Uk standards for Microbiology Investigations Acknowledgments

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UK Standards for Microbiology Investigations


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 SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see

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



UK Standards for Microbiology Investigations are produced in association with:

Logos correct at time of publishing.


Acknowledgments 1

Amendment Table 4

UK SMI: Scope and Purpose 5

Scope of Document 6

Scope 7

Introduction 7

Technical Information/Limitations 15

1 Safety Considerations1,2,70-84 16

2 Specimen Collection 16

3 Specimen Transport and Storage1,2 17

4 Specimen Processing/Procedure1,2 17

5 Reporting Procedure 22

6 Notification to PHE95,96 or Equivalent in the Devolved Administrations97-100 23

Appendix 1: Investigation of and Deep-Seated and Organ Abscesses Infections101 24

References 26

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

New or revised documents should be controlled within the laboratory in accordance with the local quality management system.

Amendment No/Date.


Issue no. discarded.

Insert Issue no.

Section(s) involved


Amendment No/Date.


Issue no. discarded.

Insert Issue no.

Section(s) involved


Whole document.

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 Directive (98/79/EC Annex 1 B 2.1) and to Directive itself EC1,2.

Edited for clarity.

Reorganisation of [some] text.

Minor textual changes.

Sections on specimen collection, transport, storage and processing.

Reorganised. Previous numbering changed.


Some references updated.

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

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 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 representative of the members of their nominating organisations nor the corporate views of their organisations. Nominees act as a conduit for two way reporting and dialogue. Representative views are sought through the consultation process. SMIs are developed, reviewed and updated through a wide consultation process.

Quality Assurance

NICE has accredited the process used by the SMI Working Groups to produce SMIs. The accreditation is applicable to all guidance produced since October 2009. The process for the development of SMIs is certified to ISO 9001:2008. SMIs represent a good standard of practice to which all clinical and public health microbiology laboratories in the UK are expected to work. SMIs are NICE accredited and represent neither minimum standards of practice nor the highest level of complex laboratory investigation possible. In using SMIs, laboratories should take account of local requirements and undertake additional investigations where appropriate. SMIs help laboratories to meet accreditation requirements by promoting high quality practices which are auditable. SMIs also provide a reference point for method development. The performance of SMIs depends on competent staff and appropriate quality reagents and equipment. Laboratories should ensure that all commercial and in-house tests have been validated and shown to be fit for purpose. Laboratories should participate in external quality assessment schemes and undertake relevant internal quality control procedures.

Patient and Public Involvement

The SMI Working Groups are committed to patient and public involvement in the development of SMIs. By involving the public, health professionals, scientists and voluntary organisations the resulting SMI will be robust and meet the needs of the user. An opportunity is given to members of the public to contribute to consultations through our open access website.

Information Governance and Equality

PHE is a Caldicott compliant organisation. It seeks to take every possible precaution to prevent unauthorised disclosure of patient details and to ensure that patient-related records are kept under secure conditions. The development of SMIs are subject to PHE Equality objectives

The SMI Working Groups are committed to achieving the equality objectives by effective consultation with members of the public, partners, stakeholders and specialist interest groups.

Legal Statement

Whilst every care has been taken in the preparation of SMIs, PHE and any supporting organisation, shall, to the greatest extent possible under any applicable law, exclude liability for all losses, costs, claims, damages or expenses arising out of or connected with the use of an SMI or any information contained therein. If alterations are made to an SMI, it must be made clear where and by whom such changes have been made.

The evidence base and microbial taxonomy for the SMI is as complete as possible at the time of issue. Any omissions and new material will be considered at the next review. These standards can only be superseded by revisions of the standard, legislative action, or by NICE accredited guidance.

SMIs are Crown copyright which should be acknowledged where appropriate.

Suggested Citation for this Document

Public Health England. (). . UK Standards for Microbiology Investigations. B Issue.

