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.
Please note that some review dates may be affected due to the COVID-19 outbreak and there will be delays in the review of some UK SMIs. This will be limited where possible and we would be grateful for your patience as the team navigates its way back to business as usual. Contact standards@phe.gov.uk for any queries.
UK SMI supporting information
UK SMI repository
The search strategy for any UK SMI document is available on request by emailing standards@phe.gov.uk
UK Standards for microbiology investigations consultations
Bacteriology
These are bacteriology standards for the laboratory covering receipt of the sample in the laboratory to the issue of a report.
- SMI B 1: investigation of ear infections and associated specimens
- SMI B 2: investigation of bacterial eye infections
- SMI B 4: investigation of superficial mouth samples
- SMI B 5: investigation of nasal samples
- SMI B 6: investigation of whooping cough
- SMI B 9: investigation of throat related specimens
- SMI B 10: processing of faeces for Clostridium difficile
- UK SMI B 11: swabs from skin and superficial soft tissue infections
- SMI B 14: investigation of pus and exudates
- SMI B 15: investigation of bile
- UK SMI B 17: tissues and biopsies from deep-seated sites and organs
- SMI B 19: investigation of sinus aspirate
- SMI B 20: investigation of intravascular cannulae and associated specimens
- SMI B 22: investigation of cerebrospinal fluid shunts
- SMI B 25: investigation of continuous ambulatory peritoneal dialysis fluid
- SMI B 26: investigation of fluids from normally sterile sites
- SMI B 27: investigation of cerebrospinal fluid
- SMI B 28: investigation of genital tract and associated specimens
- SMI B 29: investigation of specimens for screening for MRSA
- SMI B 31: investigation of specimens other than blood for parasites
- UK SMI B 37: investigation of blood cultures (for organisms other than Mycobacterium species)
- SMI B 38: investigation of bone marrow
- SMI B 39: investigation of dermatological specimens for superficial mycoses
- UK SMI B 40: investigation of specimens for Mycobacterium species
- SMI B 41: investigation of urine
- SMI B 42: investigation of bone and soft tissue associated with osteomyelitis
- UK SMI B 44: investigation of orthopaedic implant associated infections
- SMI B 51: Screening for Neisseria meningitidis
- UK SMI B 55: investigation of infectious causes of dyspepsia
- SMI B 57: investigation of bronchoalveolar lavage, sputum and associated specimens
- SMI B 58: detection of carriage of group B streptococci
- SMI B 59: detection of Enterobacteriaceae producing extended spectrum β lactamases
- UK SMI B 60: detection of bacteria with carbapenem hydrolysing β lactamases (carbapenemases)
- SMI B 61: investigation of specimens for ectoparasites
- UK SMI B 62: abdominal organ transport fluid testing
Virology
Virology and serology diagnostic algorithms and standards for the laboratory testing of viruses.
- UK SMI V 4: investigation of hepatitis B infection
- SMI V 5: screening for hepatitis C infection
- SMI V 8: vertical and perinatal transmission of hepatitis C
- SMI V 11: HIV screening and confirmation
- SMI V 26: Epstein-Barr virus serology
- SMI V 27: hepatitis A virus acute infection serology
- UK SMI V 28: investigation of cytomegalovirus infection
- UK SMI V 30: investigation of exposure to rash in pregnancy
- SMI V 37: Chlamydia trachomatis infection: testing by nucleic acid amplification tests (NAAT)
- SMI V 43: investigation of viral encephalitis
- SMI V 44: Syphilis serology
- SMI V 53: screening and monitoring for hepatitis E infection
- SMI V 57: Chlamydial zoonotic infections
- UK SMI V 58: SARS-CoV-2 serology
Identification
These documents cover techniques used for bacterial identification.
