Type of Specimen
Nose swab
Scope
The examination of the processing and bacteriological investigation of nose swabs.
Introduction
Nasal colonisation with Staphylococcus aureus increases the risk of staphylococcal infections at other sites of the body, such as postoperative wounds and dialysis access sites3. It is also associated with recurrent skin infections, nosocomial infections in nurseries and hospital wards. S. aureus is a major cause of morbidity and mortality in haemodialysis patients as most patients carry the organism in their anterior nares4.
Eradication of nasal carriage of S. aureus may be beneficial in certain clinical conditions such as recurrent furunculosis. Systemic, in addition to topical, treatment is appropriate for nasally colonised patients who have an infection elsewhere. Topical antibacterial agents such as mupirocin and chlorhexidine/neomycin are preferred to systemic formulations when a patient is identified as a carrier5.
Nose swabs may be used to investigate carriage of Lancefield group A streptococcus, and Meticillin Resistant Staphylococcus aureus (MRSA) (B 29 - Investigation of Specimens for Screening for MRSA).
There is no clear evidence regarding the significance of isolating Haemophilus influenzae and Streptococcus pneumoniae from nose swabs as a predictor of involvement in infections such as sinusitis.
Although nose swabs are not the ideal specimen for the examination of nasal discharge, they are sometimes received. Nasal discharge may show the presence of diphtheria. However, nose swabs are not routinely cultured for Corynebacterium diphtheriae. Nasal swabs should not be taken to investigate the presence of Bordetella pertussis6.
Rhinoscleroma, due to infection with Klebsiella rhinoscleromatis, is a rare form of chronic granulomatous nasal infection affecting the nasal passages and sinuses, which can also include the pharynx and larynx7,8. The disease is progressive and manifests itself by tumour-like growths with local extension. Although common in Eastern Europe, Central Africa, Latin America and South East Asia, rhinoscleroma appears to be poor communicability.
Ozaenia (ozena) is a chronic atrophic rhinitis7. The condition can destroy the mucosa and is characterised by a chronic, purulent and often foul-smelling nasal discharge. Klebsiella ozaenae may have an etiological role.
Rhinosporidium seeberi, an aquatic protistan protozoan, producing polypoid masses may affect the nasal mucosa of persons living in India, Sri Lanka, parts of South East Asia, America and parts of Europe, including Eastern Europe9. Close collaboration between physicians, ENT surgeon, microbiologist and histopathologist is necessary to reach a diagnosis. Superficial swabs are likely to be inadequate; scrapings or biopsy material are most likely to yield the organism (B 19 - Investigation of Sinus Aspirate).
Specimen Containers1,2
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.”
1 Safety Considerations1,2,10-24
1.1 Specimen Collection, Transport and Storage1,2,10-13
Use aseptic technique.
Collect swabs into appropriate transport medium and transport in sealed plastic bags.
Compliance with postal, transport and storage regulations is essential.
1.2 Specimen Processing1,2,10-24
Containment Level 2.
Laboratory procedures that give rise to infectious aerosols must be conducted in a microbiological safety cabinet16.
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
Nose swab
2.2 Optimal Time and Method of Collection25
For safety considerations refer to Section 1.1.
Collect specimens before antimicrobial therapy where possible25.
Plain, sterile cotton wool swab. Sample the anterior nares by gently rotating the swab over the mucosal surface.
Unless otherwise stated, swabs for bacterial and fungal culture should be placed in appropriate transport medium19-23.
2.3 Adequate Quantity and Appropriate Number of Specimens25
Numbers and frequency of specimen collection are dependent on clinical condition of patient.
3 Specimen Transport and Storage1,2
3.1 Optimal Transport and Storage Conditions
For safety considerations refer to Section 1.1.
Specimens should be transported and processed as soon as possible25.
If processing is delayed, refrigeration is preferable to storage at ambient temperature25.
