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Transcript of microbiological specimens
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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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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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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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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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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 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
• 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
• 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:
• Staphylococcus aureus
• β-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 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
• 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 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
• 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
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
• Staphylococcus aureus
• Clostridium 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:
• 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.