Clinical microbiology

Surgical Microbiology

An extensive topic so an overview is given here. Organisms causing common surgical infections are
reasonable topics in the examination. However, microbiology is less rigorously tested than anatomy, for
example.

Common organisms

Staphylococcus aureus

 Facultative anaerobe
 Gram positive coccus
 Haemolysis on blood agar plates
 Catalase positive
 20% population are long term carriers
 Exo and entero toxin may result in toxic shock syndrome and gastroenteritis respectively
 Ideally treated with penicillin although many strains now resistant through beta Lactamase
production. In the UK less than 5% of isolates are sensitive to penicillin.
 Resistance to methicillin (and other antibiotics) is mediated by the mec operon , essentially
penicillin binding protein is altered and resistance to this class of antibiotics ensues
 Common cause of cutaneous infections and abscesses

Streptococcus pyogenes

 Gram positive, forms chain like colonies, Lancefield Group A Streptococcus

 Produces beta haemolysis on blood agar plates
 Rarely part of normal skin microflora
 Catalase negative
 Releases a number of proteins/ virulence factors into host including hyaluronidase, streptokinase
which allow rapid tissue destruction
 Releases superantigens such as pyogenic exotoxin A which results in scarlet fever
 Remains sensitive to penicillin, macrolides may be used as an alternative.

Escherichia coli

 Gram negative rod

 Facultative anaerobe, non sporing
 Wide range of subtypes and some are normal gut commensals
 Some subtypes such as 0157 may produce lethal toxins resulting in haemolytic-uraemic syndrome
 Enterotoxigenic E-Coli produces an enterotoxin (ST enterotoxin) that results in large volume
fluid secretion into the gut lumen (Via cGMP activation)
  Enteropathogenic E-Coli binds to intestinal cells and cause structural damage, this coupled with
a moderate (or in case of enteroinvasive E-Coli significant) invasive component produces enteritis
and large volume diarrhoea together with fever.
 They are resistant to many antibiotics used to treat gram positive infections and acquire
resistance rapidly and are recognised as producing beta lactamases

Campylobacter jejuni

 Curved, gram negative, non sporulating bacteria

 One of the commonest causes of diarrhoea worldwide
 Produces enteritis which is often diffuse and blood may be passed
 Remains a differential for right iliac fossa pain with diarrhoea
 Self limiting infection so antibiotics are not usually advised. However, the quinolones are often
rapidly effective.

Helicobacter pylori

 Gram negative, helix shaped rod, microaerophillic

 Produces hydrogenase that can derive energy from hydrogen released by intestinal bacteria
 Flagellated and mobile
 Those carrying the cag A gene may cause ulcers
 It secretes urease that breaks down gastric urea> Carbon dioxide and ammonia>
ammonium>bicarbonate (simplified!) The bicarbonate can neutralise the gastric acid.
 Usually colonises the gastric antrum and irritates resulting in increased gastrin release and higher
levels of gastric acid. These patients will develop duodenal ulcers. In those with more diffuse H-
Pylori infection gastric acid levels are lower and ulcers develop by local tissue damage from H-
Pylori- these patients get gastric ulcers.
 Diagnosis may be made by serology (approx. 75% sensitive). Biopsy urease test during endoscopy
probably the most sensitive.
 In patients who are colonised 10-20% risk of peptic ulcer, 1-2% risk gastric cancer, <1% risk MALT
lymphoma.

Acute tonsillitis

 Characterised by pharyngitis, fever, malaise and lymphadenopathy.

 Over half of all cases are bacterial with Streptococcus pyogenes the most common organism
 The tonsils are typically oedematous and yellow or white pustules may be present
 Infectious mononucleosis may mimic the condition.
 Treatment with penicillin type antibiotics is indicated for bacterial tonsillitis.
 Bacterial tonsillitis may result in local abscess formation (quinsy)

Acute streptococcal tonsillitis

Diarrhoea

World Health Organisation definitions

Diarrhoea: > 3 loose or watery stool per day
Acute diarrhoea < 14 days
Chronic diarrhoea > 14 days

