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Standards for microbiology investigations (SMI)

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

Contents

SMI repository

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

   • 1 June 2014
   • Detailed guide

2. Standards for microbiology investigations (SMI): searchable index

   • 27 June 2014
   • Guidance

Bacteriology

These are bacteriology standards for the laboratory covering receipt of the sample in the laboratory to the issue of a report.

1. SMI B 1: Investigation of ear infections and associated specimens

   • 4 June 2014
   • Guidance

2. SMI B 2: Investigation of bacterial eye infections

   • 7 January 2015
   • Guidance

3. SMI B 4: Investigation of superficial mouth samples

   • 2 December 2015
   • Guidance

4. SMI B 5: Investigation of nasal samples

   • 7 January 2015
   • Guidance

5. SMI B 6: Culture of specimens for Bordetella pertussis and Bordetella parapertussis

   • 11 November 2014
   • Guidance

6. SMI B 9: Investigation of throat related specimens

   • 24 April 2015
   • Guidance

7. SMI B 10: Processing of faeces for Clostridium difficile

   • 2 April 2014
   • Guidance

8. SMI B 11: Investigation of swabs from skin and superficial soft tissue infections

   • 8 August 2016
   • Guidance

9. SMI B 14: Investigation of pus and exudates

   • 8 August 2016
   • Guidance

10. SMI B 15: Investigation of bile

    • 11 November 2014
    • Guidance

11. SMI B 17: Investigation of tissues and biopsies from deep seated sites and organs

    • 15 April 2016
    • Guidance

12. SMI B 20: Investigation of intravascular cannulae and associated specimens

    • 1 December 2015
    • Guidance

13. SMI B 22: Investigation of cerebrospinal fluid shunts

    • 28 May 2015
    • Guidance

14. SMI B 25: Investigation of continuous ambulatory peritoneal dialysis fluid

    • 26 February 2015
    • Guidance

15. SMI B 26: Investigation of fluids from normally sterile sites

    • 26 June 2015
    • Guidance

16. SMI B 27: Investigation of cerebrospinal fluid

    • 12 March 2015
    • Guidance

17. SMI B 28: Investigation of genital tract and associated specimens

    • 9 December 2014
    • Guidance

18. SMI B 29: Investigation of specimens for screening for MRSA

    • 3 April 2014
    • Guidance

19. SMI B 30: Investigation of faecal specimens for enteric pathogens

    • 24 April 2014
    • Guidance

20. SMI B 31: Investigation of specimens other than blood for parasites

    • 9 May 2014
    • Guidance

21. SMI B 37: Investigation of blood cultures (for organisms other than Mycobacterium species)

    • 5 November 2014
    • Guidance

22. SMI B 38: Investigation of bone marrow

    • 13 October 2015
    • Guidance

23. SMI B 39: Investigation of dermatological specimens for superficial mycoses

    • 13 August 2015
    • Guidance

24. SMI B 40: Investigation of specimens for Mycobacterium species

    • 22 May 2014
    • Guidance

25. SMI B 41: Investigation of urine

    • 7 September 2016
    • Guidance

26. SMI B 42: Investigation of bone and soft tissue associated with osteomyelitis

    • 14 January 2016
    • Guidance

27. SMI B 44: Investigation of orthopaedic implant associated infections

    • 1 March 2016
    • Guidance

28. SMI B 51: Screening for Neisseria meningitidis

    • 12 March 2014
    • Guidance

29. SMI B 55: Investigation of gastric biopsies for Helicobacter pylori

    • 14 January 2016
    • Guidance

30. SMI B 57: Investigation of bronchoalveolar lavage, sputum and associated specimens

    • 9 December 2015
    • Guidance

31. SMI B 58: Detection of carriage of group B streptococci

    • 26 June 2015
    • Guidance

32. SMI B 59: Detection of Enterobacteriaceae producing extended spectrum β lactamases

    • 23 August 2016
    • Guidance

33. SMI B 60: Detection of bacteria with carbapenem hydrolysing β lactamases (carbapenemases)

    • 21 September 2016
    • Guidance

Virology

Virology and serology diagnostic algorithms and standards for the laboratory testing of viruses.

