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



PHE publications gateway number: 2016127

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 6

Scope of document 9

Key recommendations 9

Introduction 9

Technical information/limitations 17

1 Safety considerations60,61,64-78 19

2 Specimen collection 19

3 Specimen transport and storage60,61 20

4 Specimen processing/procedure60,61 20

5 Reporting procedure 25

6 Notification to PHE90,91, or equivalent in the devolved administrations92-95 27

Appendix: Investigation of pus and exudates96 28

References 30

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



Incubation temperature and atmosphere on clinical conditions “Nocardiosis” has been updated.


Updated to reflect section 4.5.1 culture media, conditions and organisms table.

Amendment no/date.


Issue no. discarded.


Insert issue no.


Section(s) involved



Section regarding swabs has been clarified.

Amendment no/date.


Issue no. discarded.


Insert issue no.


Section(s) involved



Changed to ‘investigation of pus and exudates’.

Whole document.

References reviewed and updated.

Type of specimen.

Pus or exudate.

Key recommendations.

Key recommendation section included.


Document streamlined and re-structured.

Information regarding skin related abscesses and post-operative wound infections removed and transferred to B 11 - Investigation of swabs from skin and superficial soft tissue infections.

Inclusion of throat and neck abscesses.

Technical information /limitations.

Inclusion of information on selective media and rapid methods.

Safety considerations.

Recommendations included regarding the use of Class I or Class II microbiological safety cabinets where Gram negative coccobacilli are identified.

Specimen collection.

Samples of pus are preferred to swabs.

Culture and investigation.

Section 4.5.1 - Table updated to include specimen type.

Neomycin fastidious anaerobic agar replaced by selective anaerobic agar for all specimens.

Cooked meat broth or equivalent added as alternative to fastidious anaerobic broth.

GN Medium (NAV) replaced with selective Gram negative anaerobe medium.

Minor changes to incubation and culture reads throughout for consistency.

Section 4.6 - Minimum level of identity updated for the following organisms: anaerobes, β-haemolytic streptococci, enterobacteriaceae and yeast.

Consider sending staphylococci isolates from post mortem samples for toxin testing.

Section 4.7 - Antimicrobial susceptibility testing section updated. Recommendations for selective reporting are not included.

Section 4.9 - Consider sending S. aureus isolates for toxin testing where appropriate clinical details are provided.

Reporting procedure.

Updated in line with bacteriology template.

Report antimicrobial susceptibilities as clinically indicated.


Updated to reflect section 4.5.1 culture media, conditions and organisms table.

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 is 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

While every care has been taken in the preparation of SMIs, PHE and the partner organisations, 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 by an end user to an SMI for local use, it must be made clear where in the document the alterations have been made and by whom such alterations have been made and also acknowledged that PHE and the partner organisations shall bear no liability for such alterations. For the further avoidance of doubt, as SMIs have been developed for application within the UK, any application outside the UK shall be at the user’s risk.

The evidence base and microbial taxonomy for the SMI is as complete as possible at the date 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 .2.

Scope of document

Type of specimen

Pus, exudate

This SMI describes the processing and microbiological investigation of pus and exudate specimens from abscesses and infections which are deep seated or associated with specific organs (including the skin).

Investigations of these specimens for parasitic infections are in B 31 - Investigations of specimens other than blood for parasites, whereas investigations for mycobacterial cultures are in B 40 – Investigations of specimens for Mycobacterium species.

For information regarding genital tract abscesses and infections refer to B 28 – Investigation of genital tract and associated specimens.

For information on skin and soft tissue infections and regarding testing of swabs of pus refer to B 11 - Investigation of swabs from skin and superficial soft tissue infections.

This SMI should be used in conjunction with other SMIs.

Key recommendations

Samples should be transported to the laboratory and processed rapidly.

Gram stain should be undertaken on all samples.

Gram stain results should be taken into consideration when choosing which investigations to carry out.

Significant microscopy, culture and sensitivity results should be issued as soon as they become available.

A mechanism for urgent reporting should be in place to communicate key, significant results.


Abscesses are accumulations of pus in tissue 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 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, for example from subcutaneous cold abscesses, is described in B 40 – Investigation of specimens for Mycobacterium species.

Brain abscess1-4

Brain abscesses are serious and life-threatening.