Acute Diarrhoea
Gastroenteritis May be accompanied by abdominal pain or
nausea/vomiting
Diverticulitis Classically causes left lower quadrant pain, diarrhoea and
fever
Antibiotic therapy More common with broad spectrum antibiotics
Clostridium difficile is also seen with antibiotic use
Constipation causing A history of alternating diarrhoea and constipation may be
overflow given
May lead to faecal incontinence in the elderly

Chronic
Diarrhoea
Irritable Extremely common. The most consistent features are abdominal pain,
bowel bloating and change in bowel habit. Patients may be divided into those
syndrome with diarrhoea predominant IBS and those with constipation predominant
IBS.
Features such as lethargy, nausea, backache and bladder symptoms may
also be present
Ulcerative Bloody diarrhoea may be seen. Crampy abdominal pain and weight loss
colitis are also common. Faecal urgency and tenesmus may occur
Crohn's Crampy abdominal pains and diarrhoea. Bloody diarrhoea less common
disease than in ulcerative colitis. Other features include malabsorption, mouth
ulcers perianal disease and intestinal obstruction
Colorectal Symptoms depend on the site of the lesion but include diarrhoea, rectal
cancer bleeding, anaemia and constitutional symptoms e.g. Weight loss and
anorexia
Coeliac  In children may present with failure to thrive, diarrhoea and
disease abdominal distension
 In adults lethargy, anaemia, diarrhoea and weight loss are seen.
Other autoimmune conditions may coexist

Other conditions associated with diarrhoea include:

 Thyrotoxicosis
 Laxative abuse
 Appendicitis with pelvic abscess or pelvic appendix
 Radiation enteritis
Diagnosis
Stool culture
Abdominal and digital rectal examination
Consider colonoscopy (radiological studies unhelpful)
Thyroid function tests, serum calcium, anti endomysial antibodies, glucose

Antibiotics: mechanism of action

The lists below summarise the site of action of the commonly used antibiotics

Inhibit cell wall formation

 penicillins
 cephalosporins

Inhibit protein synthesis

 aminoglycosides (cause misreading of mRNA)

 chloramphenicol
 macrolides (e.g. erythromycin)
 tetracyclines
 fusidic acid

Inhibit DNA synthesis

 quinolones (e.g. ciprofloxacin)

 metronidazole
 sulphonamides
 trimethoprim

Inhibit RNA synthesis

 rifampicin

Gastro intestinal parasitic infections

Common infections

Enterobiasis  Due to organism Enterobius vermicularis

  Common cause of pruritus ani
 Diagnosis usually made by placing scotch tape at the anus,
this will trap eggs that can then be viewed microscopically
 Treatment is with mebendazole

Ancylostoma  Hookworms that anchor in proximal small bowel

duodenale  Most infections are asymptomatic although may cause iron
deficiency anaemia
 Larvae may be found in stools left at ambient temperature,
otherwise infection is difficult to diagnose
 Infection occurs as a result of cutaneous penetration,
migrates to lungs, coughed up and then swallowed
 Treatment is with mebendazole

Ascariasis  Due to infection with roundworm Ascaris lumbricoides

 Infections begin in gut following ingestion, then penetrate
duodenal wall to migrate to lungs, coughed up and
swallowed, cycle begins again
 Diagnosis is made by identification of worm or eggs within
faeces
 Treatment is with mebendazole

Strongyloidiasis  Due to infection with Strongyloides stercoralis

 Rare in west
 Organism is a nematode living in duodenum of host
 Initial infection is via skin penetration. They then migrate
to lungs and are coughed up and swallowed. Then mature
in small bowel are excreted and cycle begins again
 An auto infective cycle is also recognised where larvae will
penetrate colonic wall
 Individuals may be asymptomatic, although they may also
have respiratory disease and skin lesions
 Diagnosis is usually made by stool microscopy
 In the UK mebendazole is used for treatment

Cryptosporidium  Protozoal infection

 Organisms produce cysts which are excreted and thereby
cause new infections
 Symptoms consist of diarrhoea and cramping abdominal
pains. Symptoms are worse in immunosuppressed people
 Cysts may be identified in stools
 Treatment is with metronidazole

