Microbiology Conditions Flashcards
What are the 5 viruses that cause hepatitis?
Hepatitis A (HAV) - RNA
Hepatitis B (HBV) - DNA
Hepatitis C (HCV) - RNA
Hepatitis D (HDV) - RNA
Hepatitis E (HEV) - RNA
How are hepatitis A and E transmitted?
Via Faecal-oral transmission
How are hepatitis B,C and D transmitted?
Blood to blood transmission
What is acute hepatitis?
What Hepatitis viruses cause acute hepatitis?
A sudden illnesss with a mild to severe course followed by complete resolution
All hepatitis Viruses
What is chronic hepatitis
What Hepatitis viruses cause acute hepatitis?
A prolonged course of active disease or silent asymptomatic infection.
HBV, HCV, HDV
Outline Acute hepatitis
Variable incubation period
-Systemic symptoms first:
-**Fatigue, low-grade fever, muscle/joint aches, cough, runny nose, and
pharyngitis. **
Jaundice (1-2 weeks after infection)
LFTs (rise through hepatocyte death from virus)
**ALT and AST to elevate to very high **
levels, while GGT, ALP, and bilirubin are only mildly elevated
Outline Chronic Hepatitis
More difficult to Diagnose
Patient is often asymptomatic
Clinical manifestations arethe same regardlesss of virus causing hepatitis.
Describe the transmission of hepatitis A
Ingesting contaminated drinking water or food
Close person to person contact
Often infects young children
What is the pathogenesis of HAV?
-Initial immune response consists IgM antibody; important in the laboratory
diagnosis of hepatitis A.
-1 to 3 weeks later IgG antibody is produced→ lifelong protection
What are the clinical findings of HAV?
Incubation of 3-4 weeks
Fever, anorexia, nausea, vomiting and jaundice
Dark urine, pale faeces, elevated ALT and AST.
Cases often resolve spontaneously in 2-4 weeks.
What Ix are required for HAV diagnosis?
LFTs: High AST and ALT.
Bilirubin and ALP usually only mild.
Serology - Detection of anti-HAV IgM confirms the diagnosis and remails for 3-6 months.
What is the treatment for HAV infection?
Acute Infection:
Symptomatic treatment (avoid paracetamol)
Fulminant Hepatitis:
Supportive therapy - consider liver transplanation
Pre-exposure prophylaxis - Vaccination
What is Hepatitis B virus?
DNA virus that lives in all human body fluids in an infected individual.
Semen, urine, saliva, blood, breast milk
What are HBV 3 main antigens?
HBsAg - surface antigen - required for lab diagnosis and immunity
HBcAg - Core antigen
HbeAg - e Antigen - indicator of transmissibiility
How can HBV be transmitted and give examples?
Blood to blood transmission - parenteral transmission.
Needle sharing, accidental medical exposures, sexual contact Blood transfusions
Where is HBV prevalent
ASIA
How does HBV present?
3 clinical states:
Acute hepatitis
Fulminant hepatitis - severe acute hepatitis with rapid destruction of the liver
Chronic Hepatitis
How do you diagnose HBV infection?
HBsAg antigen means there is LIVE virus and infection.
Anti - HBsAg antibodies - patient is protected and immune
HBcAg - antibodies are not protective but can be used to understand length of infection.
What are the complications of HBV infection?
HDV co-infection
Hepatocellular carcinoma
End-stage liver disease/cirrhosis
What is Hepatitis C virus
RNA virus
Incubation period 6-12 weeks
What is the clinical signs of HCV infection?
Acute infection is usually asymptomatic - some patients will present with classic acute hepatitis symptoms
Up to 85% of patients of HCV will develop chronic hepatitis
HCV strongly predisposes HCC.
Outline HCV transmission
Blood-to-blood contact via blood transfusions, injecting drug use, nosocomial (needle sticks, dialysis, inadequate sterilisation of colonoscopes
What is the most common indication for liver transplantation?
Liver cirrhosis resulting from chronic HCV infection
What comorbidities arise with HCV infection?
HCV infection can lead to significant autoimmune reactions:
vasculitis, arthralgias, purpura, membranoproliferative glomerulonephritis
How is HCV diagnosed?
