UK Standards for Microbiology Investigations Investigation of Genital Tract and Associated Specimens REVIEW UNDER Issued by the Standards Unit, Microbiology Services, PHE Bacteriology | B 28 | Issue no: 4.6 | Issue date: 26.04.17 | Page: 1 of 40 © Crown copyright 2017 Investigation of Genital Tract and Associated Specimens Acknowledgments 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 https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- 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. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations REVIEWare produced in association with: UNDER Logos correct at time of publishing. Bacteriology | B 28 | Issue no: 4.6 | Issue date: 26.04.17 | Page: 2 of 40 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Investigation of Genital Tract and Associated Specimens Contents ACKNOWLEDGMENTS .......................................................................................................... 2 AMENDMENT TABLE ............................................................................................................. 4 UK SMI: SCOPE AND PURPOSE ........................................................................................... 7 SCOPE OF DOCUMENT ......................................................................................................... 9 SCOPE .................................................................................................................................... 9 INTRODUCTION ..................................................................................................................... 9 TECHNICAL INFORMATION/LIMITATIONS ......................................................................... 20 1 SAFETY CONSIDERATIONS .................................................................................... 22 2 SPECIMEN COLLECTION ......................................................................................... 22 3 SPECIMEN TRANSPORT AND STORAGE ............................................................... 24 4 SPECIMEN PROCESSING/PROCEDURE ................................................................. 24 5 REPORTING PROCEDURE ....................................................................................... 32 6 NOTIFICATION TO PHE OR EQUIVALENT IN THE DEVOLVED ADMINISTRATIONS .................................................................................................. 34 REFERENCES ......................................................................................................................REVIEW 35 UNDER Bacteriology | B 28 | Issue no: 4.6 | Issue date: 26.04.17 | Page: 3 of 40 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Investigation of Genital Tract and Associated Specimens 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 [email protected]. New or revised documents should be controlled within the laboratory in accordance with the local quality management system. Amendment No/Date. 10/26.04.17 Issue no. discarded. 4.5 Insert Issue no. 4.6 Section(s) involved Amendment Change to the scoring for Mobiluncus Page 32. morphotypes to match ref. 72 (>30/hpf =2 not 4; 5- 30/hpf =2 not 3; 2-4/hpf =1 not 2). Change to the interpretation of the scoring to Page 33. match ref. 72 (Abnormal: indicative of BV when Total score ≥7 not 6). Amendment No/Date. 9/08.12.14 Issue no. discarded. 4.4 REVIEW Insert Issue no. 4.5 Section(s) involved Amendment Whole document. Hyperlinks updated to gov.uk. Page 2. Updated logos added. Due to a transcription error during transfer to the PHE template, some text regarding Nugent’s Reporting Procedure. criteria score was removed. This information has been re-instated in the document. AmendmentUNDER No/Date. 8/24.04.14 Issue no. discarded. 4.3 Insert Issue no. 4.4 Section(s) involved Amendment Whole document. Document has been transferred to a new template Bacteriology | B 28 | Issue no: 4.6 | Issue date: 26.04.17 | Page: 4 of 40 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Investigation of Genital Tract and Associated Specimens to reflect the Health Protection Agency’s transition to Public Health England. Front page has been redesigned. Status page has been renamed as Scope and Purpose and updated as appropriate. Professional body logos have been reviewed and updated. Standard safety and notification references have been reviewed and updated. Scientific content remains unchanged. Amendment No/Date. 7/18.12.12 Issue no. discarded. 4.2 Insert Issue no. 4.3 Section(s) involved Amendment Whole document. Minor formatting amendments. 2.5.3. Section number amended in table. Amendment No/Date. 6/11.07.12 REVIEW Issue no. discarded. 4.1 Insert Issue no. 4.2 Section(s) involved Amendment Document presented in a new format. The term “CE marked leak proof container” replaces “sterile leak proof container” (where appropriate) and is referenced to specific text in the EU in vitro Diagnostic Medical Devices Whole document. Directive (98/79/EC Annex 1 B 2.1) and to Directive itself EC1,2. UNDEREdited for clarity. Reorganisation of [some] text. Minor textual changes. Sections on specimen collection, transport, storage Reorganised. Previous numbering changed. and processing. Bacteriology | B 28 | Issue no: 4.6 | Issue date: 26.04.17 | Page: 5 of 40 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Investigation of Genital Tract and Associated Specimens References. Some references updated. Amendment No/Date. 5/03.05.05 Issue no. discarded. 4 Insert Issue no. 4.1 Section(s) involved Amendment Front page. Redesigned. Status of document. Reworded. Amendment page. Redesigned. Amendment No/Date. 4/15.12.03 Issue no. discarded. 3.1 Insert Issue no. 4 Section(s) involved Amendment Whole document. Text revision. REVIEW UNDER Bacteriology | B 28 | Issue no: 4.6 | Issue date: 26.04.17 | Page: 6 of 40 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Investigation of Genital Tract and Associated Specimens # 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 REVIEW 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 https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories. 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