Sources of abscess formation include5:

  • 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 rare6. The mortality rate of these abscesses is high even when appropriately treated7.

Treatment of brain abscesses involves the drainage of pus and appropriate antimicrobial therapy5. 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 include9-11:

  • 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 isolated9,10,12. 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 species13.

Brain abscesses due to fungi are rare. Aspergillus brain abscess can occur in patients who are neutropenic. Zygomycosis (mucormycosis) is an uncommon opportunistic infection caused by mucoraceous moulds, for example Lichtheimia (formerly Mycocladus, Absidia) and related fungi. Scedosporium apiospermum (Pseudallescheria boydii) enters the body and spreads haematogenously14.

The use of culture based methods for organism identification is time consuming; molecular tests are becoming popular resulting in improved management of brain abscesses3.

Breast abscess

Breast abscesses occur in both lactating and non-lactating women. In the former, infections are commonly caused by S. aureus, but may be polymicrobial, involving anaerobes and streptococci7,15. 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 isolated16. Some patients require surgery involving complete duct excision16. Abscesses may also be caused by Pseudomonas aeruginosa and Proteus species17.

Dental abscess18-20

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 periodontitis21.

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 include18,19:

  • α-haemolytic streptococci

  • anaerobic Gram negative bacilli

  • anaerobic streptococci

  • "S. anginosus" group

  • Aggregatibacter actinomycetemcomitans

  • Actinomyces species

  • spirochaetes

Aspiration of dental abscesses may be taken, where possible, to assist in the identification of the causative organism(s). Swabs may be contaminated with superficial commensal flora. In cases of intraosseal abscess, swabs can be useful, but only if taken from a disinfected site.

Liver abscess22

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 include:

  • biliary tract disease

  • extrahepatic foci of metastatic infection

  • surgery

  • trauma

Many different bacteria may be isolated from pyogenic liver abscesses. The most common include23-25:

  • 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 abscess

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 bronchoalveolar 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 sepsis. 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 diabetics26.

Nocardia infection is most often seen in the lung where it may produce an acute, often necrotising, pneumonia27. 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 sepsis.

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 syndrome28.

Aspergillus 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 species29.

Perirectal abscess

Perirectal abscesses are encountered in patients with predisposing factors. These include30:

  • immunodeficiency

  • malignancy

  • rectal surgery

  • ulcerative colitis

They are often caused by31:

  • anaerobes

  • Enterobacteriaceae

  • streptococci

  • S. aureus

Pilonidal abscess

Pilonidal abscesses result from infection of a pilonidal sinus. Anaerobes and Enterobacteriaceae are usually isolated, but they may be caused by S. aureus and

β-haemolytic streptococci32.

Prostatic abscess33

Abscesses within the prostate may be caused by, or associated with34:

  • 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 include35:

  • E. coli and other Enterobacteriaceae

  • enterococci

  • anaerobes

  • Neisseria gonorrhoea

  • S. aureus33

Prostatic abscesses can act as reservoirs for Cryptococcus neoformans resulting in relapses of infection with this organism36.

Psoas abscess

Psoas abscesses may be seen as secondary infections to:

  • 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 by37,38:

  • 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 sepsis39.

Renal abscesses are localised in the renal cortex and may occur as a result of, for example, 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.

Perinephric abscess are an uncommon complication of UTI, which usually affects patients with one or more anatomical or physiological abnormalities40. The abscess may be confined to the perinephric space or extend into adjacent structures. Pyuria, with or without positive culture, is normally, but not invariably 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.

Salivary gland abscess

There are three pairs of major salivary glands; the parotid, submandibular and sublingual. Parotic abscesses are more commonly seen in the elderly. Common organisms include:

  • S. aureus

  • anaerobes

Spinal epidural abscess41

Spinal epidural abscesses may occur in patients with:

  • predisposing disease (such as diabetes)

  • prior infection elsewhere in the body which may serve as a source for haematogenous spread

  • abnormality of, or trauma to, the spinal column (often involving invasive medical procedures such as epidural catheterisation)

The most common isolate is S. aureus42. Staphylococcus epidermidis may be isolated in patients following invasive spinal manipulation. Streptococci (α-haemolytic,
β-haemolytic and S. pneumoniae), Enterobacteriaceae and pseudomonads may also be isolated42,43.

