_full Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria
title_fullStr Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria
title_full_unstemmed Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria
title_short Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria
title_sort analysis of selection methods to develop novel phage therapy cocktails against antimicrobial resistant clinical isolates of bacteria
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8044893/
https://www.ncbi.nlm.nih.gov/pubmed/33868187
http://dx.doi.org/10.3389/fmicb.2021.613529
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