Periodic Reporting for period 1 - SaPhaDe (Know your enemy: systematic discovery of Salmonella anti-Phage Defences for the improved design of phage therapeutics)
Période du rapport: 2019-05-01 au 2021-04-30
Summary SaPhaDe project
Antimicrobial drug resistance is a serious global threat that make us to fear the return of the mortality rates from pre-penicillin times. A promising alternative to antibiotic drugs is the phage therapy, which is based in viruses that kill bacteria. The rational design of effective phage therapeutics requires a fundamental understanding of evolutionary co-adaptation of phages and bacteria. These co-adaptations have led to the development of multiple anti-phage defence systems in bacteria which modulate their susceptibility to be killed by phages at strain level. In this way, the study of the diversity and mechanisms of action of defence islands in bacterial pathogens represents crucial knowledge for improving rapid delivery of phage-based therapeutics. The proposed work aims to deeply characterize the anti-phage defences in an emerging human pathogen, antibiotic resistant Klebsiella pneumoniae, (according to Infectious Disease Society of America, one of the most dangerous worldwide disseminated pathogen, ESKAPE group composed by Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) to provide the strategy to discover and classify phage counter-defences for an optimal design of phage therapy.
To develop the project is necessary to characterize of the population genetics of K. pneumoniae to understand the distribution and diversity of anti-phage defence islands. The project was developed from 01-May-2019 to 31-August-2019 at Dr. German Bou laboratory (INIBIC, Spain). His extensive experience in clinical microbiology allowed to quickly stablish the protocols and to access to a collection of 334 carbapenem-resistant Enterobacteria and their genomic sequences. The project found effective phages against K. pneumoniae high risk clone (Kp3380). The isolated phages present different susceptibility patterns in close and distant related strains, allowing to design a future research line to unravel the genetic mechanisms behind anti-phage defence in K. pneumoniae.
The study of K. pneumoniae pan-genome will allow to understand the antimicrobial resistance mechanisms and the genetic basis of anti-phage defences. This research line will continue with a close collaboration between Dr. Germán Bou and Prof. Martin Polz, who is a world expert in the ecology and evolution of environmental microbiology, in order to discover the genetic mechanisms of pathogens in order to improve clinical decisions to maximize the efficacy of antibiotic and phage therapeutics. This project will open a new field for the treatment of MDR infections by a tailor-phage strategy
Antimicrobial drug resistance is a serious global threat that make us to fear the return of the mortality rates from pre-penicillin times. A promising alternative to antibiotic drugs is the phage therapy, which is based in viruses that kill bacteria. The rational design of effective phage therapeutics requires a fundamental understanding of evolutionary co-adaptation of phages and bacteria. These co-adaptations have led to the development of multiple anti-phage defence systems in bacteria which modulate their susceptibility to be killed by phages at strain level. In this way, the study of the diversity and mechanisms of action of defence islands in bacterial pathogens represents crucial knowledge for improving rapid delivery of phage-based therapeutics. The proposed work aims to deeply characterize the anti-phage defences in an emerging human pathogen, antibiotic resistant Klebsiella pneumoniae, (according to Infectious Disease Society of America, one of the most dangerous worldwide disseminated pathogen, ESKAPE group composed by Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) to provide the strategy to discover and classify phage counter-defences for an optimal design of phage therapy.
To develop the project is necessary to characterize of the population genetics of K. pneumoniae to understand the distribution and diversity of anti-phage defence islands. The project was developed from 01-May-2019 to 31-August-2019 at Dr. German Bou laboratory (INIBIC, Spain). His extensive experience in clinical microbiology allowed to quickly stablish the protocols and to access to a collection of 334 carbapenem-resistant Enterobacteria and their genomic sequences. The project found effective phages against K. pneumoniae high risk clone (Kp3380). The isolated phages present different susceptibility patterns in close and distant related strains, allowing to design a future research line to unravel the genetic mechanisms behind anti-phage defence in K. pneumoniae.