4 Specimen Processing/Procedure1,2
4.5.3 Culture media, conditions and organisms
Clinical details/conditions / Specimen / Standard media / Incubation / Cultures read / Target organism(s)
Temp °C / Atmos / Time
Boils
S. aureus carriage / Nose swab / Blood agar / 35-37 / 5-10% CO2 / 16-24hr / ³16hr / S. aureus
Lancefield group A streptococcus carriage / Nose swab / Blood agar / 35-37 / 5-10% CO2 / 16-24hr / ³16hr / Lancefield group A streptococcus
For these situations, add the following:
Clinical details/
conditions / Specimen / Supplementary media / Incubation / Cultures read / Target organism(s)
Temp °C / Atmos / Time
Nasal diphtheria / Nose swab / Hoyle's tellurite agar / 35-37 / air / 40-48hr / daily / C. diphtheriae
Rhinoscleroma / Nose swab / CLED/
MacConkey agar / 35-37 / air / 16-24hr / ³16hr / K. rhinoscleromatis
Other organisms for consideration - MRSA (B 29 - Investigation of Specimens for Screening for MRSA)
Reporting Procedure
5.1 Microscopy
N/A
5.2 Culture
Report presence or absence of specific pathogens, also report results of supplementary investigations:
Negatives
"Staphylococcus aureus NOT isolated."
"Lancefield group A streptococcus NOT isolated."
Positives
"Staphylococcus aureus isolated."
"Lancefield group A streptococcus isolated."
Also, report results of supplementary investigations.
5.2.1 Culture reporting time
Written report: 16–72hr stating, if appropriate, that a further report will be issued
5.3 Antimicrobial Susceptibility Testing
Report susceptibilities as clinically indicated. Prudent use of antimicrobials according to local and national protocols is recommended.
Investigation of Mouth Swabs
Introduction
Candidosis
Candidosis is the most frequent type of oral infection. Infection of the buccal mucosa, tongue or oropharynx is usually due to Candida albicans. Species of yeast other than C. albicans, such as Candida krusei and Candida glabrata, can also occasionally colonise the mouth but are rarely associated with infection. However, they are becoming increasingly important, particularly in patients who are immunocompromised3,4.
Cancrum oris (Noma or Gangrenous Stomatitis)
Cancrum oris (noma or gangrenous stomatitis) is a necrotising polymicrobic infection, rarely seen in the UK, arising in the severely debilitated and malnourished, with children most often affected particularly in Africa5,6. It is usually preceded by ulcerative (Vincent’s) gingivitis7. Vincent's gingivitis is diagnosed by microscopy, and the appearance of a fusospirochaetal complex is pathognomonic for the disease8.
Sialadenitis
Sialadenitis, or infections of the salivary glands (parotid, submandibular, sublingual and accessory parotid), include suppurative, chronic bacterial and viral parotitis5.
Parotitis
Parotitis may result in pus exuding from the parotid glands, which is sampled via the mouth5. The predominant organisms causing suppurative parotitis are staphylococci, but members of the enterobacteriaceae and other Gram negative bacilli, viridans streptococci and anaerobes have been isolated. Chronic bacterial parotitis is due to staphylococci, or mixed oral aerobes and anaerobes. Mumps, influenza and enteroviruses are the usual viral agents of parotitis.
Other infective causes of oral ulceration include syphilis, herpes simplex virus and Mycobacterium species. Fungi may attack the sinuses and encroach on the palate, eg Aspergillus species. Infection with Histoplasma can lead to ulceration of oral mucosa9.
Specimens which may be submitted for the investigation of dental abscesses include pus (refer to B 14 - Investigation of Abscesses and Deep-Seated Wound Infections).
Specimen Containers1,2
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.”
1 Safety Considerations1,2,10-24
1.1 Specimen Collection, Transport and Storage1,2,10-13
Use aseptic technique.
Collect swabs into appropriate transport medium and transport in sealed plastic bags.
Compliance with postal and transport regulations is essential.
1.2 Specimen Processing1,2,10-24
Containment Level 2.
Laboratory procedures that give rise to infectious aerosols must be conducted in a microbiological safety cabinet16.
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
Mouth swab
Sample pus if present, otherwise sample any lesions or inflamed areas. A tongue depressor or spatula may be helpful to aid vision and avoid contamination from other parts of the mouth.
2.2 Optimal Time and Method of Collection25
For safety considerations refer to Section 1.1.
Collect specimens before antimicrobial therapy where possible25.
Unless otherwise stated, swabs for bacterial and fungal culture should be placed in appropriate transport medium26-30.
2.3 Adequate Quantity and Appropriate Number of Specimens25
Numbers and frequency of specimen collection are dependent on clinical condition of patient.
3 Specimen Transport and Storage1,2
3.1 Optimal Transport and Storage Conditions
For safety considerations refer to Section 1.1.
Specimens should be transported and processed as soon as possible25.
If processing is delayed, refrigeration is preferable to storage at ambient temperature25.
4 Specimen Processing1,2
For the isolation of individual colonies, spread inoculum with a sterile loop.