Scope of Document

Type of Specimen

Deep-seated and organ pus or swabs


This SMI describes the processing and bacteriological investigation of specimens from abscesses and infections which are deep seated or associated with specific organs.

For information regarding superficial abscesses refer to B11 – Investigation of skin and soft tissue infections.

This SMI should be used in conjunction with other SMIs.


Abscesses are accumulations of pus in the tissues and any organism isolated from them may be of significance. They occur in many parts of the body as superficial infections or as deep-seated infections associated with any internal organ. Many abscesses are caused by Staphylococcus aureus alone, but others are caused by mixed infections. Anaerobes are predominant isolates in intra-abdominal abscesses and abscesses in the oral and anal areas. Members of the "Streptococcus anginosus" group and Enterobacteriaceae are also frequently present in lesions at these sites.

Bartholin gland abscesses and tubo-ovarian abscesses are considered in B 28 – Investigation of Genital Tract and Associated Specimens. Processing of specimens for Mycobacterium species from, for example, subcutaneous cold abscesses is described in B 40 – Investigation of Specimens for Mycobacterium species.

Brain Abscess3-6

Brain abscesses are serious and life-threatening.

Sources of abscess formation include:

  • Direct contiguous spread from chronic otitic or paranasal sinus infection

  • Metastatic haematogenous spread either from general sepsis or secondary to chronic suppurative lung disease

  • Penetrating wounds

  • Surgery

  • Cryptogenic (ie source unknown)

Brain abscesses of dental origin are rare. The mortality rate of theses abscesses is high even when appropriately treated7.

Treatment of brain abscesses involves the drainage of pus and appropriate antimicrobial therapy. Brain stem abscesses have a poor prognosis due to their critical anatomical location8.

Bacteria isolated from brain abscesses are usually mixtures of aerobes and obligate anaerobes, and the prevalent organism may vary depending upon geographical location, age and underlying medical conditions. The most commonly isolated organisms include9-13:

  • Anaerobic streptococci

  • Anaerobic Gram negative bacilli

  • "Streptococcus anginosus" group

  • Enterobacteriaceae

  • Streptococcus pneumoniae

  • β-haemolytic streptococci

  • S. aureus

Organisms commonly isolated vary according to the part of the brain involved. Many other less common organisms, for example Haemophilus species, may be isolated3,11-18. Nocardia species often exhibit metastatic spread to the brain from the lung. Any organism isolated from a brain abscess must be regarded as clinically significant.

Organisms causing brain abscesses following trauma may often be environmental in origin, such as Clostridium species or skin derived, such as staphylococci and Propionibacterium species19.

Brain abscesses due to fungi are rare. Aspergillus brain abscess can occur in patients who are neutropenic. Zygomycosis is an uncommon opportunistic infection caused by Rhizopus and Absidia species and related fungi. Scedosporium apiospermum (Pseudallescheria boydii) enters the lungs and spreads haematogenously20.

The use of culture based methods for organism identification is time consuming; molecular tests are becoming popular resulting in improved management of brain abscesses21.

Breast Abscess7

Breast abscesses occur in both lactating and non-lactating women. In the former infections are commonly caused by S. aureus, but may alternatively be polymicrobial, involving anaerobes and streptococci22-24. Signs include discharge from the nipple, swelling, oedema, firmness and erythema.

In non-lactating women a subareolar abscess forms often with an inverted or retracted nipple. Mixed growths of anaerobes are usually isolated25. Some patients require surgery involving complete duct excision25. Abscesses may also be caused by Pseudomonas aeruginosa and Proteus species26.

Dental Abscess

Dental abscesses involve microorganisms colonising the teeth that may become responsible for oral and dental infections, leading to dentoalveolar abscesses and associated diseases. They may also occur as a direct result of trauma or surgery.

Periodontal disease involves the gingiva and underlying connective tissue, and infection may result in gingivitis or periodontitis27.