The study of K. pneumoniae pan-genome will allow to understand the antimicrobial resistance mechanisms and the genetic basis of anti-phage defences. This research line will continue with a close collaboration between Dr. Germán Bou and Prof. Martin Polz, who is a world expert in the ecology and evolution of environmental microbiology, in order to discover the genetic mechanisms of pathogens in order to improve clinical decisions to maximize the efficacy of antibiotic and phage therapeutics. This project will open a new field for the treatment of MDR infections by a tailor-phage strategy
1.2.1 Work Package 1
As indicated in the GANNT chart, the first three months of the project were developed at INIBIC in the laboratory of Dr. German Bou. The plan during these three months was to develop part of the Work Package 1 (WP1), which was focused in the activities to develop Major milestone 1a (M1a). WP1 includes one presentation of the project (PP1), data management plan, preparation of deliverables and reports. In addition, during the three months two communication activities were performed (CA1).
WP1: During the duration of this project:
o A total of 334 K. pneumoniae strains were collected. A selection of 12 K. pneumoniae were used for phage isolation (part of the major milestone M1a).
o A total of 11 phages were isolated (part of the major milestone M1a).
o The sequencing data and hybrid assembly (Oxford Nanopore Technology + illumina) from the 334 K. pneumoniae strains were obtained (part of the major milestone M1a).
PP1: A presentation of the project to all Dr. German Bou group was performed at 06-May-2019.
Data management plan: The data management plan was discussed with Dr. Germán Bou and prepared as a deliverable.
Deliverables and reports: Preparation of reports “Methods to identify-recruit subjects”, “Patient data management report” and “Health-Safety procedures”. During the preparation of the reports the Ethic Committee evaluated the project, giving a favourable evaluation.
CA1: One communication activity of SaPhaDe project was performed at Centro de Investigacións Científicas Avanzadas (CICA), A Coruña, Spain at 17-July-2019.
Communication activity: SaPhaDe project was presented at Falling Walls Lab Marie Skłodowska-Curie Actions Event at 26-September-2019 in Brussels, Belgium.
As indicated in the GANNT chart, the first three months of the project were developed at INIBIC in the laboratory of Dr. German Bou. The plan during these three months was to develop part of the Work Package 1 (WP1), which was focused in the activities to develop Major milestone 1a (M1a). WP1 includes one presentation of the project (PP1), data management plan, preparation of deliverables and reports. In addition, during the three months two communication activities were performed (CA1).
WP1: During the duration of this project:
o A total of 334 K. pneumoniae strains were collected. A selection of 12 K. pneumoniae were used for phage isolation (part of the major milestone M1a).
o A total of 11 phages were isolated (part of the major milestone M1a).
o The sequencing data and hybrid assembly (Oxford Nanopore Technology + illumina) from the 334 K. pneumoniae strains were obtained (part of the major milestone M1a).
PP1: A presentation of the project to all Dr. German Bou group was performed at 06-May-2019.
Data management plan: The data management plan was discussed with Dr. Germán Bou and prepared as a deliverable.
Deliverables and reports: Preparation of reports “Methods to identify-recruit subjects”, “Patient data management report” and “Health-Safety procedures”. During the preparation of the reports the Ethic Committee evaluated the project, giving a favourable evaluation.
CA1: One communication activity of SaPhaDe project was performed at Centro de Investigacións Científicas Avanzadas (CICA), A Coruña, Spain at 17-July-2019.
Communication activity: SaPhaDe project was presented at Falling Walls Lab Marie Skłodowska-Curie Actions Event at 26-September-2019 in Brussels, Belgium.
Even the short duration of the project, a long-term collaboration was stablished with Dr. German Bou laboratory and with Prof. Martin Polz. A relevant publication is being prepared with Dr. Germán Bou based in the collection of 334 K. pneumoniae. SaPhaDe project will continue with Prof. Martin Polz at University of Vienna during the next 6 years. In addition, the ER applied for the Ramon y Cajal grant (Spanish national tenure track) to open this independent research line in the Universidad de A Coruña, which is directly linked to INIBIC (host institution during the three months’ project).