Subphrenic abscess

Subphrenic abscesses occur immediately below the diaphragm, often as a result of44:

  • gastric, duodenal or colonic perforation

  • acute cholecystitis

  • procedures on the liver and upper part of the gastrointestinal tract

  • ruptured appendix

  • trauma

Subphrenic abscesses are caused by mixed infections from the normal gastrointestinal flora44.

Throat/neck abscess

Throat and neck abscess are relatively common45-47.

Causative organisms include45,48:

  • β-haemolytic streptococci

  • anaerobes

Surgical incision and drainage may be undertaken through intraoral or extra oral procedures.

Unusual cases of abscess formation

Unusual cases of abscess formation can occur in patients with many underlying conditions and may be caused by a vast range of organisms49-56. Any organism isolated from abscess pus is potentially significant.

Actinomycosis is a chronic suppurative infection characterised by chronic abscess formation with surrounding fibrosis. It is rare and usually follows perforation of a viscous, trauma or surgery. It is caused by Actinomyces israelii, usually in mixed culture with other bacteria57.

Abscess formation is most often associated with the gastrointestinal tract, the jaw and the pelvis. Other areas of the body may be involved and the formation of abdominal abscesses may occur. Thoracic involvement occurs in 15% of cases of actinomycosis. Pulmonary actinomycosis can be difficult to diagnose prior to cutaneous involvement, which results in direct extension through the chest wall. The disease progresses to form a chronic indurated mass with draining fistulae. Material should be drained from abscesses and biopsies taken. Skin biopsies may reveal the presence of organisms (refer to B 17 – ).

"Sulphur granules" are sought in the pus specimen58. These are discharged from actinomycosis abscesses. Sulphur granules are colonies of organisms forming a filamentous inner mass which is surrounded by host reaction. They are formed only in vivo. They are hard, buff to yellow in colour, and have a clubbed surface.

Intra-abdominal sepsis

Intra-abdominal sepsis is infection occurring in the normally sterile peritoneal cavity59. The term covers primary and secondary peritonitis, as well as intra-abdominal abscesses.

Primary peritonitis is infection of the peritoneal fluid in which no perforation of a viscous has occurred. Infection usually arises via haematogenous spread from an extra-abdominal source and is often caused by a single pathogen59. It is common in patients with ascites following hepatic failure. In females it may also result from organisms ascending the genital tract (refer to B 28 - Investigation of genital tract associated specimens).

Secondary peritonitis is acute, suppurative inflammation of the peritoneal cavity usually resulting from bowel perforation or postoperative gastrointestinal leakage. Secondary peritonitis is most often treated with a combination of drainage and antibiotics.

The most frequent isolates encountered in intra-abdominal sepsis with secondary peritonitis are derived from the normal gastrointestinal flora. Anaerobic bacteria are isolated from the majority of cases with Bacteroides species being isolated. However, infections are usually polymicrobial and organisms that have been isolated include:

  • Enterococcus species

  • Bacteroides species

  • pseudomonads

  • Peptostreptococcus species

  • yeasts (mostly Candida species)

  • β-haemolytic streptococci

  • Clostridium species

  • Enterobacteriaceae

Tuberculous peritonitis is a rare disease in the UK. It is more common on the Indian sub-continent, so it is important to consider this in immigrants from that area. In most cases a primary pulmonary focus is present with secondary spread of Mycobacterium tuberculosis (refer to B 40 – Investigation of specimens for Mycobacterium species).

Technical information/limitations

Limitations of UK SMIs

The recommendations made in UK SMIs are based on evidence (eg sensitivity and specificity) where available, expert opinion and pragmatism, with consideration also being given to available resources. Laboratories should take account of local requirements and undertake additional investigations where appropriate. Prior to use, laboratories should ensure that all commercial and in-house tests have been validated and are fit for purpose.

Selective media in screening procedures

Selective media which does not support the growth of all circulating strains of organisms may be recommended based on the evidence available. A balance therefore must be sought between available evidence, and available resources required if more than one media plate is used.

Specimen containers60,61

SMIs use the term “CE marked leak proof container” to describe containers bearing the CE marking used for the collection and transport of clinical specimens. The requirements for specimen containers are given in the EU in vitro Diagnostic Medical Devices Directive (98/79/EC Annex 1 B 2.1) which states: “The design must allow easy handling and, where necessary, reduce as far as possible contamination of, and leakage from, the device during use and, in the case of specimen receptacles, the risk of contamination of the specimen. The manufacturing processes must be appropriate for these purposes”.

