Uk standards for Microbiology Investigations Acknowledgments

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UK Standards for Microbiology Investigations


UK Standards for Microbiology Investigations (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 the professional organisations whose logos are displayed below and listed on the website SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see

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.

For further information please contact us at:

Standards Unit

Microbiology Services

Public Health England

61 Colindale Avenue

London NW9 5EQ



UK Standards for Microbiology Investigations are produced in association with:


Acknowledgments 1

Amendment Table 4

UK SMI: Scope and Purpose 5

Scope of Document 7

Introduction 7

Technical Information/Limitations 13

1 Safety Considerations1,2,54-68 16

2 Specimen Collection 16

3 Specimen Transport and Storage1,2 17

4 Specimen Processing/Procedure1,2 17

5 Reporting Procedure 25

6 Notification to PHE84,85 or Equivalent in the Devolved Administrations86-89 26

Appendix 1: BAL Specimens for Culture 27

Appendix 2: Sputum Specimens for Culture 27

References 29

Amendment Table

Each SMI method has an individual record of amendments. The current amendments are listed on this page. The amendment history is available from

New or revised documents should be controlled within the laboratory in accordance with the local quality management system.

Amendment No/Date.


Issue no. discarded.

Insert Issue no.

Section(s) involved


Amendment No/Date.


Issue no. discarded.

Insert Issue no.

Section(s) involved


Whole document.

Document presented in a new format.

The term “CE marked leak proof container” is referenced to specific text in the EU in vitro Diagnostic Medical Devices Directive (98/79/EC Annex 1 B 2.1) and to the Directive itself EC1,2.

Edited for clarity.

Reorganisation of [some] text.

Minor textual changes.

Sections on specimen collection, transport, storage and processing.

Reorganised. Previous numbering changed.


Some references updated.

UK SMI: Scope and Purpose

Users of SMIs

Primarily, SMIs are intended as a general resource for practising professionals operating in the field of laboratory medicine and infection specialties in the UK. SMIs also provide clinicians with information about the available test repertoire and the standard of laboratory services they should expect for the investigation of infection in their patients, as well as providing information that aids the electronic ordering of appropriate tests. The documents also provide commissioners of healthcare services with the appropriateness and standard of microbiology investigations they should be seeking as part of the clinical and public health care package for their population.

Background to SMIs

SMIs comprise a collection of recommended algorithms and procedures covering all stages of the investigative process in microbiology from the pre-analytical (clinical syndrome) stage to the analytical (laboratory testing) and post analytical (result interpretation and reporting) stages. Syndromic algorithms are supported by more detailed documents containing advice on the investigation of specific diseases and infections. Guidance notes cover the clinical background, differential diagnosis, and appropriate investigation of particular clinical conditions. Quality guidance notes describe laboratory processes which underpin quality, for example assay validation.

Standardisation of the diagnostic process through the application of SMIs helps to assure the equivalence of investigation strategies in different laboratories across the UK and is essential for public health surveillance, research and development activities.

Equal Partnership Working

SMIs are developed in equal partnership with PHE, NHS, Royal College of Pathologists and professional societies. The list of participating societies may be found at Inclusion of a logo in an SMI indicates participation of the society in equal partnership and support for the objectives and process of preparing SMIs. Nominees of professional societies are members of the Steering Committee and Working Groups which develop 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. SMIs are developed, reviewed and updated through a wide consultation process.

Quality Assurance

NICE has accredited the process used by the SMI Working Groups to produce SMIs. The accreditation is applicable to all guidance produced since October 2009. The process for the development of SMIs is 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. SMIs are NICE accredited and 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 should ensure that all commercial and in-house tests have been validated and shown to be fit for purpose. Laboratories should participate in external quality assessment schemes and undertake relevant internal quality control procedures.

Patient and Public Involvement

The SMI Working Groups are committed to patient and public involvement in the development of SMIs. By involving the public, health professionals, scientists and voluntary organisations the resulting SMI will be robust and meet the needs of the user. An opportunity is given to members of the public to contribute to consultations through our open access website.

Information Governance and Equality

PHE 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. The development of SMIs are subject to PHE Equality objectives

The SMI Working Groups are committed to achieving the equality objectives by effective consultation with members of the public, partners, stakeholders and specialist interest groups.

Legal Statement

Whilst every care has been taken in the preparation of SMIs, PHE and any supporting organisation, 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 to an SMI, it must be made clear where and by whom such changes have been made.

The evidence base and microbial taxonomy for the SMI is as complete as possible at the time 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.

Suggested Citation for this Document

Public Health England. (). . UK Standards for Microbiology Investigations. B Issue xx.

Scope of Document

Type of Specimen

Bronchial aspirate, transthoracic aspirate, bronchoalveolar lavage, transtracheal aspirate, bronchial brushings, protected catheter specimens, bronchial washings, endotracheal tube specimens, sputum – expectorated


This SMI describes the isolation of organisms known to cause bacterial and fungal respiratory infection from sputum, bronchoalveolar lavage and associated specimens (see S 2 – Pneumonia, G 8 - Respiratory Viruses and V 22 - Immunofluorescence and Isolation of Viruses from Respiratory Samples). Different tests are carried out on different sample types depending on the patient group.

This SMI should be used in conjunction with other SMIs.


Recovery and recognition of organisms responsible for pneumonia depends on:

  • The adequacy of the lower respiratory tract specimen

  • Avoidance of contamination by upper respiratory tract flora

  • The use of microscopic techniques and culture methods

  • Current and recent antimicrobial treatment

Distinction between tracheobronchial colonisation and true pulmonary infection can prove difficult.

The expression lower respiratory tract infection (LRTI) includes pneumonia, where there is inflammation of the lung parenchyma, and infections such as bronchiolitis that affect the small airways. Lung abscess, where the lung parenchyma is replaced by pus filled cavities, and empyema, where pus occupies the pleural space, are less common manifestations of LRTI.


Pneumonia can be classified according to whether it is community acquired or nosocomial (often defined as presenting more than 48 hours after hospitalisation). It may be primary, occurring in a person without previously identified risk factors, or secondary. Many conditions are associated with an increased risk of pneumonia. Common risk factors include chronic lung diseases such as chronic obstructive pulmonary disease (COPD), diabetes mellitus, cardiac or renal failure and immunosuppression (either congenital or acquired). Reduced level of consciousness and weakness of the gag and cough reflexes are risk factors for aspiration pneumonia. Recent infection with respiratory viruses, particularly influenza, is also a risk factor. There are clinical signs and laboratory indices that can be used to assess the severity of pneumonia in an individual patient, some of which are predictive of an increased risk of death if present3.

The aetiology of pneumonia varies according to whether it has been acquired in the community or in hospital and the risk factors present. Many of the bacteria found as colonisers of the upper respiratory tract have been implicated in pneumonia. Antibiotic treatment and hospitalisation affect the colonising flora, leading to an increase in numbers of aerobic Gram negative bacilli4. These factors affect the sensitivity and specificity of sputum culture as a diagnostic test and results must always be interpreted in the light of the clinical information5. Sputum culture results are often unreliable and sensitivity of culture is poor for many pathogens, although culture and antibiotic sensitivities may be of value in sputum specimens from patients with severe exacerbation of COPD6.

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