Genomic investigation of Carbapenemase producing organism outbreaks
Research type
Research Study
Full title
Evaluation of long-read next generation sequencing technology to epidemiologically track carbapenemase producing organisms and their mobile genetic elements from two hospital outbreaks; use of complete genome sequences to investigate transfer of resistance genes.
IRAS ID
251099
Contact name
Lim Jones
Contact email
Sponsor organisation
Public Health Wales
Duration of Study in the UK
1 years, 0 months, 0 days
Research summary
Antibiotic resistance is a key area of public health concern. Infections caused by multi-drug resistant pathogens are occurring more often and are associated with an increased risk of death. Carbapenemase producing organisms (CPOs), as they include bacteria which cause common infections, are resistant to most safe and effective antibiotics including the carbapenems, which were formally reliable treatments for resistant organisms. Globally, hospital acquired outbreaks with CPOs have been increasing and difficult to control outbreaks have occurred. Outbreaks can be caused by direct spread of closely related bacteria but can involve sharing of genetic information between unrelated bacteria, so that previously sensitive bacteria acquire resistance to multiple antibiotics. With modern sequencing technology, it is possible to sequence complete pathogen genomes, revealing how closely related bacteria are and identifying causes of antibiotic resistance and whether they are associated with mobile elements, which could spread to a new bacterial host. This can reveal means of transmission and inform strategies to prevent spread of infection. Different sequencing technologies have different strengths and limitations. The Illumina MiSeq sequencing platform is being introduced in Public Health Wales for the typing of bacterial pathogens. However, analysis of sequencing data produced with short reads (the output of each sequencing reaction is a small fragment of DNA) by MiSeq is not suited to other applications, such as defining sequences of mobile genetic elements. MinION sequencing with longer reads is better suited to this, but sequence error rates are higher. We aim to use both sequencing strategies in parallel on a unique collection of CPO from across Wales associated with hospital outbreaks to better understand transmission of CPO and transmission of carbapenemase genetic determinants, as well as evaluating the outputs of 2 sequencing platforms for clinically relevant information.
REC name
N/A
REC reference
N/A