Giardiasis  Diarrhoeal infection caused by Giardia

lamblia (protozoan)
 Infections occur as a result of ingestion of cysts
 Symptoms are usually gastrointestinal with abdominal
pain, bloating and passage of soft or loose stools
 Diagnosis is by serology or stool microscopy
 First line treatment is with metronidazole
Meleney's Gangrene and Necrotising Fasciitis

Necrotising fasciitis

 Advancing soft tissue infection associated with fascial necrosis

 Uncommon, but can be fatal
 In many cases there is underlying background immunosuppression e.g. Diabetes
 Caused by polymicrobial flora (aerobic and anaerobic) and MRSA is seen increasingly in cases of
necrotising fasciitis
 Streptococcus is the commonest organism in isolated pathogen infection (15%)

Meleneys gangrene

 Meleneys is a similar principle but the infection is more superficially sited than necrotising fasciitis
and often confined to the trunk

Fournier gangrene

 Necrotising fasciitis affecting the perineum

 Polymicrobial with E-coli and Bacteroides acting in synergy

Clinical features
Fever
Pain
Cellulitis
Oedema
Induration
Numbness

Late findings

Purple/black skin discolouration

Blistering
Haemorrhagic bullae
Crepitus
Dirty Dishwater fluid discharge
Septic shock

A typical case of gas gangrene presenting late demonstrating some of the features described above
 Image sourced from Wikipedia
Diagnosis is mainly clinical

Management

 Radical surgical debridement forms the cornerstone of management

 Sterile dressing is used to dress the wound
 Reconstructive surgery is considered once the infection is completely treated

Osteomyelitis

Infection of the bone

Causes

 S aureus and occasionally Enterobacter or Streptococcus species

 In sickle cell: Salmonella species

Clinical features

 Erythema
 Pain
 Fever
Investigation

 X-ray: lytic centre with a ring of sclerosis

 Bone biopsy and culture

Treatment

 Prolonged antibiotics
 Sequestra may need surgical removal

Breast abscess

 In lactational women Staphylococcus aureus is the most common cause

 Typical presentation is with a tender, fluctuant mass in a lactating women
 Diagnosis and treatment is performed using USS and associated drainage of the abscess cavity.
Antibiotics should also be administered
 Where there is necrotic skin overlying the abscess, the patient should undergo surgery

Cholangitis

- Combination of bacterial infection and biliary obstruction

 Most common organisms are: (most frequent at top of list)

Escherichia coli
Klebsiella species
Enterococcus species
Streptococcus species

Clinical features
Charcot's triad:
Fever (90% cases)
Right upper quadrant pain
Jaundice

Reynolds pentad: Above plus confusion and hypotension

Investigations
USS 1st line
CT scan
ERCP: may be 1st line if high clinical suspicion and suitable for treatment
Treatment
ERCP -usually after 72 hours of antibiotics
Percutaneous transhepatic cholangiogram and biliary drain
Clostridium difficile

Clostridium difficile is a Gram positive rod often encountered in hospital practice. In the UK it can be
found in 3% of normal adults and up to 66% of babies. It produces an exotoxin which causes intestinal
damage leading to a syndrome called pseudomembranous colitis.

Risk factors

 Broad spectrum antibiotics

 Use of proton pump inhibitors
 Contacted with persons infected with c.difficile

Features

 Diarrhoea
 Abdominal pain
 A raised white blood cell count is characteristic
 If severe, toxic megacolon may develop

Diagnosis is made by detecting Clostridium difficile toxin (CDT) in the stool

Management

 Consider stopping proton pump inhibitor treatment

 First-line therapy is now oral vancomycin 125mg orally 4 times daily for 10 days
 Patients who do not respond to vancomycin may respond to oral fidaxomicin
 Patients with severe and unremitting colitis should be considered for combination therapy of oral
vancomycin and metronidazole. Some cases may require emergency colectomy

Further reading
NICE guidance NG199 published 2021.
Fasciola hepatica

 Also known as the common liver fluke (parasitic trematode)

 Infects humans as part of a plant/ food trematode infection
 Found throughout the world
 There are two illness phases; during the acute phase, the immature worms begin penetrating the
gut, causing symptoms of fever, nausea, swollen liver, skin rashes, and extreme abdominal pain.
 The chronic phase occurs when the worms mature in the bile duct, and can cause symptoms of
intermittent pain, jaundice, and anemia.
 Diagnosis is either by stool sample or serology
 Treatment is with triclabendazole. Some patients may need ERCP

Hepatitis B

Hepatitis B is a double-stranded DNA virus and is spread through exposure to infected blood or body
fluids, including vertical transmission from mother to child. The incubation period is 6-20 weeks.