Testing for antiHCV antibodies
(detectable within 6-8 weeks after exposure and remain positive thereafter)
Measure HCV viral RNA
An ELISA antibody test for detectable viral RNA is positive for at least 6 months.
What is the treatment for HCV infection
Acute HCV infection - pegINF alpha decreases the number of patients who become chronic carriers.
Patients with chronic HCV - reduce or eliminate alcohol consumption to reduce HCC or cirrhosis risk.
Chronic HCV treatment is direct-acting antivirals (DAAs)
No vaccine currently exists.
What is Hepatitis D virus?
An RNA virus
It is a defetive virus an it cannot replicate itself due to not having the genes to envelop protein.
HDV can only be replicated in cells co-infected with HBV.
HDV uses HBsAg to evelope its protein.
Outline the transmission of HDV?
Transmitted in the same way as HBV
Coinfection of HBV and HDV is more severe than those infected with HBV alone.
What is the presentation of a HDV infection?
Can range from asymptomatic to fulminant liver failure
Simultaneous co-infection with HBV/HDV - causes acute hepatitis.
HDV superinfection of a carrier of HBV can cause liver flare.
What diagnostic tests are required for HDV infection?
Detecting delta antigen or IgM antibody against delta antigen in the patient’s serum.
What is the treatment for HDV infection?
PegINF alpha can mitigate chronic effects but does not eradicate the carrier state.
no vaccine against HDV but a person immunized against HBV will not get HDV infection.
What is Hepatitis E infection?
RNA virus similar to HAV.
How is HEV transmitted?
Via the faecal oral route
Waterborne transmission is most common.
What is the clinical presentation of HEV infection?
Clinically similar to HAV infection.
Chronic infection can be caused in immunocompromised individuals.
How is HEV diagnosed?
Detecting IgM antibodies to HEV.
What is the treatment to HEV infection?
No antiviral drug available for acute infection in immunocompetent patients.
Treatment is supportive.
How can diarrhoea present?
It can be acute (lasting 2 weeks) or chronic (persisting for > 4 weeks)
What are the 2 classifications of acute diarrhoea?
Noninflammatory (watery, non-blood)
Inflammatory (bloody - dysentery)
What most commonly causes acute diarrhoea?
Infections in the small intestine (where the majority of the fluid is normally absorbed)
What is the pathophysiology of Diarrhoea?
Pathogens secrete exotoxins directly into food or into the body (enterotoxins) to disrupt the intestinal homeostasis and cause mucosal damage.
What pathogens can produce preformed exotoxins?
Staphylococcus aureus
Bacillus cereus
Clostridium perfringens
What pathogens cause non-inflammatory acute diarrhoea by enterotoxin production?
Enterotoxigenic Escherichia coli (ETEC)
Vibrio cholerae
What pathogens cause acute inflammatory diarrhoea?
Salmonella, shigella, campylocbacter
Shiga-toxin producing E.coli (STEC)
What causes pseudomembranous colitis and what can predispose this condition?
Clostridium difficile
Predisposed by antibiotic use
What are the risk factors for developing diarrhoea?
PPIs (reducing gastric acid levels)
Travel to developing countries
Antibiotic treatment
Immunosuppressed patients.
What is the presentation of diarhoea?
Symptoms tend to begin 6 hours after ingestion of suspected contaminated food.
diarrhoea
urgency
abdominal bloating
cramping
What are the signs of acute inflammatory diarrhoea
Blood and pus in the stool
fever
What other systemic effects may be present in someone with diarrhoea
dehydration
tachycardia
orthostatic hypotension
What kind of diarrhoea is caused by Staphylococcus aureas.
What is the presentation and Tx
Acute noninflammatory
Vomiting, epigastric pain
diarrhoea
Tx - supportive care fluids and electrolytes
Within 6 hours of eating uncooked meat or diary.
What kind of diarrhoea is caused by ETEC.
What is the presentation and Tx?
Acute noninflammatory
Watery diarrhoea
Tx is ciprofloxacin
(this is traveller’s diarrhoea)
What kind of diarrhoea is caused by Listeria monocytogenes?