Organisms most commonly isolated in acute dentoalveolar abscesses are facultative or strict anaerobes. The most frequently isolated organisms are anaerobic Gram negative rods, however other organisms have also been isolated. Examples include27-31:

  • α-haemolytic streptococci

  • Anaerobic Gram negative bacilli

  • Anaerobic streptococci

  • "S. anginosus" group

  • Actinobacillus actinomycetemcomitans

  • Spirochaetes

  • Actinomyces species

Aspiration of dental abscesses is necessary to obtain samples containing the likely causative organisms. Swabs are likely to be contaminated with superficial commensal flora.

Liver Abscess

Liver abscesses can be amoebic or bacterial (so-called pyogenic) in origin or, more rarely, a combination of the two.

Pyogenic liver abscesses usually present as multiple abscesses and are potentially life-threatening. They require prompt diagnosis and therapy by draining and/or aspirating purulent material, although it is possible to treat liver abscesses with antibiotics alone. They occur in older patients than those with amoebic liver abscesses, and are often secondary to a source of sepsis in the portal venous distribution.

Examples of the sources of pyogenic liver abscess include29:

  • Biliary tract disease

  • Extrahepatic foci of metastatic infection

  • Surgery

  • Trauma

Many different bacteria may be isolated from pyogenic liver abscesses. The most common include32-35:

  • Enterobacteriaceae

  • Bacteroides species

  • Clostridium species

  • Anaerobic streptococci

  • "S. anginosus" group

  • Enterococci

  • P. aeruginosa

  • B. pseudomallei (in endemic areas)

Other causes include Candida species.

Amoebic liver abscesses arise as a result of the spread of Entamoeba histolytica via the portal vein from the large bowel which is the primary site of infection (investigation of amoebae is described in B 31 – Investigation of Specimens other than Blood for Parasites).

Hydatid cysts may also occur as fluid-filled lesions in the liver. However, the clinical presentation is usually different from that of liver abscesses (refer to B 31 – Investigation of Specimens other than Blood for Parasites). Cysts may become super-infected with gut flora and progress to abscess formation.

Lung Abscess36

Lung abscesses involve the destruction of lung parenchyma and present on chest radiographs as large cavities often exhibiting air-fluid levels. This may be secondary to aspiration pneumonia, in which case the right middle zone is most frequently affected. Other organisms may give rise to multifocal abscess formation and the presence of widespread consolidation containing multiple small abscesses (<2 cm diameter) is sometimes referred to as necrotising pneumonia. Pneumonia caused by S. aureus and Klebsiella pneumoniae may show this picture (refer to B 57 – Investigation of Brochoalveolar Lavage, Sputum and Associated Specimens).

Lung abscesses most often follow aspiration of gastric or nasopharyngeal contents as a consequence of loss of consciousness, resulting for example from alcohol excess, cerebrovascular accident, drug overdose, general anaesthesia, seizure, diabetic coma, or shock. Other predisposing factors include oesophageal or neurological disease, tonsillectomy and tooth extraction.

Lung abscesses may arise from endogenous sources of infection. The bacteria involved in these cases are generally from the upper respiratory tract and anaerobes are often implicated, secondarily infecting consolidated lung after aspiration from the upper respiratory tract. Nosocomial infections involving S. aureus, S. pneumoniae, Klebsiella species and other organisms may also occur.

B. pseudomallei may cause lung abscesses or necrotising pneumonia in those who have visited endemic areas (mainly South East Asia and Northern Australia) especially in diabetics37.

Nocardia infection is most often seen in the lung where it may produce an acute, often necrotising, pneumonia38. This is commonly associated with cavitation. It may also produce a slowly enlarging pulmonary nodule with pneumonia, associated with empyema. Nocardiosis, almost always occurring in a setting of immunosuppression, may present as pulmonary abscesses.

