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Standards for microbiology investigations (SMI)

• From: Public Health England
• Part of: Services
• Published: 1 August 2014
• Last updated: 23 September 2014, see all updates

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

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

   • 1 June 2014
   • Guidance

2. UK Standards for microbiology investigations (UK SMI): Searchable index

   • 10 May 2017
   • 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

   • 5 May 2017
   • 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

   • 22 November 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

    • 10 January 2017
    • Guidance

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

    • 28 June 2017
    • 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

    • 8 March 2017
    • Guidance

16. SMI B 27: Investigation of cerebrospinal fluid

    • 1 June 2017
    • Guidance

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

    • 26 April 2017
    • 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

    • 29 June 2017
    • 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

    • 29 December 2016
    • Guidance

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

    • 17 January 2017
    • Guidance

25. SMI B 41: Investigation of urine

    • 17 August 2017
    • 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

    • 24 August 2017
    • 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

34. SMI B 61: Investigation of specimens for ectoparasites

    • 28 October 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: Screening for hepatitis C infection

   • 3 August 2017
   • 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: HIV screening and confirmation

   • 4 January 2017
   • 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 (NAAT)

    • 17 January 2017
    • 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

14. SMI V 57: Chlamydial zoonotic infections

    • 28 October 2016
    • Guidance

Identification

These documents cover techniques used for bacterial identification.

1. SMI ID 1: Introduction to the preliminary identification of medically important bacteria and fungi from culture

   • 26 April 2017
   • 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

    • 31 October 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: Evaluations, validations and verifications of diagnostic tests

   • 22 March 2017
   • Guidance

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

   • 9 December 2015
   • Guidance

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

   • 16 December 2013
   • Guidance

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

   • 17 January 2017
   • Guidance

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

   • 15 April 2016
   • Guidance

National user manual and Syndromic algorithm

The national user manual template contains standard headings and suggestions to guide laboratories in completing a national user manual. Two worked examples of use have been developed and work on this has now been completed.

The syndromic algorithm documents provide the overarching framework for all other UK 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. UK SMI U 1: National user manual template

   • 2 November 2016
   • Guidance

2. UK SMI U 2: National user manual worked example for conjunctivitis

   • 9 August 2017
   • Guidance

3. UK SMI U 3: National user manual worked example for urine tests

   • 9 August 2017
   • Guidance

4. SMI S 1: Acute infective hepatitis

   • 1 September 2015
   • Guidance

5. SMI S 2: Pneumonia

   • 1 September 2015
   • Guidance

6. SMI S 3: Conjunctivitis

   • 1 September 2015
   • Guidance

7. SMI S 5: Meningoencephalitis

   • 8 May 2014
   • Guidance

8. SMI S 6: Sexually transmitted infections

   • 1 November 2013
   • Guidance

9. 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

   • 22 November 2016
   • 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

21. SMI TP 40: MALDI TOF MS test procedure

    • 13 October 2016
    • Guidance

Withdrawn and recalled documents

1. UK SMI withdrawn and recalled documents

   • 11 September 2014
   • Guidance

Document information

Published: 1 August 2014

Updated: 23 September 2014

+ full page history

1. 23 September 2014 The standards for microbiology investigations (SMI): searchable index has been added.
2. 1 August 2014 First published.

From: Public Health England

Part of: Services