1. SMI V 4: Hepatitis B diagnostic serology in the immunocompetent (including hepatitis B in pregnancy)

   • 23 November 2015
   • Guidance

2. SMI V 5: Investigation of hepatitis C infection by antibody or combined antigen and antibody assay

   • 31 March 2014
   • Guidance

3. SMI V 8: Vertical and perinatal transmission of hepatitis C

   • 5 November 2014
   • Guidance

4. SMI V 10: Blood borne virus testing in dialysis patients

   • 1 May 2015
   • Guidance

5. SMI V 11: Anti-HIV screening

   • 15 April 2014
   • Guidance

6. SMI V 26: Epstein-barr virus serology

   • 10 July 2015
   • Guidance

7. SMI V 27: Hepatitis A virus acute infection serology

   • 12 May 2014
   • Guidance

8. SMI V 28: Cytomegalovirus serology

   • 21 September 2016
   • Guidance

9. SMI V 30: Investigation of pregnant women exposed to non-vesicular rash

   • 3 February 2015
   • Guidance

10. SMI V 37: Chlamydia trachomatis infection: testing by nucleic acid amplification tests (NAATs)

    • 16 April 2014
    • Guidance

11. SMI V 43: Investigation of viral encephalitis

    • 16 April 2014
    • Guidance

12. SMI V 44: Syphilis serology

    • 21 July 2016
    • Guidance

13. SMI V 53: Screening for hepatitis E infection

    • 2 November 2015
    • Guidance

Clinical related guidance

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

1. SMI G 2: Microbiological investigation of patients with acute lymphadenopathy and fever

   • 21 October 2013
   • Guidance

2. SMI G 3: Chlamydial zoonotic infections

   • 14 November 2014
   • Guidance

3. SMI G 4: Investigation of viral encephalitis and meningitis

   • 3 March 2014
   • Guidance

4. SMI G 5: Investigation of hepatitis

   • 3 March 2014
   • Guidance

5. SMI G 6: Investigation of vesicular rashes

   • 1 November 2013
   • Guidance

6. SMI G 7: Investigation of red rash

   • 4 March 2014
   • Guidance

7. SMI G 8: Respiratory viruses

   • 4 March 2014
   • Guidance

8. SMI G 9: Investigation of specimens for ectoparasites

   • 1 May 2015
   • Guidance

Identification

These documents cover techniques used for bacterial identification.

1. SMI ID 1: Introduction to the preliminary identification of medically important bacteria

   • 12 March 2014
   • Guidance

2. SMI ID 2: Identification of Corynebacterium species

   • 29 October 2014
   • Guidance

3. SMI ID 3: Identification of Listeria species, and other non sporing Gram positive rods, except Corynebacterium

   • 1 July 2016
   • Guidance

4. SMI ID 4: Identification of Streptococcus species, Enterococcus species and morphologically similar organisms

   • 3 November 2014
   • Guidance

5. SMI ID 5: Identification of Bordetella species

   • 10 November 2014
   • Guidance

6. SMI ID 6: identification of Neisseria species

   • 10 July 2015
   • Guidance

7. SMI ID 7: Identification of Staphylococcus species, Micrococcus species and Rothia species

   • 14 November 2014
   • Guidance

8. SMI ID 8: Identification of Clostridium species

   • 1 March 2016
   • Guidance

9. SMI ID 9: Identification of Bacillus species

   • 26 February 2015
   • Guidance

10. SMI ID 10: Identification of aerobic actinomycetes

    • 21 March 2016
    • Guidance

11. SMI ID 11: Identification of Moraxella species and morphologically similar organisms

    • 5 February 2015
    • Guidance

12. SMI ID 12: Identification of Haemophilus species and the HACEK group of organisms

    • 5 February 2015
    • Guidance

13. SMI ID 13: Identification of Pasteurella species and morphologically similar bacteria

    • 5 February 2015
    • Guidance

14. SMI ID 14: Identification of anaerobic cocci

    • 5 February 2015
    • Guidance

15. SMI ID 15: identification of anaerobic Actinomyces species

    • 10 July 2015
    • Guidance

16. SMI ID 16: Identification of Enterobacteriaceae

    • 24 April 2015
    • Guidance

17. SMI ID 17: Identification of Pseudomonas species and other non glucose fermenters

    • 24 April 2015
    • Guidance

18. SMI ID 18: Identification of Legionella species

    • 24 April 2015
    • Guidance

19. SMI ID 19: Identification of Vibrio and Aeromonas species

    • 14 April 2015
    • Guidance

20. SMI ID 20: Identification of Shigella species

    • 24 April 2015
    • Guidance

21. SMI ID 21: Identification of Yersinia species

    • 10 July 2015
    • Guidance

22. SMI ID 22: Identification of VTEC including Escherichia coli O157

    • 26 June 2015
    • Guidance

23. SMI ID 23: identification of Campylobacter species

    • 26 June 2015
    • Guidance

24. SMI ID 24: Identification of Salmonella species

    • 10 July 2015
    • Guidance

25. SMI ID 25: Identification of anaerobic Gram negative rods

    • 10 July 2015
    • Guidance

26. SMI ID 26: identification of Helicobacter species

    • 10 July 2015
    • Guidance

Quality-related guidance

These standards describe essential laboratory practices to ensure quality like assay validation, quality assurance and understanding uncertainty of measurement.