Actinomyces species cause a thoracic infection that may involve the lungs, pleura, mediastinum or chest wall. Cases often go unrecognised until empyema or a chest wall fistula develops. Aspiration of oral contents is a risk factor for the development of thoracic actinomycosis, thus predisposing conditions include alcoholism, cerebral infarction, drug overdose, general anaesthesia, seizure, diabetic coma or shock.

Abscesses as a result of blood borne spread of infection from a distant focus may occur in conditions such as infective endocarditis.

Lemierre's syndrome (or necrobacillosis) originates as an acute oropharyngeal infection usually in a young adult. Infective thrombophlebitis of the internal jugular vein leads to septic embolisation and metastatic infection. The lung is most frequently involved but multifocal abscesses may develop. Fusobacterium necrophorum is the most common pathogen isolated from blood cultures in patients with this syndrome36.

Aspergilllus species have been isolated from lung abscesses in patients who are immunocompromised.

Pancreatic Abscess

Pancreatic abscesses are potential complications of acute pancreatitis. Infections are often polymicrobial and common isolates include Escherichia coli, other Enterobacteriaceae, enterococci and anaerobes: longer-standing collections, especially after prolonged antibiotic therapy, are often infected with coagulase negative staphylococci and Candida species39.

Perinephric Abscess40

Perinephric abscess are an uncommon complication of UTI, which affects patients with one or more anatomical or physiological abnormalities. The abscess may be confined to the perinephric space or extend into adjacent structures. Pyuria, with or without positive culture, is seen on examination of urine. Causative organisms are usually Gram negative bacilli, but can also be staphylococci or Candida species. Mixed infections have also been reported.

Perirectal Abscess

Perirectal abscesses are encountered in patients with predisposing factors. These include41:

  • Immunodeficiency

  • Malignancy

  • Rectal surgery

  • Ulcerative colitis

They are often caused by42:

  • Anaerobes

  • Enterobacteriaceae

  • Streptococci

  • S. aureus

Pilonidal Abscess

Pilonidal abscesses are common in children and result from infection of a pilonidal sinus. Anaerobes and Enterobacteriaceae are usually isolated, but they may be caused by S. aureus and β-haemolytic streptococci43.

Prostatic Abscess

Prostatic abscesses may be caused by, or associated with44:

  • Diabetes Mellitus

  • Acute and chronic prostatitis

  • Instrumentation of the urethra and bladder

  • Lower urinary tract obstruction

  • Haematogenous spread of infection

Organisms that may cause prostatic abscesses include45:

  • E. coli and other Enterobacteriaceae

  • Anaerobes

  • Neisseria gonorrhoea

  • S. aureus

Prostatic abscesses can act as reservoirs for Cryptococcus neoformans resulting in relapses of infection with this organism46.

Psoas Abscess

Psoas abscesses may be seen as secondary infections to47:

  • Appendicitis

  • Diverticulitis

  • Osteomyelitis of the spine

  • Infection of a disc space

  • Bacteraemia

  • Perinephric abscess

Pus tracks under the sheath of the psoas muscle. Infection often occurs in drug abusers after injection into the ipsilateral femoral vein.

Psoas abscesses are predominantly caused by48-50:

  • Enterobacteriaceae

  • Bacteroides species

  • S. aureus

  • Streptococci

  • Mycobacterium tuberculosis

Renal Abscess

Renal abscesses are typically caused by Gram negative bacilli and result from ascending urinary tract infection, pyelonephritis, renal calculi or septicaemia51.

Renal abscesses are localised in the renal cortex and may occur as a result of Staphylococcus aureus bacteraemia. Pyuria may also be present, but urine culture is usually negative. Renal abscesses are increasingly being seen as complications of acute pyelonephritis caused by Gram negative bacilli. The rare condition of emphysematous pyelonephritis, which results in multifocal intrarenal abscesses and gas formation within the renal parenchyma, is usually seen in diabetic patients or as a complication of renal stones. The commonest cause is Escherichia coli and the condition carries a 70% mortality rate.

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