Immunisation against hepatitis B

 Contains HBsAg absorbed onto aluminium hydroxide adjuvant and is prepared from yeast cells
using recombinant DNA technology
 Most schedules give 3 doses of the vaccine with a recommendation for a one-off booster 5 years
following the initial primary vaccination
 At risk groups who should be vaccinated include: healthcare workers, intravenous drug users, sex
workers, close family contacts of an individual with hepatitis B, individuals receiving blood
transfusions regularly, chronic kidney disease patients who may soon require renal replacement
therapy, prisoners, chronic liver disease patients
 Around 10-15% of adults fail to respond or respond poorly to 3 doses of the vaccine. Risk factors
include age over 40 years, obesity, smoking, alcohol excess and immunosuppression
 Testing for anti-HBs is only recommended for those at risk of occupational exposure (i.e.
Healthcare workers) and patients with chronic kidney disease. In these patients anti-HBs levels
should be checked 1-4 months after primary immunisation
 The table below shows how to interpret anti-HBs levels:

Anti-HBs Response
level
(mIU/ml)
> 100 Indicates adequate response, no further testing required. Should still
receive booster at 5 years
10 - 100 Suboptimal response - one additional vaccine dose should be given. If
immunocompetent no further testing is required
< 10 Non-responder. Test for current or past infection. Give further vaccine
course (i.e. 3 doses again) with testing following. If still fails to respond
then HBIG would be required for protection if exposed to the virus

Complications of hepatitis B infection

 Chronic hepatitis (5-10%)

 Fulminant liver failure (1%)
 Hepatocellular carcinoma
 Glomerulonephritis
 Polyarteritis nodosa
 Cryoglobulinaemia
Management of hepatitis B

 Pegylated interferon-alpha used to be the only treatment available. It reduces viral replication in
up to 30% of chronic carriers. A better response is predicted by being female, < 50 years old, low
HBV DNA levels, non-Asian, HIV negative, high degree of inflammation on liver biopsy
 However, due to the side-effects of pegylated interferon it is now used less commonly in clinical
practice. Oral antiviral medication is increasingly used with an aim to suppress viral replication
(not in dissimilar way to treating HIV patients)
 Examples include lamivudine, tenofovir and entecavir

Hepatitis B

Hepatitis B is a double-stranded DNA virus and is spread through exposure to infected blood or body
fluids, including vertical transmission from mother to child. The incubation period is 6-20 weeks.

Immunisation against hepatitis B

 Contains HBsAg absorbed onto aluminium hydroxide adjuvant and is prepared from yeast cells
using recombinant DNA technology
 Most schedules give 3 doses of the vaccine with a recommendation for a one-off booster 5 years
following the initial primary vaccination
 At risk groups who should be vaccinated include: healthcare workers, intravenous drug users, sex
workers, close family contacts of an individual with hepatitis B, individuals receiving blood
transfusions regularly, chronic kidney disease patients who may soon require renal replacement
therapy, prisoners, chronic liver disease patients
 Around 10-15% of adults fail to respond or respond poorly to 3 doses of the vaccine. Risk factors
include age over 40 years, obesity, smoking, alcohol excess and immunosuppression
 Testing for anti-HBs is only recommended for those at risk of occupational exposure (i.e.
Healthcare workers) and patients with chronic kidney disease. In these patients anti-HBs levels
should be checked 1-4 months after primary immunisation
 The table below shows how to interpret anti-HBs levels:

Anti-HBs Response
level
(mIU/ml)
> 100 Indicates adequate response, no further testing required. Should still
receive booster at 5 years
10 - 100 Suboptimal response - one additional vaccine dose should be given. If
immunocompetent no further testing is required
< 10 Non-responder. Test for current or past infection. Give further vaccine
course (i.e. 3 doses again) with testing following. If still fails to respond
then HBIG would be required for protection if exposed to the virus