1. SMI Q 1: Commercial and in-house diagnostic tests: evaluations and validations

   • 10 February 2014
   • Guidance

2. SMI Q 2: Quality assurance in the diagnostic virology and serology laboratory

   • 9 December 2015
   • Guidance

3. SMI Q 3: European directive on in vitro diagnostic medical devices (IVD directive)

   • 9 October 2013
   • Guidance

4. SMI Q 4: Good laboratory practice when performing molecular amplification assays

   • 16 December 2013
   • Guidance

5. SMI Q 5: Inoculation of culture media for bacteriology

   • 16 December 2013
   • Guidance

6. SMI Q 7: Good practice when undertaking serology assays for infectious diseases

   • 15 April 2016
   • Guidance

Syndromic algorithm

These documents provide the overarching framework for all other SMIs.

These standards help clinicians and diagnostic laboratory staff choose the correct approach for investigating a sample from a clinical setting.

Further development of syndromic algorithms has ceased and the current documents will remain on the website until they are superseded or withdrawn.

1. SMI S 1: Acute infective hepatitis

   • 1 September 2015
   • Guidance

2. SMI S 2: Pneumonia

   • 1 September 2015
   • Guidance

3. SMI S 3: Conjunctivitis

   • 1 September 2015
   • Guidance

4. SMI S 5: Meningoencephalitis

   • 8 May 2014
   • Guidance

5. SMI S 6: Sexually transmitted infections

   • 1 November 2013
   • Guidance

6. SMI S 7: Gastroenteritis and diarrhoea

   • 23 December 2013
   • Guidance

Test procedures

These standards outline the test procedures for identifying the organisms.

1. SMI TP 1: Example reference strains for UK standards for microbiology investigations test procedures

   • 13 January 2015
   • Guidance

2. SMI TP 2: Aesculin hydrolysis test

   • 10 November 2014
   • Guidance

3. SMI TP 3: Agglutination test for Salmonella species

   • 12 November 2014
   • Guidance

4. SMI TP 5: Bile solubility test

   • 12 November 2014
   • Guidance

5. SMI TP 8: Catalase test

   • 19 November 2014
   • Guidance

6. SMI TP 10: Coagulase test

   • 19 November 2014
   • Guidance

7. SMI TP 12: Deoxyribonuclease test

   • 26 November 2014
   • Guidance

8. SMI TP 19: Indole test

   • 24 November 2014
   • Guidance

9. SMI TP 21: Motility test

   • 24 November 2014
   • Guidance

10. SMI TP 24: ONPG (Beta-Galactosidase) test

    • 24 November 2014
    • Guidance

11. SMI TP 25: Optochin test

    • 13 January 2015
    • Guidance

12. SMI TP 26: Oxidase test

    • 13 January 2015
    • Guidance

13. SMI TP 27: Oxidation fermentation of glucose test

    • 13 January 2015
    • Guidance

14. SMI TP 29: Porphyrin synthesis (ALA) test

    • 13 January 2015
    • Guidance

15. SMI TP 30: Potassium hydroxide test

    • 13 January 2015
    • Guidance

16. SMI TP 32: Changing the phase of Salmonella

    • 13 January 2015
    • Guidance

17. SMI TP 34: Thermonuclease test

    • 13 January 2015
    • Guidance

18. SMI TP 36: Urease test

    • 15 January 2015
    • Guidance

19. SMI TP 38: X and V factor test

    • 13 January 2015
    • Guidance

20. SMI TP 39: staining procedures

    • 30 July 2015
    • Guidance

Withdrawn and recalled documents

1. UK SMI withdrawn and recalled documents

   • 11 September 2014
   • Guidance

• Published: 1 August 2014
• Updated: 23 September 2014

+ full page history

• 23 September 2014 2:33pm: The standards for microbiology investigations (SMI): searchable index has been added.
• 1 August 2014 12:00am: First published.

• From: Public Health England