Investigations of ear swabs and associated specimens

Infections of the ear can be divided into otitis externa and otits media Otitis externa: In general, infection of the external auditory canal resembles infection of skin and soft tissue elsewhere. Otitis externa can be subdivided into categories: acute localised; acute diffuse; chronic; and invasive (malignant). a) Acute localised otitis externa Acute localised otitis externa is usually caused by Staphylococcus aureus and may result in a furuncle or pustule of a hair follicle. Erysipelas due to Group A Streptococcus may be found in the concha and canal. b) Acute diffuse otitis externa It is known as "swimmer's ear" and is mainly encountered in hot, humid conditions. The most common bacteria being Pseudomonas aeruginosa and S. aureus. Anaerobes are frequently associated with polymicrobial infections and usually originate from the oropharynx. c) Chronic otitis externa Chronic otitis externa is due to colonisation with coliforms and fungi which is best treated by topical cleansing, and not antibiotics.
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d) Malignant otitis externa Malignant otitis externa is a severe necrotising infection that spreads from the squamous epithelium of the canal into surrounding soft tissues, blood vessels, cartilage and bone. Patients at risk include people with diabetes, the elderly and patients who are immunocompromised. It is almost always caused by P. aeruginosa.

Otitis media: It can occur when oropharyngeal flora ascends the Eustachian tube and are not eliminated by the defence mechanisms of the middle ear. The role of antibiotic treatment at the first presentation of infection is a contentious issue as most infections are of viral origin. However, common bacteria causing otitis media, such as Streptococcus pneumoniae and Haemophilus influenzae can be isolated from ear swabs if the tympanic membrane has perforated. Often the strains of S. pneumoniae exhibit reduced susceptibility to penicillin although this is not common in the UK. Other less common causes include S. aureus, S. pyogenes and Moraxella catarrhalis. An external ear swab is not useful in the investigation of otitis media unless there is perforation of the eardrum. Tympanocentesis, to sample middle ear effusion, is rarely justified. a) Acute otitis media infection Acute otitis media infection is defined by the coexistence of fluid in the middle ear and signs and
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symptoms of acute illness. Organisms that cause this type of infection are S. pneumoniae, H. influenzae and M. catarrhalis. Less frequent causes are S. pyogenes, S. aureus, and Gram-negative bacilli. Respiratory syncytial virus and parainfluenza viruses have been isolated from middle ear effusions and may have a role in the aetiology of otitis media especially in children.

b) Chronic suppurative otitis media are very destructive, persistent and can produce irreversible adverse outcomes such as hearing loss. The most common bacterial isolates are pseudomonads closely followed by meticillin-resistant Staphylococcus aureus (MRSA), with anerobic bacteria found in 25% of patients. P. aeruginosa usually only colonises the ear canal and is rarely isolated from the middle ear.

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Investigations of eye swabs and canlicular pus

Infections of the eye can be caused by a variety of microorganisms. Swabs from eyes may be contaminated with skin microflora, but any organism may be considered for further investigation if clinically indicated. Exogenous organisms may be introduced to the eye via hands, fomites (eg contact lenses), traumatic injury involving a foreign body, following surgery, or simply by spread from adjacent sites. Eye infections occurring in the first four weeks of life caused by Chlamydia trachomatis or Neisseria gonorrhoeae are notifiable as ophthalmia neonatorum. Blepharitis is associated with: Staphylococcus aureus Staphylococcus epidermidis Corynebacterium species Propionibacterium acnes Conjunctivitis may be acute or chronic Common bacterial causes include: S. aureus Streptococcus pneumoniae Haemophilus influenza

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Less common causes: Lancefield group A, C and G streptococci Neisseria cinerea P. acnes Moraxella species other Gram-negative rods anaerobes such as Eubacterium species and Peptostreptococcus species. Moraxella catarrhalis causes acute conjunctivitis and Moraxella lacunata causes a chronic infection.
However, many of these organisms may also be isolated from the surrounding areas (skin), and so the interpretation of the significance of their presence is difficult.

Conjunctivitis caused by Neisseria gonorrhoeae is associated with concomitant genital infection. In neonates it is an important cause of ophthalmia neonatorum, which may cause blindness if left untreated. Neisseria meningitidis has also been implicated in hyperacute conjunctivitis. Conjunctivitis in neonates is caused by the pathogens commonly found in adult cases. Additional organisms include: N. gonorrhoeae Haemophilus parainfluenzae Lancefield group B streptococci and enterococci Enterobacteriaceae eg Klebsiella pneumoniae and Proteus mirabilis
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 Pseudomonas aeruginosa Chlamydial and viral conjunctivitis also occur. The most common causes of viral conjunctivitis are adenoviruses. Acanthamoeba species can cause severe keratitis, usually in contact lens wearers or after ocular trauma. These protozoa may be isolated from corneal scrapings, as well as from contact lenses and storage cases . Orbital cellulitis The most common pathogens in adults are: S. aureus, streptococci and anaerobes. In children H. influenzae still remains prevalent, but the capsulated (type b) strain is rarely seen. Streptococci, staphylococci, peptostreptococci and P. aeruginosa may cause necrosis. Eye swabs are of limited value in the investigation of orbital and preseptal cellulitis. Ideally aspirates from the affected tissues should be obtained and treated Canaliculitis: is a rare condition. Infections are usually chronic and caused by anaerobic actinomycetes such as Actinomyces israelii or by Propionibacterium propionicus. Swabs of samples of the canalicular pus are preferable to eye swabs for diagnosis.

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Investigations of mouth swabs

Candidosis: is the most frequent type of oral infection. Infection of the buccal mucosa, tongue or oropharynx is usually due to Candida albicans. Cancrum oris (noma or gangrenous stomatitis): is a necrotising polymicrobic infection, arising in the severely debilitated and malnourished, with children most often affected. It is usually preceded by ulcerative (Vincents) gingivitis and diagnosed by microscopy, and the appearance of a fusospirochaetal complex is pathognomonic for the disease. Parotitis: may result in pus exuding from the parotid glands which is sampled via the mouth. 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
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species. Fungi may attack the sinuses and encroach on the palate, eg Aspergillus species. Infection with Histoplasma can lead to ulceration of oral mucosa

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Investigations of nose swabs

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 colonized patients who have infection elsewhere. Topical antibacterial agents such as mupirocin and chlorhexidine/neomycin are preferred to systemic formulations when a patient is identified as a carrier. Nose swabs may be used to investigate carriage of Lancefield group A streptococcus and Meticillin Resistant Staphylococcus aureus (MRSA). Nasal discharge may be a presentation of diphtheria. However, nose swabs are NOT routinely cultured for Corynebacterium diphtheriae. Nasal swabs should not be taken to investigate the presence of Bordetella pertussis. 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. Rhinoscleroma, due to infection with Klebsiella rhinoscleromatis, is a rare form of chronic granulomatous nasal infection. Ozaenia (ozena) is a chronic atrophic rhinitis. 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.
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Rhinosporidium seeberi, an aquatic protistan protozoan, producing polypoid masses may affect the nasal mucosa. Superficial swabs are likely to be inadequate; scrapings or biopsy material are most likely to yield the organism.

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Investigations of throat swabs

Pharyngitis The commonest cause of bacterial pharyngitis is the Lancefield group A, Streptococcus pyogenes. The isolation rate of Lancefield group A streptococci may be increased by incubating culture plates for 40-48 h. Lancefield group C streptococci have been reported as a cause of pharyngitis. Most of the evidence for Lancefield groups C and G streptococci causing pharyngitis comes from reports of outbreaks. Diphtheria It is caused by toxigenic strains of Corynebacterium diphtheriae (of which there are 4 biotypes - gravis, mitis, intermedius and belfanti) and some toxigenic strains of Corynebacterium ulcerans and pseudotuberculosis. Criteria for screening throat swabs for C. diphtheria Throat or nose swabs from a patient with one or more of the following risk factors reported: a. Membranous or pseudomembranous pharyngitis/tonsillitis b. Travel overseas (especially Russia and Former Soviet States, Africa, South America and South- East Asia) within the last 10 days c. Recent contact with someone who has travelled overseas recently

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d. Recent consumption of raw milk products (C. ulcerans) e. Recent contact with farms/farm animals or domestic animals (C. ulcerans) f. The patient works in a clinical microbiology laboratory, or similar, where Corynebacterium species may be handled Epiglottitis Most cases of epiglottitis in young children under the age of five used to be caused by Haemophilus influenzae type b. Because trauma from the swab may precipitate obstruction, throat swabs are contraindicated in cases of suspected acute epiglottitis. Blood cultures should be taken in all cases of suspected epiglottitis. Throat swabs to determine upper airway colonization with H. influenzae type b are usually only taken for epidemiological studies. Vincents angina Borrelia vincentii and Fusobacterium species are associated with the infection known as Vincent's angina. It is characterised by ulceration of the pharynx or gums and occurs in adults with poor mouth hygiene or serious systemic disease.

Other causes of pharyngitis

Non-toxigenic C. diphtheria
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 Arcanobacterium haemolyticum (previously Corynebacterium haemolyticum Fungal throat and pharyngeal infections Fusobacterium necrophorum Neisseria gonorrhoeae Neisseria meningitides Staphylococcus aureus

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Investigation of bronchoalveolar lavage, sputum and associated specimens

Pneumonia Many of the bacteria found as colonisers of the upper respiratory tract have been implicated in pneumonia. Antibiotic treatment and hospitalisation affect the colonizing flora, leading to an increase in numbers of aerobic Gram-negative bacilli. These factors affect the sensitivity and specificity of sputum culture as a diagnostic test and results must always be interpreted in the light of the clinical information. Sputum culture results are often unreliable and sensitivity of culture is poor for many pathogens, although culture and antibiotic sensitivities may be of value in sputum specimens from patients with severe exacerbation of COPD. Community acquired pneumonia The commonest cause overall is Streptococcus pneumonia. Patients with COPD are additionally at risk of pneumonia caused by Haemophilus influenzae and Moraxella catarrhalis as are patients infected with HIV. Staphylococcus aureus pneumonia occurs either in the context of recent influenza infection or, less commonly, as a result of blood borne spread from a distant focus, COPD or aspiration. Aerobic Gram-negative rods are rare causes of community acquired pneumonia. Occasionally, Klebsiella pneumoniae causes severe

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necrotising pneumonia, typically in patients with a history of alcohol abuse and homelessness (Friedlnders pneumonia). Mycoplasma pneumonia second only to Streptococcus pneumoniae. Chlamydia pneumoniae is an exclusively human pathogen, but pneumonia caused by Chlamydia psittaci and Coxiella burnetii occurs in individuals with the relevant exposure history (birds and farm animals). Legionella pneumophila is rare. Respiratory viruses, such as RSV, influenza and adenoviruses may occasionally cause primary viral pneumonia. Other rare causes of community-acquired pneumonia include Pasteurella species and Neisseria meningitidis. Hospital acquired pneumonia Patients with critical illnesses requiring prolonged mechanical ventilation are susceptible to multi-resistant Pseudomonas aeruginosa and Acinetobacter species (eg A. baumanii). Aerobic Gram-negative bacilli, including members of the Enterobacteriaceae (such as Klebsiella and Enterobacter species) and P. aeruginosa are implicated in up to 60% of cases. Intravascular catheters and nasal carriage are risk factors for pneumonia caused by meticillin resistant S. aureus (MRSA). Aspiration pneumonia

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Lung abscess 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. caused by S. aureus and K. pneumonia, Nocardiosis, almost always occurring in a setting of immunosuppression. The S. anginosus group (S. anginosus, S. constellatus and S. intermedius) have been isolated from cases of lung abscess as a polymicrobial infection with oral anaerobes. Burkholderia pseudomallei may cause lung abscesses or necrotising pneumonia. Lemierre's syndrome or necrobacillosis originates as an acute oropharyngeal infection. Fusobacterium necrophorum is the most common pathogen isolated from blood cultures in patients with this syndrome. Cystic fibrosis (CF) The major pathogens are S. aureus, H. influenzae (usually non-encapsulated in CF patients), S.pneumoniae and pseudomonads, particularly mucoid P. aeruginosa strains. Strains of P. aeruginosa with differing antibiotic susceptibilities may be isolated from a single sample. Anaerobes may also be present, together with Aspergillus fumigatus and mycobacteria other than Mycobacterium tuberculosis (MOTT).

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Burkholderia cepacia complex, Stenotrophomonas maltophilia, Fungi, particularly Aspergillus species, have also been implicated in infections in cystic fibrosis patients. Nocardia and Actinomyces infections Parasitic infections Fungal infections

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Investigations of skin, superficial and non-surgical wound swabs

Commonly isolated organisms include: Staphylococcus aureus Lancefield groups A, B, C and G streptococci Bacteroides species Clostridium species Anaerobic cocci Coagulase-negative staphylococci Corynebacterium species Enterobacteriaceae Pseudomonads Cellulitis is a diffuse spreading infection involving the loose connective tissue of the deeper layers of the skin and subcutaneous tissues. Blood culture is the investigation of choice. The most common causative organisms are -haemolytic streptococci and Staphylococcus aureus. Haemophilus influenzae cellulitis, particularly of the orbit, occurs in children up to three years of age. Facial cellulitis due to Streptococcus pneumoniae has also been described and occurs mainly in children. Cellulitis due to S. pneumoniae may also occur in patients with underlying conditions such as alcoholism, diabetes mellitus, intravenous drug abuse or systemic lupus erythematosus.

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Cellulitis around wound infections is commonly caused by: -haemolytic streptococci S. aureus Bacteroides species Anaerobic cocci Bite wounds in human and animal can become contaminated by oral flora. Organisms most commonly isolated include: Pasteurella multocida S. aureus -haemolytic streptococci Anaerobes DF-2 (Capnocytophaga canimorsus) Eikenella corrodens Haemophilus species Coagulase-negative staphylococci Streptobacillus moniliformis S. intermedius Burns sepsis is an important cause of death in patients suffering from burns. Organisms encountered include: Staphylococcus aureus -haemolytic streptococci Pseudomonads, especially Pseudomonas aeruginosa Acinetobacter species Bacillus species
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 Enterobacteriaceae Filamentous fungi, eg: Fusarium species Candida albicans and other yeasts Coagulase-negative staphylococci Paronychia is a superficial infection of the nail fold occurring as either an acute or chronic condition. Common isolates include: S. aureus Lancefield Group A streptococci Yeasts Anaerobic bacteria H. influenzae

Other skin infections Aeromonas and non-cholera Vibrio species are predominantly isolated from traumatic water-related wounds or lacerations received whilst swimming in fresh or salt water.

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INVESTIGATION OF CEREBROSPINAL FLUID SHUNTS

Organisms isolated from CSF shunts and ventricular catheters include: Coagulase-negative staphylococci Staphylococcus aureus Enterobacteriaceae Coryneforms and Propionibacterium species Enterococci Haemophilus influenzae Neisseria meningitidis Pseudomonads Streptococci Streptococcus pneumoniae Yeasts Mycobacterium species

Organisms which may be isolated but less frequently include anaerobes and fungi other than yeasts. Coagulase-negative staphylococci are isolated most commonly. Production of extracellular slime has been reported as being important in the pathogenesis of shunt infections. Coryneforms also produce extracellular slime which may contribute to their pathogenesis in devicerelated infections. Many isolates are Corynebacterium jeikeium (formerly JK coryneforms). C.

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jeikeium, and other species, are notable for their resistance to a wide range of antimicrobials.

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INVESTIGATION OF ABSCESSES AND DEEP-SEATED WOUND INFECTIONS

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 intraabdominal 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.

Brain abscess 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
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 Surgery Cryptogenic (ie source unknown) 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 include Anaerobic streptococci Anaerobic Gram-negative bacilli "Streptococcus anginosus" group Enterobacteriaceae Streptococcus pneumoniae -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 isolated. 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 species.

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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 haematogenously.

Breast abscess Breast abscesses occur in both lactating and nonlactating women. In the former infections are commonly caused by S. aureus, but may alternatively be polymicrobial, involving anaerobes and streptococci. 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 isolated. Some patients require surgery involving complete duct excision. Abscesses may also be caused by Pseudomonas aeruginosa and Proteus species. Carbuncles, furuncles, cutaneous, soft tissue and other abscesses Carbuncles are deep and extensive subcutaneous abscesses involving several hair follicles and sebaceous glands. Carbuncles are most often caused by S. aureus.
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Furuncles are abscesses which begin in hair follicles as firm, tender, red nodules that become painful and fluctuant. Furuncles are caused by the same pathogens as carbuncles. Recurrent staphylococcal furunculosis is highly infectious and may be the first sign of an underlying disease such as diabetes mellitus. Cutaneous abscesses are usually painful, tender, fluctuant erythematous nodules often with a pustule on top. In some cases they are associated with extensive cellulitis, lymphangitis, lymphadenitis and fever. They are caused by a variety of organisms. The location of an abscess often determines the flora likely to be isolated. Thus S. aureus is most often isolated from cutaneous abscesses of the axillae, the extremities and the trunk, whereas cutaneous abscesses involving the vulva and buttocks may yield faecal or urogenital mucosal flora. Soft tissue abscesses involve one or more tissue planes underlying the epidermis, usually developing after trauma to the skin. They may arise from animal bites, in which case common isolates include Pasteurella and Actinobacillus species as well as other organisms of the HACEK group (Haemophilus, Actinobacillus, Cardiobacterium, Eikenella and Kingella species). Burkholderia pseudomallei causes melioidosi. The disease may present in a variety of forms with skin
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lesions and/or cellulitis. Diagnosis is made by blood culture, serology or culture of pus. Pyomyositis is a purulent infection of skeletal muscle in which solitary or multiple muscle abscesses form. It most often occurs in tropical areas, and in HIVinfected or other patients who are immunocompromised. The main causative organism is S. aureus. Abscesses in intravenous drug users Cutaneous abscesses frequently occur as a complication of injecting drug use. They commonly result from the use of non-sterile solutions in which the drug is dissolved or from lubrication of the needle using saliva. Common bacterial isolates include: Oral streptococci Streptococcus anginosus group Fusobacterium nucleatum Prevotella species Porphyromonas species Staphylococcus aureus Clostridium species

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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 periodontitis. 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 include: -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.

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Liver abscess Liver abscesses can be amoebic or bacterial (socalled 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 include: Enterobacteriaceae Bacteroides species Clostridium species Anaerobic streptococci "S. anginosus" group Enterococci
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 P. aeruginosa B. pseudomallei (in endemic areas) 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. Hydatid cysts may also occur as fluid-filled lesions in the liver. However, the clinical presentation is usually different from that of liver abscesses. Cysts may become super-infected with gut flora and progress to abscess formation.

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