Complications of hepatitis B infection

  Chronic hepatitis (5-10%)
 Fulminant liver failure (1%)
 Hepatocellular carcinoma
 Glomerulonephritis
 Polyarteritis nodosa
 Cryoglobulinaemia

Management of hepatitis B

 Pegylated interferon-alpha used to be the only treatment available. It reduces viral replication in
up to 30% of chronic carriers. A better response is predicted by being female, < 50 years old, low
HBV DNA levels, non-Asian, HIV negative, high degree of inflammation on liver biopsy
 However, due to the side-effects of pegylated interferon it is now used less commonly in clinical
practice. Oral antiviral medication is increasingly used with an aim to suppress viral replication
(not in dissimilar way to treating HIV patients)
 Examples include lamivudine, tenofovir and entecavir

HIV testing

HIV seroconversion is symptomatic in 60-80% of patients and typically presents as a glandular fever type
illness. Increased symptomatic severity is associated with poorer long term prognosis. It typically occurs 3-
12 weeks after infection

Features

 sore throat
 lymphadenopathy
 malaise, myalgia, arthralgia
 diarrhoea
 maculopapular rash
 mouth ulcers
 rarely meningoencephalitis

Diagnosis

 antibodies to HIV may not be present

 HIV PCR and p24 antigen tests can confirm diagnosis

HIV antibody test

 most common and accurate test

  usually consists of both a screening ELISA (Enzyme Linked Immuno-Sorbent Assay) test and a
confirmatory Western Blot Assay
 most people develop antibodies to HIV at 4-6 weeks but 99% do by 3 months

p24 antigen test

 usually positive from about 1 week to 3 - 4 weeks after infection with HIV
 sometimes used as an additional screening test in blood banks

Malignant otitis externa

- Uncommon type of otitis externa that is found in immunocompromised individuals (90% cases found in
diabetics)

 Infective organism is usually Pseudomonas aeruginosa

 Infection commences in the soft tissues of the external auditory meatus, then progresses to
involve the soft tissues and into the bony ear canal
 Progresses to temporal bone osteomyelitis

Key features in history

Diabetes (90%) or immunosuppression (illness or treatment related)
Severe, unrelenting, deep-seated otalgia
Temporal headaches
Purulent otorrhea
Possibly dysphagia, hoarseness, and/or facial nerve dysfunction

Treatment
Anti pseudomonal antimicrobial agents
Topical agents
Hyperbaric oxygen is sometimes used in refractory cases
Mastitis

Mastitis refers to infection within the breast, the commonest variant, lactational mastitis is related to
breast feeding and occurs as a result of inoculation of the breast tissue (which may have breaks in
epithelial integrity) with staphylococcus aureus that is carried in the infants oropharynx. The result is a
tender erythematous breast. Fever is common. Treatment is usually with encouraging breast drainage (e.g.
breast pumps) and antibiotics. Imaging with USS will demonstrate any underlying abscess. The preferred
treatment for this complication is percutaneous aspiration where this is possible. Where the overlying
epithelium is non viable, debridement may be needed, there is a risk that this may be complicated by the
development of a subsequent mammary duct fistula.
MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) was one of the first organisms which highlighted the
dangers of hospital-acquired infections.

Who should be screened for MRSA?

 all patients awaiting elective admissions (exceptions include day patients having terminations of
pregnancy and ophthalmic surgery. Patients admitted to mental health trusts are also excluded)
 in the UK all emergency admissions are currently screened

How should a patient be screened for MRSA?

 nasal swab and skin lesions or wounds

 the swab should be wiped around the inside rim of a patient's nose for 5 seconds
 the microbiology form must be labelled 'MRSA screen'

Suppression of MRSA from a carrier once identified

 nose: mupirocin 2% in white soft paraffin, tds for 5 days

 skin: chlorhexidine gluconate, od for 5 days. Apply all over but particularly to the axilla, groin and
perineum

The following antibiotics are commonly used in the treatment of MRSA infections:

 vancomycin
 teicoplanin

Some strains may be sensitive to the antibiotics listed below but they should not generally be used alone
because resistance may develop:

 rifampicin
 macrolides
 tetracyclines
 aminoglycosides
 clindamycin
Relatively new antibiotics such as linezolid, quinupristin/dalfopristin combinations and tigecycline have
activity against MRSA but should be reserved for resistant cases
Salmonella

The Salmonella group contains many members, most of which cause diarrhoeal diseases. They are
facultative anaerobes, Gram negative rods which are not normally present as commensals in the gut.