What is the presentation and Tx?
Febrile diarrhoea
Tx is supportive
caused by eating cheese, raw veggies and cold food.
What kind of diarrhoea is caused by vibrio cholerae?
What is the presentation and Tx?
Acute - noninflammatory
Severe watery diarrhoea (loss of volume)
Tx is supportive care and rehydration therapy.
Rice water stool
What kind of diarrhoea is caused by norovirus?
What is the presentation and Tx?
Acute noninflammatory
Vomiting, headache and diarrhoea
Tx is supportive care.
Typically infected on cruise ships and nursing homes.
What kind of diarrhoea is caused by STEC?
What is the Px, Dx and Tx?
Px: acute inflammatory diarrheoa
bloody and abdominal pain
Dx: Stool cultures grow e.coli
Tx. none - do not give children antibiotics as this can cause HUS
What kind of diarrhoea is caused by shigella?
What is the Px, Dx and Tx?
Px: inflammatory diarrhoea with blood and pus
Dx: stool culture
Tx: Ciprofloxacin
What kind of diarrhoea is caused by Salmonella?
What is the Px, Dx and Tx?
Inflammatory diarrhoea with blood and fever
Dx: Stool culture
Tx: ciprofloxacin
Caused by undercooked eggs, raw veggies, undercooked poultry
What kind of diarrhoea is caused by campylobacter jejuni?
What is the Px, Dx and Tx?
Inflammatory diarrhoea
Fever
Dx: Stool culutre
Tx: Azithromycin or ciprofloxacin
What kind of diarrhoea is caused by C.difficle?
What is the Px, Dx and Tx?
Inflammatory bloody diarrhoea,
Fever
Dx: Stool culture, colonoscopy - pseudomembranous colitis
Tx: Metronidazole
Associated with antibiotic use especially in hospitals
What is cellulitis?
An infection caused by bacteria getting into the deeper layers of skin such as the dermis or subcutaneous fat.
It is caused by a break in the normal skin integrity.
What are the common sites where cellulitis occurs?
Legs
face
arms
What are the risk factors for developing cellulitis?
Skin wounds
diabetes
bites
elderly
swollen legs
immunosuppression
What causative organisms can cause cellulitis
Beta-haemolytic streptococci
(S.pyogenes, sS. agalactiae)
S.aureus.
What is the presentation of cellulitis?
Symptoms spread quickly:
Erythema - tracking occurs along lymphatics
Pain, swelling and warm to touch.
Associated wounds - ulcers, bite marks, injection site
What is the diagnosis of cellulitis?
Usually clinical diagnosis
What is the treatment of cellulitis?
Elevate and mobilise limb
wash out wonds
empiric treatment with IV flucloxacillin or clindamycin.
Vancomycin for MRSA cellulitis.
What is necrotising fasciitis?
A necrotising infection of the deep structures of the skin including the underlying fascia
What are the causes of necrotising fasciitis?
break in the skin caused by trauma or surgery
passage of organisms to deeper structures
infection of the fascial layer resulting in thrombosis of vascular supply
manifests as necrosis
can spread to superficial layers of the skin
What pathogens cause necrotising fasciitis?
Type I: aerobic and anaerobic organisms
Type II: due to streptococcus pyogenes, clostridium perfringens
What is the clinical presentation of necrotising fasciitis?
-Erythema, warmth, and tenderness; pain out of proportion of the
examination findings.
-Skin changes often spread and progress very quickly
-Followed by evidence of skin hypoperfusion, blue-gray coloring, bullae, loss
of sensation
-Crepitus may be felt.
-Signs and symptoms of systemic infection and/or sepsis
-Fournier’s gangrene is a form of necrotizing fasciitis that affects the male
genitals and is usually polymicrobial.
What is the diagnosis of necrotising fasciitis?
Surgery - clinical diagnosis confirmed by surgical exploration
Tissues appear swollen, easy separation of tissue planes by blunt dissection
Microbiology - surgical samples sent for gram stain and culture.
What is the treatment for necrotising fasciitis?
Emergency surgical exploration and debridement
Empirical therapy - broad antibiotics (piperacillin), clindamycin
S.pyogenes - penicillin and clindamycin
What is appedicitis?
