Theme 2: Translating sequencing technologies into clinical and public health microbiology
Funded by a Wellcome/Department of Health and Social Care HICF (Health Innovation Challenge Fund) award, this project is working to make it feasible for routine microbiology laboratories to use bacterial sequencing to improve outbreak detection and control in hospitals. We routinely sequence pathogens associated with hospital infections (such as MRSA) and compare their genetic relatedness on an on-going basis. Patients may be cared for on several different wards of the hospital during their care, which can make it difficult to detect outbreaks that relies on time and place analysis. But sequencing MRSA and detecting highly related isolates can provide an early warning, and can help target investigations for the infection control team, bringing them to a rapid close. Sequencing can also quickly refute outbreaks suspected by the clinical team, which can prevent unnecessary actions such as ward closures.
The group are currently focused on establishing MRSA into our routine work, using the latest whole-genome sequencing technology to shorten the turnaround time between sample and result. We are also starting to develop sequencing for other species of concern including Clostridium difficile and Enterococcus faecium, together with developing methodology to predict antibiotic resistance and detect genes that code for virulence factors such as toxins. There is also a strong emphasis on the evaluation of cost effectiveness, which is essential if such methods are to be adopted in the National Health Service and elsewhere.
The project is led by Professor Sharon Peacock and Dr Kathy Raven. Analysis and interpretation of sequence data is provided by Dr’s Kathy Raven and Narender Kumar, and the laboratory team is headed by Beth Blane and includes Danielle Leek, Sophia Girgis and Asha Akram.
- Addenbrooke’s Hospital infection control team
- Clinical Microbiology and Public Heath Laboratory, Addenbrooke’s Hospital
- Next Generation Diagnostics
- Illumina, inc.
- Raven KE*, Blane B*, Leek D, Churcher C, Kokko-Gonzales P, Pugazhendhi D, Fraser L, Betley J, Parkhill J, Peacock SJ. Methodology for whole genome sequencing of MRSA in a routine hospital microbiology laboratory. Journal of Clinical Microbiology. In press.
- Raven K, Blane B, Churcher C, Parkhill J, Peacock SJ. Are commercial providers a viable option for clinical sequencing? Microbial Genomics. 2018.
- Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE et al. Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community. Sci Transl Med. 2017.