UK Standards for Microbiology Investigations (SMI): quality and consistency in clinical laboratories

UK SMIs are algorithms and procedures for clinical microbiology, developed through consultation. Patients and the public can comment on any open consultations.

SMIs are algorithms and procedures for clinical microbiology, developed through consultation. Patients, public and partner organisations can comment on any open consultations.

UK Standards for Microbiology Investigations include:

  • syndromic algorithms, that are the overarching framework that connect other SMIs, and describe the investigations chosen at the pre-analytical (clinical syndrome) stage
  • recommended investigations for microbiology
  • minimum testing algorithms for virology (analytical and post analytical)
  • clinical guidance that covers the clinical background, differential diagnosis, and appropriate investigation of particular clinical conditions
  • quality guidance that describes laboratory methodologies to ensure quality, like assay validation, quality assurance and understanding uncertainty of measurement

Updates include:

  • newly issued and re-issued SMIs
  • documents under consultation
  • general news updates


UK Standards for Microbiology Investigations objectives are:

  • to provide good quality evidence based, NICE accredited standards for the investigation of infections for diagnostic and public health microbiology laboratories, without commercial company bias or emphasis
  • to develop overarching documents based on the investigation of syndromes which in turn are supported by more detailed guidance on the investigation of diseases and infections
  • to develop, review and update UK SMIs through a wide consultation process where the views of all participants are considered and the resulting documents reflect the majority agreement of contributors
  • to advise commissioners of microbiological services on the range and standard they should require in their contracts with microbiology laboratories
  • to provide the UK SMIs electronically as a one stop shop for microbiology investigations

Who uses the standards

Three groups of users find SMIs relevant to their work.

Practicing laboratory medicine professionals in the UK use SMIs as a general resource.

Clinicians use SMIs to learn about the standard of laboratory services they can expect for their patients. SMIs can help them order the appropriate tests electronically from hospital wards.

Commissioners of healthcare services use SMIs to find the standard of microbiology investigations they can seek as part of the clinical and public health care package for their population.

SMI consultation process

Public Health England (PHE) acts as custodian of SMIs. We review documents which are in use every 3 to 5 years.

SMIs are developed, reviewed and updated through a consultation process.

We develop these standards together with partner organisations, Public Health Wales, representatives from Scotland and Northern Ireland, NHS and the Royal College of Pathologists which display their logos on the SMIs.

An organisation’s logo in an SMI indicates the society participated in equal partnership and support for the objectives and process of preparing SMIs.

Each of the devolved administrations endorses SMIs. Public Health Wales bases its own All-Wales SOPs on the SMIs. The Welsh Microbiological Association, the Scottish Microbiology and Virology Network, the Scottish Microbiology Association and the Northern Ireland Microbiology Forum and Audit Group also endorse the standards.

Nominees of professional societies are members of the steering committee and working groups that develop SMIs. The nominees participate in the development of the SMIs although their views cannot be rigorously representative of the members of the partner organisation nor the corporate view of the organisation.

Nominees act as conduits for two way reporting and dialogue.

The standards unit updates and reviews SMIs by consultation with members of the public, partners, stakeholders and specialist groups. This includes microbiology professionals and doctors. The resulting documents reflect the majority view of contributors.

Consultation stages and document markings

The ‘Draft’ watermark means that a document is new to the SMI repository or is actively undergoing review.

The ‘Under review’ watermark refers to a document that is already in the SMI repository but requires a review.

The ‘Under Consultation’ watermark refers to documents which are either draft or under review which are undergoing wide consultation.

Public and patient involvement (PPI)

The standards unit encourages public and patient involvement (PPI) in the development of all UK SMI.

All PPI activities within the standards unit follow the PHE public involvement policy and take place following discussion with the PHE public involvement team.

UK Standards for Microbiology Investigations are available in Italian.

Quality assurance and accreditation

National Institute for Health and Care Excellence (NICE) has accredited the process to produce SMIs used by the SMI working groups.

The accreditation applies to all guidance produced since October 2009 using the SMI development processes.

Accreditation is valid for 5 years from July 2011.

The process for developing SMIs is also certified to ISO 9001:2008.

SMIs represent a good standard of practice to which all clinical and public health microbiology laboratories in the UK are expected to work. They represent neither minimum standards of practice nor the highest level of complex laboratory investigation possible.

In using SMIs, laboratories should take account of local requirements and undertake additional investigations where appropriate. SMIs help laboratories to meet accreditation requirements by promoting high quality practices which are auditable. SMIs also provide a reference point for method development.

The performance of SMIs depends on competent staff and appropriate quality reagents and equipment. Laboratories must ensure that they have validated all commercial and in-house tests, to ensure the tests are fit for purpose.

Laboratories should participate in external quality assessment schemes and undertake relevant internal quality control procedures.

Information governance and equality

PHE is a Caldicott compliant organisation. It seeks to take every possible precaution to prevent unauthorised disclosure of patients details and to ensure that patient-related records are kept under secure conditions.

PHE equality objectives apply to the SMI development process.

The SMI working groups achieve the equality objectives by effective consultation with members of the public, partners, stakeholders and specialist interest groups.

While every care has been taken in the preparation of SMIs, PHE and the partner organisations, shall, to the greatest extent possible under any applicable law, exclude liability for all losses, costs, claims, damages or expenses arising out of or connected with the use of an SMI or any information contained therein. If alterations are made by an end user to an SMI for local use, it must be made clear where in the document the alterations have been made and by whom such alterations have been made and also acknowledged that PHE and the partner organisations shall bear no liability for such alterations. For the further avoidance of doubt, as SMIs have been developed for application within the UK, any application outside the UK shall be at the user’s risk.

The evidence base and microbial taxonomy for the SMI is as complete as possible at the date of issue. Any omissions and new material will be considered at the next review. These standards can only be superseded by revisions of the standard, legislative action, or by NICE accredited guidance.

SMIs are Crown copyright which should be acknowledged where appropriate.


UK standards for microbiology investigations

Standards unit
National Infection Service
Public Health England
61 Colindale Avenue