- UK SMI ID 1: introduction to the preliminary identification of medically important bacteria and fungi from culture
- SMI ID 2: identification of Corynebacterium species
- UK SMI ID 3: identification of Listeria species
- UK SMI ID 4: identification of Streptococcus species, Enterococcus species and morphologically similar organisms
- UK SMI ID 5: identification of Bordetella species
- SMI ID 6: identification of Neisseria species
- UK SMI ID 7: identification of Staphylococcus species, Micrococcus species and Rothia species
- SMI ID 8: identification of Clostridium species
- SMI ID 9: identification of Bacillus species
- SMI ID 10: identification of aerobic actinomycetes
- SMI ID 11: identification of Moraxella species and morphologically similar organisms
- UK SMI ID 12: identification of Haemophilus species and the HACEK group of organisms
- SMI ID 13: identification of Pasteurella species and morphologically similar bacteria
- SMI ID 14: identification of anaerobic cocci
- SMI ID 15: identification of anaerobic Actinomyces species
- SMI ID 16: identification of Enterobacteriaceae
- SMI ID 17: identification of Pseudomonas species and other non glucose fermenters
- SMI ID 18: identification of Legionella species
- SMI ID 19: identification of Vibrio and Aeromonas species
- UK SMI ID 20: identification of Shigella species
- SMI ID 21: identification of Yersinia species
- SMI ID 22: identification of VTEC including Escherichia coli O157
- SMI ID 23: identification of Campylobacter species
- UK SMI ID 24: identification of Salmonella species
- SMI ID 25: identification of anaerobic Gram negative rods
- SMI ID 26: identification of Helicobacter species
Quality-related guidance
These standards describe essential laboratory practices to ensure quality like assay validation, quality assurance and understanding uncertainty of measurement.
- SMI Q 1: evaluations, validations and verifications of diagnostic tests
- UK SMI Q 2: quality assurance in the diagnostic infection sciences laboratory
- SMI Q 4: good practice when performing molecular amplification assays
- SMI Q 5: inoculation of culture media for bacteriology
- UK SMI Q 7: good practice when ordering and undertaking diagnostic tests for infectious disease serology
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.
Development of syndromic algorithms has now resumed. Documents that have exceeded their review date will remain on the website until they are superseded or withdrawn.
- UK SMI U 1: National user manual template
- UK SMI U 2: National user manual worked example for conjunctivitis
- UK SMI U 3: National user manual worked example for urine tests
- SMI S 1: Acute infective hepatitis
- SMI S 2: Pneumonia
- SMI S 3: Conjunctivitis
- SMI S 5: Meningoencephalitis
- SMI S 6: sexually transmitted infections
- UK SMI S 7: gastroenteritis
Test procedures
These standards outline the test procedures for identifying the organisms.
- UK SMI TP 1: example reference strains for UK SMI test procedures
- SMI TP 2: aesculin hydrolysis test
- SMI TP 3: agglutination test for Salmonella species
- SMI TP 5: bile solubility test
- UK SMI TP 8: catalase test
- SMI TP 10: coagulase test
- SMI TP 12: deoxyribonuclease test
- SMI TP 19: indole test
- SMI TP 21: motility test
- SMI TP 24: ONPG (Beta-Galactosidase) test
- SMI TP 25: optochin test
- SMI TP 26: oxidase test
- SMI TP 27: oxidation-fermentation of glucose test
- SMI TP 29: porphyrin synthesis (ALA) test
- UK SMI TP 30: potassium hydroxide test
- UK SMI TP 32: changing the phase of Salmonella
- UK SMI TP 34: thermonuclease test
- UK SMI TP 36: urease test
- UK SMI TP 38: X and V factor test
- UK SMI TP 39: staining procedures
- UK SMI TP 40: MALDI TOF MS test procedure
Withdrawn and recalled documents
Last updated 15 December 2021 + show all updates
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Updated UK SMI repository section.
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Removed 'report on survey into susceptibility testing methodology'.
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The standards for microbiology investigations (SMI): searchable index has been added.
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First published.