UK Standards for Microbiology Investigations (UK SMI): general information

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

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

  • syndromic algorithms, 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 (analytical and post analytical)
  • quality guidance that describes laboratory methodologies to underpin quality, like assay validation, quality assurance and understanding uncertainty of measurement

Updates include:

  • newly issued and re-issued UK 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

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 notes that describe the recommended standard set of investigations consistent with current good practice in different infective disease presentations, as well as examples of standard laboratory practice and general information on clinical syndromes.

The syndromic algorithms 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 and/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.

This document should be read in conjunction with relevant UK SMIs 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.

UK Standards for Microbiology Investigations are available in Italian.

UK SMI consultation process

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

UK 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 UK SMIs.

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

Each of the devolved administrations endorses UK SMIs. Public Health Wales bases its own All-Wales SOPs on the UK 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 UK SMIs. The nominees participate in the development of the UK 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 UK 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 UK SMI repository or is actively undergoing review.

The ‘Under review’ watermark refers to a document that is already in the UK 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.


UK Standards for Microbiology Investigations (UK SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with professional organisations. UK SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee.

The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the medical editors for editing the medical content.

Partner organisations

UK SMIs are developed in equal partnership with PHE, NHS, Royal College of Pathologists and professional societies. Inclusion of a logo in a UK SMI indicates participation of the society in equal partnership and support for the objectives and process of preparing UK SMIs. Nominees of professional societies are members of the Steering Committee and Working Groups which develop UK SMIs. The views of nominees cannot be rigorously representative of the members of their nominating organisations nor the corporate views of their organisations. Nominees act as a conduit for two way reporting and dialogue. Representative views are sought through the consultation process. UK SMIs are developed, reviewed and updated through a wide consultation process.

Public and patient involvement (PPI)

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

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

Quality assurance and accreditation

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

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

Accreditation is valid until 30 June 2021.

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

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.

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

The performance of UK 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 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.

Implementation tool

UK SMIs are evidence based standards of practice that are produced in compliance with NICE accreditation requirements. The implementation of UK SMIs should consist of adoption by laboratories of the methods in their entirety and without amendment of the content. Circumstances in which deviation from the UK SMIs may occur are those for which local arrangements and conditions preclude the use of a particular UK SMI as published. In all cases of deviation, laboratories are advised to establish an evidence base for their local practice, including test evaluation as applicable.

Incorporation of the UK SMIs into local laboratory document systems and translation into local style guides is acceptable but attention must be given to effective document control taking account of any future revisions to each UK SMI.

The Standards Unit at PHE would welcome any evidence in support of practices that differ from those published.

While every care has been taken in the preparation of UK 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 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 PHE 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.


UK standards for microbiology investigations

Standards unit
National Infection Service
Public Health England
61 Colindale Avenue


Published 1 June 2014