Genomics has the potential to influence every step of the infectious disease pathway. Infection control is the principal area where next generation sequencing (NGS) technologies could be used now for infectious disease management and surveillance, complemented by established techniques. The detailed and high-resolution information obtained by sequencing a pathogen from a patient can be used to make a diagnosis and inform treatment, but is also important in a public health context for understanding how diseases spread in the community.
Genomic information is therefore of interest to the full range of organisations involved in the delivery and use of microbiology services. As each organisation has its own priorities, which influence how they use microbiology services, a coordinated approach and open communication between stakeholders is required to ensure that genomic services meet the needs of all. Without this, uneven provision, knowledge gaps, and missed opportunities to understand outbreaks could result.
Microbiology services in England are provided by the National Health Service (NHS) and Public Health England (PHE) in a mixed model, with some private provision:
Provided by PHE through a network of specialist microbiology laboratories embedded in NHS hospital trusts. There are also a number of national PHE reference laboratories. Service functions cover: diagnosis and monitoring of pathogens of public health importance in community and healthcare settings including novel or re-emerging threats; monitoring antibiotic resistance and vaccine uptake and advising government on infectious disease policy.
Provided through hospital-based laboratories, these services offer identification of a range of common pathogens and support clinical management of patients. They also play a crucial role in hospital infection control efforts by identifying common pathogens and providing drug susceptibility information. More complex cases are sent to PHE-led specialist or reference laboratories. NHS services also play a significant role in contributing to public health microbiology practice; they may test samples as part of a PHE-led outbreak investigation, and are required by law to report on certain ‘notifiable’ pathogens of public health significance, including measles, tuberculosis, and foodborne infections.
Joint ventures exist with providers, such as The Doctors Laboratory, Serco and Spire Health. Services are the same as those provided by NHS laboratories themselves.
The funding and commissioning of microbiology services reflects the dynamics of their organisation. The current payment structure will be challenging to apply in a situation where genomics is used, since the information is useful in both a primary care and public health context. Effective stakeholder communication is key to resolving this challenge.
At a local level, the advantages to hospitals of using genomics for infection control efforts include targeted and swifter resolution of outbreaks and optimal use of control measures (1).
The use of genomic information can also benefit national surveillance, a core function of PHE, for example by demonstrating or refuting connections between outbreaks in different geographical areas. The higher resolution of whole genome sequencing means that accurate transmission networks can be determined, and if applicable the source can be dealt with (1).
Microbiology services are undergoing a process of consolidation which will reduce the number of hospital laboratories. Those that remain will be larger and able to carry out more specialist tests. They will benefit from economies of scale, which will have implications for how services are provided in the future. This consolidation will affect how genomics is implemented into health services - different business models and needs will have to be taken into account.
Genomic based services are already operational or in development by PHE. The central PHE reference laboratory has set up a sequencing service to investigate organisms of public health importance such as Salmonella spp. and Staphylococcus aureus with the aim of ensuring a resilient and self-sufficient NGS capability to meet national needs. Other PHE centres are developing sequence-based approaches for the management of specific pathogens, including HIV and tuberculosis. Moreover, the infectious diseases component of the 100,000 Genomes Project is being fulfilled in collaboration with PHE. However, widespread national implementation of pathogen genomics has yet to occur.
For genomics to be effective within the health system as a whole, it should be implemented in a way that serves both the local and national needs of the different organisations involved in the delivery of services.
The following issues should be considered in parallel to ensure that genomics services are optimised by all users and that provision is equitable: