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Page 1

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 andcanal.

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 withpolymicrobial 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 canalinto 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 Haemophilusinfluenzae 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 theinvestigation 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 co-

existence 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 syncytialvirus 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 eyevia 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 conjunctivitisand 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 pathogenscommonly 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 severelydebilitated and malnourished, with children most often

affected. It is usually preceded by ulcerative (Vincent’s)

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 parotidglands 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 includesyphilis, 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 forCorynebacterium 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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10

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 likelyto yield the organism.



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11

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 comesfrom 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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12

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.

Vincent’s angina

Borrelia vincentii and Fusobacterium species areassociated 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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13

Arcanobacterium haemolyticum (previously

Corynebacterium haemolyticum

Fungal throat and pharyngeal infections

Fusobacterium necrophorum

Neisseria gonorrhoeae

Neisseria meningitides

Staphylococcus aureus



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14

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 asa 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

(“Friedländer’s 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. aeruginosaare 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, inwhich case the right middle zone is most frequently

affected. Other organisms may give rise to multifocal

abscess formation. caused by S. aureus and K.

pneumoni a, 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 isthe 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 theskin and subcutaneous tissues. Blood culture is the

investigation of choice. The most common causative

organisms are β-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:

• β-haemolytic streptococci

• S. aureus


• Anaerobic cocci

Bite wounds in human and animal can become

contaminated by oral flora. Organisms most commonly

isolated include:• Pasteurella multocida

• S. aureus

• α-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 encounteredinclude:



• Pseudomonads, especially Pseudomonas

aeruginosa

• Acinetobacter species

• Bacillus species



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• 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 arepredominantly 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



•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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23

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 intra-

abdominal abscesses and abscesses in the oral and

anal areas. Members of the "Streptococcusanginosus" 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 usuallymixtures 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


• Streptococcus pneumoniae


•

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 clinicallysignificant.

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 relatedfungi. Scedosporium apiospermum (Pseudallescheria

boydii ) enters the lungs and spreads haematogenously.

Breast abscess

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 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 oftenisolated 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 developingafter 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 skeletalmuscle in which solitary or multiple muscle abscesses

form. It most often occurs in tropical areas, and in HIV-

infected 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





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Dental abscess

Dental abscesses involve microorganisms colonising

the teeth that may become responsible for oral anddental 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:

• 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.



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Liver abscess

Liver abscesses can be amoebic or bacterial (so-

called pyogenic) in origin or, more rarely, a combinationof 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 frompyogenic liver abscesses. The most common include:




• Anaerobic streptococci

• "S. anginosus" group

•

Enterococci



• 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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microbiological specimens