Inflammation of the appendix caused by an obstruction which cna lead to bacterial overgrowth and then infection and inflammation!
What is a complication of appedicitis?
If the appendix becomes necrosed it can perforate and lead to diffuse peritonitis
What pathogens are responsible for causing appedicitis?
Colonic flora:
E. coli,
peptostreptococcus,
bacteriodes fragillis,
pseudomonas
What is the presentation of appendicitis?
Abdominal pain - periumbilical pain migrating to the right lower quadrant.
Anorexia, nausea, vomiting
Potentially low grade fever and leukocytosis
How is appendicitis diagnosed?
Clinical presentation of appendicitis
Confirmed by CT or ultrasound
What is the treatment of appendicitis?
Surgical (usually) - an appendectomy
Some cases can be managed by antibiotics (metronidazole, cefoxitin) but there is a risk of recurrence
What is diverticulitis?
Inflammation of the diverticula
(diverticula is a sac like protrusion of the colonic wall usually in the sigmoid colon)
What is a complication of diverticulitis?
Perforation of the diverticulum leading to abscess formation and peritonitis
What can cause diverticula?
Low fibre diet
constipation
obesity
What is acute diverticulitis and who typically is at risk?
Inflammation of the diverticula
Common in the elderly and those with extensive disease
What is complicated diverticulitis?
Acute diverticulitis with one of the following complications:
Abscess
colovesical or colovaginal fistula
perforation
obstruction
What pathogens are typically involved in diverticulitis?
Bowel flora:
B.fragillis
E.coli
What is the presentation of diverticulitis?
Dull aching and pain in the left lower quadrant of the abdomen
Diarrhoea or constipation may be present
Nausea and vomiting.
if perforated then diffuse abdominal pain
How is diverticulitis diagnosed?
Clinical Hx
Confirmed by abdominal CT scan or ultrasound
WCC (White cell count) is elevated
What is the treatment for acute and complicated diverticulitis?
Acute: Co-amoxiclav, ciprofloxacin + Metronidazole
Complicated: Piperacillin-tazobactam
What is osteomyelitis?
Infection of the bone and or bone marrow.
It can occur as a result of haematogenous seeding, contiguous spread from nearby tissue or traumatic or surgical introduction of an organism.
Who can get osteomyelitis?
More common in children than adults but can be seen in both.
Can be acute or chronic (elderly)
What pathogens can cause osteomyelitis and in what context?
Most common - S.aureus
IVD users - Pseudomonas, E.coli
Sickle cell Patients - salmonella
Hip or knee prosthesis patients - S. epidermidis
What is the presentation of osteomyelitis?
Pain around the affected region.
swelling, tenderness, warmth erythema
Systemic signs
Chronic osteomyelitis can have sinus tracts or ulcers (diabetics)
What Ix are required for a diagnosis of osteomyelitis?
Suspected clinically
Dx - confirmed by radiological and microbiological findings
Ix:
Blood tests - raised WCC, raised inflammatory markers (ESR, CRP)
CT/MRI - sensitive but expensive
Bone/percutaneous biopsy should be taken
What is the Tx for osteomyelitis?
Surgical debridement and antibiotic therapy combination.
Antibiotics: flucloxacillin, fusidic acid, or vancomycin.
What is septic arthritis?
Infectious arthritis is an infection of the joints
What is the pathophysiology of septic arthritis?
Organisms reach the joint via the bloodstream from a skin site.
Organisms can enter joints through penetrating trauma, medical procedures or contiguous osteomyelitis
What are the risk factors for septic arthritis?
elderly - >80yrs
Diabetes Mellitus
RA
Prosthetic joint
recent joint surgery
skin infections or ulcers.
Intra-articular corticosteroid infection.
Injection drug use
alcoholism
What pathogens are usually responsible for septic arthritis?
S.aureas
N.gonorrhoeae (in sexually active adults)
S.epidermidis in prosthesis
IVD users - P.aeruginosa
What is the Px of septic arthritis?
Acute onset inflamed joint - usually hip or knee
Fever is often present
Joint is red, warm swollen and painful
reluctant movement of joint
What Ix confirm a diagnosis of septic arthritis?