Typhoid and paratyphoid are caused by Salmonella typhi and Salmonella paratyphi (types A, B & C)
respectively. They are often termed enteric fevers, producing systemic symptoms such as headache, fever,
arthralgia

Features

 initially systemic upset as above

 relative bradycardia
 abdominal pain, distension
 constipation: although Salmonella is a recognised cause of diarrhoea, constipation is more
common in typhoid
 rose spots: present on the trunk in 40% of patients, and are more common in paratyphoid

Possible complications include

 osteomyelitis (especially in sickle cell disease where Salmonella is one of the most common
pathogens)
 GI bleed/perforation
 meningitis
 cholecystitis
 chronic carriage (1%, more likely if adult females)

Schistosomiasis

Schistosomiasis, or bilharzia, is a parasitic flatworm infection. The following types of schistosomiasis are
recognised:

 Schistosoma mansoni and Schistosoma intercalatum: intestinal schistosomiasis

 Schistosoma haematobium: urinary schistosomiasis

Schistosoma haematobium
This typically presents as a 'swimmer's itch' in patients who have recently returned from Africa.
Schistosoma haematobium is a risk factor for squamous cell bladder cancer
Features

 Frequency
 Haematuria
 Bladder calcification

Management

 Single oral dose of praziquantel

Septic arthritis

Overview

 Most common organism overall is Staphylococcus aureus

 In young adults who are sexually active Neisseria gonorrhoeae should also be considered

Management

 Synovial fluid should be obtained before starting treatment

 Intravenous antibiotics which cover Gram-positive cocci are indicated. The BNF currently
recommends flucloxacillin or clindamycin if penicillin allergic
 Antibiotic treatment is normally be given for several weeks (BNF states 6-12 weeks)
 Needle aspiration should be used to decompress the joint
 Arthroscopic lavage may be required

Streptococci

Streptococci may be divided into alpha and beta haemolytic types

Alpha haemolytic streptococci

The most important alpha haemolytic streptococcus is Streptococcus pneumoniae (pneumococcus).

Pneumococcus is a common cause of pneumonia, meningitis and otitis media. Another clinical example is
Streptococcus viridans

Beta haemolytic streptococci

These can be subdivided into group A and B

Group A
  most important organism is Streptococcus pyogenes
 responsible for erysipelas, impetigo, cellulitis, type 2 necrotizing fasciitis and pharyngitis/tonsillitis
 immunological reactions can cause rheumatic fever or post-streptococcal glomerulonephritis
 erythrogenic toxins cause scarlet fever

Group B

 Streptococcus agalactiae may lead to neonatal meningitis and septicaemia

Syphilis

 Venereal syphilis is a cause by the spirochete Treponema Pallidum

 Most cases are transmitted sexually, congenital infection is also recognized
 The typical lesion of primary syphilis is the chancre which appears after 10-90 days. It is an
indurated papule that breaks down to form an ulcer. It is typically hard and painless. The
appearances of a hard ulcer with enlarged regional lymph nodes can mimic carcinoma.
 The histological appearances on biopsy are non specific and include dense inflammatory
infiltrates.
 Diagnosis can be made demonstrating spirochetes from the chancre by dark ground illumination
microscopy. Serological testing for anti treponemal antibodies are also used.
 Secondary syphilis usually develops around 6 weeks following exposure to the disease. It often
comprises a widespread roseolar eruption.
 Treatment can precipitate a Jarisch- Herxheimer reaction with fever and malaise occurring after
treatment has been started and is due to the release of antigens as the organisms die.
 Individuals who are not treated can eventually develop tertiary syphilis, this is characterized by the
development of gummas or diffuse inflammatory lesions. Syphilic lesions characteristically affect
the proximal aspect of the aorta and can result in atypical aneurysms.