Assessing the efficacy and safety of new antibiotic regimens against serious bacterial infections

Project title
Assessing the efficacy and safety of new antibiotic regimens against serious bacterial infections caused by carbapenem-resistant Enterobacterales and/or Pseudomonas aeruginosa (CREP)

People involved
Support requested by: Fadheela Patel
Principal investigator: Prof Adrian Brink
Bioinformatics support team: Ephifania Geza

Short description of project
The overall goals of this observational study are to collect prospective, longitudinal cohort and feasibility data to inform study design and comparator selection for future interventional clinical trial(s). The future trials will assess the efficacy and safety of new antibiotic regimens against serious bacterial infections caused by carbapenem-resistant Enterobacterales
and/or Pseudomonas aeruginosa (CREP).

Objectives

1. To archive the sequence data (raw sequencing data in fastq format) in GenBank
2. To predict the species of each isolate
3. To determine determine the MLST
4. To identify resistance-conferring genes
5. To identify the surface polysaccharide synthesis loci from bacterial whole genome sequences
6. To generate a ML phylogenetic tree
7. To generate a phylogenetic tree associated with the presence of AMR genes.