Raised WCC
Raised inflammatory markers (ESR, CRP)
Synovial fluid is cloudy and has at least 20,000 neutrophils/ul with a low glucose conc
ultrasound shows effusion
CT/MRI - sensitive but expensive
What is the treatment of septic arthritis?
Drainage of the joint urgently
remove prosthetics
Antibiotics - flucloxacillin, vancomycin
Vancomycin - S.aureus
Ceftriaxone - N.gonorrhoeae
What is chlamydia?
The most common bacterial STI
What pathogen causes chlamydia?
Chlamydia Trachomatis
What is the presentation of chlamydia?
Majority are Asymptomatic - 70% of women and 50% of men
Men - urethritis, testicular pain
Women - Vaginal discharge, post coital bleeding, intermenstrual bleeding, pelvic pain
What can be some complications of chlamydia?
Pelvic inflammatory disease
infertility
reactive arthritis
epididymo-orchitis
What is the Dx of chlamydia?
NAAT (nucleic acid amplification tests) are the most sensitive and specific test for C.trachomatis.
Vaginal swabs, urethral swabs, first catch urine sample.
What is the Tx for Chlamydia?
Avoid intercourse until Tx is finished
screen for other STIs
Antibiotics: doxycycline, Azithromycin
Contact trace
What is gonorrhoea?
Second commonest STI in the UK.
Many women are asymptomatic and act as a reservoir of infection.
What pathogen causes gonorrhoea?
Neisseria gonorrhoea
What is the presentation of gonorrhoea?
Asymptomatic
Men - urethritis, puruplent discharge and dysuria
Women - pelvic pain, vaginal dischage, itch and dysuria
What Ix are required for a Dx of gonorrhoea?
NAATs
Microscopy shows gram-negative diplococci
What is the Treatment of gonorrhoea?
Antibiotics
First line is ceftriaxone and azithromycin
What is viral meningitis?
Most common form of meningitis which is often mild and usually is resolved with a full recovery
What pathogens cause viral meningitis?
enteroviruses
Herpes simplex virus
Mumps
What is the Px of viral meningitis?
Influenza like illness followed by meningism (stiff neck, headache and photophobia)
Fever and nonspecific signs
What is the Dx of viral meningitis?
Lumbar puncture
CSF microscopy, PCR
lymphocytosis with normal protein and glucose levels
viral culture
What is the Tx for viral meningitis?
No specific antiviral therapy
Supportive treatment:
antipyretics, hydration and analgesics
Acyclovir for HSV meningitis
What is bacterial meningitis
Upper respiratory tract infection that can be very severe and result in other defects such as neurological deficits.
What pathogens cause bacterial meningitis?
Neisseria meningitidis - most common in young adults (students)
Streptococcus pneumoniae - most common in the young (<2yrs) and elderly
How is N.meningitidis spread?
Through droplets or the bloodstream if it is meningococcal menignitis
What is the Px of bacterial meningitis?
Rapid onset headache, fever, meningism
Signs of cerebral dysfunction (confusion, delirium, falling consciousness)
seizures
focal neurological deficits - CN palsies
papilledema
Non-blanching rash with meningococcal septicemia if bacteria spills into the blood.
What is the Dx of bacterial meningitis?
Blood culture performed urgently
lumbar puncture unless contraindicated:
Low glucose, increased protein, cloudy fluid, and raised neutrophils.
Perform culture on CSF
Kernigs and budzinskis sign.
What is the treatment of bacterial meningitis?
Benzylpenicillin or cefotaxime
Vancomycin if suspected strep resistance
steroids
What is malaria?
A serious disease caused by the P.falcioarum bacteria spread via a bite of the female anopheles mosquito.
What pathogens cause malaria?
P.falciparum - 80% of cases and has the highest mortality
P.vivax and P.ovale - similar but much milder infections
P.malariae - rarely causes acute illnes
P.knowlesi
What is the pathogenesis of malaria?
Sporozoites travel through the blood stream and entre hepatocytes where they cause rupture and release merozoites into the blood stream to invade RBCs
What is the Px of malaria?
