Standards for microbiology investigations (UK SMI)

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

UK SMI supporting information

UK SMI repository

Please contact us if you can’t find the document that you require.

UK Standards for Microbiology Investigations consultations

View our open consultations

View our closed consultations


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
  2. SMI B 2: investigation of bacterial eye infections
  3. SMI B 4: investigation of superficial mouth samples
  4. SMI B 5: investigation of nasal samples
  5. SMI B 6: investigation of whooping cough
  6. SMI B 9: investigation of throat related specimens
  7. SMI B 10: processing of faeces for Clostridium difficile
  8. UK SMI B 11: swabs from skin and superficial soft tissue infections
  9. SMI B 14: investigation of pus and exudates
  10. SMI B 15: investigation of bile
  11. UK SMI B 17: tissues and biopsies from deep-seated sites and organs
  12. SMI B 19: investigation of sinus aspirate
  13. SMI B 20: investigation of intravascular cannulae and associated specimens
  14. SMI B 22: investigation of cerebrospinal fluid shunts
  15. SMI B 25: investigation of continuous ambulatory peritoneal dialysis fluid
  16. SMI B 26: investigation of fluids from normally sterile sites
  17. SMI B 27: investigation of cerebrospinal fluid
  18. SMI B 28: investigation of genital tract and associated specimens
  19. SMI B 29: investigation of specimens for screening for MRSA
  20. SMI B 30: investigation of faecal specimens for enteric pathogens
  21. SMI B 31: investigation of specimens other than blood for parasites
  22. UK SMI B 37: investigation of blood cultures (for organisms other than Mycobacterium species)
  23. SMI B 38: investigation of bone marrow
  24. SMI B 39: investigation of dermatological specimens for superficial mycoses
  25. SMI B 40: investigation of specimens for Mycobacterium species
  26. SMI B 41: investigation of urine
  27. SMI B 42: investigation of bone and soft tissue associated with osteomyelitis
  28. SMI B 44: investigation of orthopaedic implant associated infections
  29. SMI B 51: Screening for Neisseria meningitidis
  30. UK SMI B 55: investigation of infectious causes of dyspepsia
  31. SMI B 57: investigation of bronchoalveolar lavage, sputum and associated specimens
  32. SMI B 58: detection of carriage of group B streptococci
  33. SMI B 59: detection of Enterobacteriaceae producing extended spectrum β lactamases
  34. SMI B 60: detection of bacteria with carbapenem hydrolysing β lactamases (carbapenemases)
  35. SMI B 61: investigation of specimens for ectoparasites
  36. UK SMI B 62: abdominal organ transport fluid testing


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

  1. UK SMI V 4: investigation of hepatitis B infection
  2. SMI V 5: screening for hepatitis C infection
  3. SMI V 8: vertical and perinatal transmission of hepatitis C
  4. SMI V 11: HIV screening and confirmation
  5. SMI V 26: Epstein-Barr virus serology
  6. SMI V 27: hepatitis A virus acute infection serology
  7. UK SMI V 28: investigation of cytomegalovirus infection
  8. SMI V 30: investigation of pregnant women exposed to non-vesicular rash
  9. SMI V 37: Chlamydia trachomatis infection: testing by nucleic acid amplification tests (NAAT)
  10. SMI V 43: investigation of viral encephalitis
  11. SMI V 44: Syphilis serology
  12. SMI V 53: screening and monitoring for hepatitis E infection
  13. SMI V 57: Chlamydial zoonotic infections


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
  2. SMI ID 2: identification of Corynebacterium species
  3. UK SMI ID 3: identification of Listeria species
  4. SMI ID 4: identification of Streptococcus species, Enterococcus species and morphologically similar organisms
  5. UK SMI ID 5: identification of Bordetella species
  6. SMI ID 6: identification of Neisseria species
  7. UK SMI ID 7: identification of Staphylococcus species, Micrococcus species and Rothia species
  8. SMI ID 8: identification of Clostridium species
  9. SMI ID 9: identification of Bacillus species
  10. SMI ID 10: identification of aerobic actinomycetes
  11. SMI ID 11: identification of Moraxella species and morphologically similar organisms
  12. UK SMI ID 12: identification of Haemophilus species and the HACEK group of organisms
  13. SMI ID 13: identification of Pasteurella species and morphologically similar bacteria
  14. SMI ID 14: identification of anaerobic cocci
  15. SMI ID 15: identification of anaerobic Actinomyces species
  16. SMI ID 16: identification of Enterobacteriaceae
  17. SMI ID 17: identification of Pseudomonas species and other non glucose fermenters
  18. SMI ID 18: identification of Legionella species
  19. SMI ID 19: identification of Vibrio and Aeromonas species
  20. SMI ID 20: identification of Shigella species
  21. SMI ID 21: identification of Yersinia species
  22. SMI ID 22: identification of VTEC including Escherichia coli O157
  23. SMI ID 23: identification of Campylobacter species
  24. SMI ID 24: identification of Salmonella species
  25. SMI ID 25: identification of anaerobic Gram negative rods
  26. SMI ID 26: identification of Helicobacter species

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

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.

Test procedures

These standards outline the test procedures for identifying the organisms.

  1. UK SMI TP 1: example reference strains for UK SMI test procedures
  2. SMI TP 2: aesculin hydrolysis test
  3. SMI TP 3: agglutination test for Salmonella species
  4. SMI TP 5: bile solubility test
  5. UK SMI TP 8: catalase test
  6. SMI TP 10: coagulase test
  7. SMI TP 12: deoxyribonuclease test
  8. SMI TP 19: indole test
  9. SMI TP 21: motility test
  10. SMI TP 24: ONPG (Beta-Galactosidase) test
  11. SMI TP 25: optochin test
  12. SMI TP 26: oxidase test
  13. SMI TP 27: oxidation-fermentation of glucose test
  14. SMI TP 29: porphyrin synthesis (ALA) test
  15. UK SMI TP 30: potassium hydroxide test
  16. UK SMI TP 32: changing the phase of Salmonella
  17. UK SMI TP 34: thermonuclease test
  18. UK SMI TP 36: urease test
  19. UK SMI TP 38: X and V factor test
  20. UK SMI TP 39: staining procedures
  21. UK SMI TP 40: MALDI TOF MS test procedure

Report on survey into susceptibility testing methodology

Withdrawn and recalled documents

  1. UK SMI withdrawn and recalled documents
Published 1 August 2014
Last updated 23 September 2014 + show all updates
  1. The standards for microbiology investigations (SMI): searchable index has been added.

  2. First published.