About us

UK Standards for Microbiology Investigations (UK SMIs) are a comprehensive referenced collection of recommended algorithms and procedures for clinical microbiology.

They consist of:

  • syndromic documents, that are the overarching framework that relate to other UK SMIs, and describe the investigations chosen at the pre-analytical (clinical syndrome) stage
  • recommended investigations for microbiology
  • minimum testing algorithms for virology
  • quality guidance that describes laboratory methodologies to underpin quality, such as assay validation, quality assurance and understanding uncertainty of measurement

UK 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.


UK SMI objectives are:

  • to provide good quality evidence-based, National Institute for Health and Care Excellence (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

Scope of document

UK SMIs comprise a collection of recommended algorithms for initial test selection and testing methods and confirmatory strategies. UK SMIs also contain guidance that describes the recommended standard set of investigations consistent with current good practice in different infectious disease presentation, as well as examples of standard laboratory practice and general information on clinical syndromes.

The syndromic documents form part of the pre-analytical stage of the investigative process and are intended to guide clinicians and diagnostic laboratory staff in the choice of the correct pathway for the investigation of a sample based upon the clinical context.

It is recognised that clinical details are essential to the optimal processing of samples and the documents perform best when sufficient, relevant, clinical details are provided at the time of sample submission. The algorithms are presented in flowchart format to give a clear overview of how to proceed with the testing of specimens and the possible outcomes using the clinical history provided.

If the primary testing set does not identify a causative pathogen, secondary testing should be performed if clinical or epidemiological features support such testing. Laboratories may wish to undertake second line tests either after, or at the same time as, the primary testing set according to the clinical and local epidemiological setting and laboratory operational capabilities.

The flowcharts are intended to reflect current recommended practice, accounting for prevalence of infections in the UK, public health needs, and availability of tests, with references and links to more detailed guidance. National surveillance programmes for specific organisms should be taken into consideration when using the algorithms.

Individual UK SMIs should be read in conjunction with relevant UK SMIs within the repository for laboratory processing and reporting of target organisms and public health actions.

Who uses the standards

Three groups of users find UK SMIs relevant to their work.

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

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

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

Information governance and equality

UKHSA is a Caldicott compliant organisation. It seeks to take every possible precaution to prevent unauthorised disclosure of patient details and to ensure that patient-related records are kept under secure conditions. UKHSA equality objectives apply to the UK SMI development process.

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


The committee encourages members of the public to get involved in the development of UK Standards for Microbiology Investigations. Please see the UK SMI consultation page.

Legal statement

Whilst every care has been taken in the preparation of UK SMIs, UKHSA 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 UK SMI or any information contained therein. If alterations are made by an end user to a UK 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 UKHSA and the partner organisations shall bear no liability for such alterations. For the further avoidance of doubt, as UK 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 UK 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.

UK SMIs are Crown copyright which should be acknowledged where appropriate.

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UK Standards for Microbiology Investigations, Standards Unit, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ. Email [email protected]