4.5.3 Culture media, conditions and organisms for all specimens:
Clinical details/conditions / Standard media / Incubation / Cultures read / Target organism(s)
Specimen / Temp °C / Atmos / Time
Oral candidosis
Fungal infection / Mouth swabs / Sabouraud agar / 35-37 / air / 40-48hr / ³40hr* / Yeasts
Fungi
For this situation, add the following:
Clinical details/
conditions / Supplementary media / Incubation / Cultures read / Target organism(s)
Specimen / Temp °C / Atmos / Time
Mouth ulcer / Mouth swabs / Blood agar / 35-37 / 5-10% CO2 / 16-24hr / ³16hr / Lancefield group A streptococcus
S. aureus
*Fungal culture may need to be prolonged if clinically indicated; in such cases plates should be read at ³40hr and then left in the incubator/cabinet until required.
4.6.1 Minimum level in the laboratory
Lancefield group A streptococcus / Lancefield group levelS. aureus / species level
Yeasts / "yeasts" level
Reporting Procedure
5.1 Microscopy
Stain for Vincent's organisms: report on Vincent's organisms detected.
5.1.1 Microscopy reporting time
Urgent microscopy results to be telephoned or sent electronically.
Written report, 16–72hr for Vincent's organisms.
5.2 Culture
Report clinically significant organisms isolated or
Report other growth, eg: “Mixed upper respiratory tract flora,” or
Report absence of growth.
5.2.1 Culture reporting time
Clinically urgent culture results to be telephoned or sent electronically.
Written report, 16–72hr stating, if appropriate, that a further report will be issued.
5.3 Antimicrobial Susceptibility Testing
Report susceptibilities as clinically indicated. Prudent use of antimicrobials according to local and national protocols is recommended.
Throat Swab
Scope
Introduction
Pharyngitis
The commonest cause of bacterial pharyngitis is the Lancefield group A, Streptococcus pyogenes. Healthy carriers of group A streptococci are usually children, in whom rates of up to 20% have been reported, but rates are much lower in adults. In these individuals, isolation of the Lancefield group A streptococcus does not necessarily imply a role in infection.
Extrapharyngeal manifestations of Lancefield group A streptococcus infection can be divided into those associated with acute infection and the non-suppurative post-streptococcal sequelae, such as acute rheumatic fever and glomerulonephritis, which occur two to three weeks after pharyngeal infection1. In acute infection, bacteraemia and streptococcal toxic shock may occur. Post-streptococcal sequelae appear to be limited to a circumscribed set of serotypes2.
The isolation rate of Lancefield group A streptococci may be increased by incubating culture plates for 40-48hr3.
Lancefield group C streptococci have been reported as a cause of pharyngitis4. The majority of the species, however, are zoonotic and rarely cause disease in humans, these include Streptoccocus equi subspecies zooepidemicus, Streptococcus equi subspecies equi and Streptococcus dysgalactiae subspecies dysgalactiae. The beta-haemolytic group C streptococci which infect humans include the large colony form Streptococcus dysgalactiae subspecies equisimilis and the minute colony form or Streptococcus anginosus group (formerly the S. milleri group); which includes Streptococcus constellatus subspecies pharyngis and Streptococcus anginosus. These organisms are very rarely implicated in bacterial pharyngitis, and may express A, C, F or G Lancefield group antigens. The Lancefield group G streptococci are known to cause pharyngitis and are subdivided into the "large colony" form (which comprises the animal species Streptococcus canis and the human species Streptococcus dysgalactiae subspecies equisimilis, which is the only recognised causative agent of pharyngitis within the group) and the "minute colony" form (S. anginosus)5.
Most of the evidence for Lancefield groups C and G streptococci causing pharyngitis comes from reports of outbreaks6-9.
Diphtheria
Diphtheria is an acute infectious disease of the upper respiratory tract and, occasionally, the skin. It is caused by toxigenic strains of Corynebacterium diphtheriae (of which there are four biotypes - gravis, mitis, intermedius and belfanti) and some toxigenic strains of Corynebacterium ulcerans and pseudotuberculosis10. All can carry the phage-borne diphtheria toxin gene. In a fully developed case of diphtheria, this toxin damages the pharyngeal epithelium to produce a leathery membrane, giving the disease its name. This membrane may occlude the airway, sometimes causing death by respiratory obstruction. Systemic absorption by the host of the toxin from the primary site of replication may damage a wide range of cells, including those of the heart and nervous system. Myocarditis and neurological dysfunction may cause or contribute to disability or death.