Fever and sweats - cyclical
Anaemia - erythrocyte haemolysis
hepatosplenomegaly
What are some complications of malaria infection?
Cerebral malaria
jaundice
kidney injury
acidosis
What is the Dx of malaria?
Thick and thin blood smears - stained with fields or geimsa stain.
Laboratory findings - haemolytic anaemia, thrombocytopenia, uraemia, hyperbilirubinaemia, abnormal LFTs and coagulopathy
What is the Tx for malaria?
Quinolone derivatives - chloroquine, quinine
Antifolates - pyrimethamine, sulfonomides
Ribosomal inhibitors - tetracycline, doxycycline, clindamycin
Supportive therapy
What is Tuberculosis?
A serious bacterial infection that mainly affects the lungs caused by Mycobacterium tuberculosis.
What pathogen causes TB?
Mycobacterial tuberculosis
What percentage of the worlds population is infected with TB?
1/3
How are TB infections usually spread?
By inhalation of droplet nuceli which are aerosolised by coughing or sneezing.
these dry in the air and can remain suspended for long periods of time.
What is the pathogenesis of primary TB?
Inhalation of M.TB resulting in mild acute inflammatory reaction in the lung parenchyma
Alveolar macrophages phagocytose the bacilli
Bacilli survive and multiply within the phagocytes and are carried to the hilar lymph nodes which then enlarge.
Local lesions (granulomas) form (epithelial cells and giant cells)
These eventually undergo caseous necrosis.
The immune system kills the bacteria and the lesion becomes fibrotic and calcified
(in some cases the granuloma is made but the TB is not killed and can lie dormant leading to latent TB)
In some patients the microorganism can spread locally and via the blood to other organs leading to widespread disease (miliary TB)
How does secondary TB occur?
Dormant M.TB may reactivate often in the lung apex or in other organs such as the kidney and bone.
A patient may also become re-infected after further exposure.
What is the presentation of TB?
Fever and night sweats.
Pleuritic chest pain - dyspnoea
Cough - can be with or without blood
fatigue, arthralgia and weight loss.
What Ix are required for a Dx of TB?
Sputum smear microscopy - Zn stain shows AFB (acid fast bacilli)
mycobacterial culture
Chest X-ray shows nodules
Elevated ESR and CRP
anaemia
TB skin test (mantoux test) shows latent TB.
What is the Tx for TB?
2 month initiation phase with 4 drugs:
Rifampicin, isoniazid, pyrazinamide, ethambutol
Followed by a 4 month continuation phase with 2 drugs:
rifampicin and isoniazid
What is pneumonia?
An infection of the lungs that primarily affects the alveoli
What are the different classifications of pneumonia?
Community-acquired pneumonia
Hospital-acquired pneumonia
Pneumonia in immunocompromised individuals
aspiration pneumonia
What are the risk factors for pneumonia?
extremes of age
smoking
COPD
diabetes
CVD
severe intercurrent illness
recent intubation
immunosuppression
What pathogens can cause TB?
Mycoplasma pneumoniae
H.influenza
Streptococcus pneumoniae.
Respiratory syncytial virus - common cause in young children.
What is the presentation of pneumonia?
Sudden onset chills, fever, cough, mucopurulent sputum, pleuritic chest pain, fatigue, anorexia and sweats
Tachypnoea, tachycardia, postural BP drop
Elderly may present with subtle signs - confusion, abdominal pain and nausea
What Ix are required to diagnose pneumonia?
Sputum specimens - culture and microscopy
blood cultures
Urine antigen detection for pneumococcal and legionella infection
PCR for viruses, mycoplasma, chlamydophila and coxiella infections.
Bronchoalveolar lavage (BAL)
Chest X-ray - lobar patchy or diffuse shadowing.
What is the Tx for pneumonia?
IV fluids
appropriate oxygen therapy.
Antibiotics:
Amoxicillin - for non-severe
Clarithromycin + co-amoxiclav - for severe illness
Once a microorganism is identified then:
S.pneumoniae - amoxicillin or benzylpenicillin
M.pneumoniae - clarithromycin
C.pneumoniae - clarithromycin