Rapid methods

To reduce turnaround times, rapid identification and sensitivity tests may be performed in conjunction with routine methods where appropriate. A variety of rapid identification and sensitivity methods have been evaluated; these include molecular techniques and the Matrix Assisted Laser Desorption Ionisation Time-of-Flight (MALDI-TOF)62,63. It is important to ensure that fresh cultures of pure single isolates are tested to avoid reporting misleading results.

Laboratories should follow manufacturers’ instructions and all rapid tests must be validated and be shown to be fit for purpose prior to use.

1 Safety considerations60,61,64-78

1.1 Specimen collection, transport and storage60,61,64-67

Use aseptic technique.

Collect specimens in appropriate CE marked leak proof containers and transport in sealed plastic bags.

Avoid accidental injury when pus is aspirated.

Compliance with postal, transport and storage regulations is essential.

1.2 Specimen processing60,61,64-78

ContGram positiveainment Level 2.

If infection with a Hazard Group 3 organism eg Mycobacterium species, Paracoccidioides brasiliensis or Brucella species is suspected, all specimens must be processed in a microbiological safety cabinet under full Containment Level 3 conditions. Thus initial examination and all follow up work on specimens from patients with suspected Mycobacterium species, or suggesting a diagnosis of blastomycosis, coccidioidomycosis, histoplasmosis, paracoccidioidomycosis or penicilliosis must be performed inside a microbiological safety cabinet under full Containment Level 3 conditions.

It is recommended that all Gram negative coccobacilli from sterile sites should be processed in a Class I or Class II microbiological safety cabinet until Hazard Group 3 pathogens (ie Brucella) have been definitively excluded79.

Laboratory procedures that give rise to infectious aerosols must be conducted in a microbiological safety cabinet70.

Any grinding of sulphur granules should be performed in a microbiological safety cabinet.

Prior to staining, fix smeared material by placing the slide on an electric hotplate (65-75°C), under the hood, until dry. Then place in a rack or other suitable holder.

Note: Heat-fixing may not kill all Mycobacterium species80. Slides should be handled carefully.

Specimen containers must also be placed in a suitable holder.

Refer to current guidance on the safe handling of all organisms documented in this SMI.

The above guidance should be supplemented with local COSHH and risk assessments.

2 Specimen collection

2.1 Type of specimens

Pus, exudate

2.2 Optimal time and method of collection81

For safety considerations refer to Section 1.1.

Collect specimens before antimicrobial therapy where possible81.

Samples of pus are preferred to swabs. However, pus swabs are often received. When using a swab disinfect the superficial areas first. The deepest part of the wound should be sampled, avoiding the superficial microflora.

The specimen will usually be collected by a medical practitioner. Cleaning the site with sterile saline or 70% alcohol is recommended by some sources82.

Collect specimens other than swabs into appropriate CE marked leak proof containers and place in sealed plastic bags.

Unless otherwise stated, swabs for bacterial and fungal culture should then be placed in appropriate transport medium83-87.

2.3 Adequate quantity and appropriate number of specimens81

Ideally, a minimum volume of 1mL of pus should be submitted.

Swabs are not the optimal sample type. However, if received, swabs should be well soaked in pus. Refer to B 11 - Investigation of swabs from skin and superficial soft tissue infections.

Numbers and frequency of specimen collection are dependent on clinical condition of patient.

3 Specimen transport and storage60,61

3.1 Optimal transport and storage conditions

For safety considerations refer to Section 1.1.

Specimens should be transported and processed as soon as possible81.

The volume of specimen influences the transport time that is acceptable. Large volumes of purulent material maintain the viability of anaerobes for longer88,89.

The recovery of anaerobes in particular is compromised if the transport time is delayed.

If processing is delayed, refrigeration is preferable to storage at ambient temperature.

4 Specimen processing/procedure60,61

4.1 Test selection

Divide specimen on receipt for appropriate procedures such as examination for parasites (B 31 – Investigation of specimens other than blood for parasites) and culture for Mycobacterium species (B 40 – Investigation of specimens for Mycobacterium species), depending on clinical details.

4.2 Appearance

Describe presence or absence of sulphur granules (if sought).

4.3 Sample preparation

4.3.1 Pre-treatment

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