Microbiology Flashcards
Define pathogen
Organism that causes or is able to cause disease
Define commensal pathogen
Pathogen which colonises host but causes no disease under normal circumstances
Define opportunist pathogen
Microbe only causes disease if host defences are immunocompromised
Define virulence/pathogenicity
Degree to which a given organism is pathogenic
What is coagulase
Enzyme in bacteria that causes blood to clot around plasma by turning fibrinogen into fibrin
How do staphylococcus appear on microscopy
Purple clusters of cocci
How do streptococcus appear on agar
Purple chains/pairs of cocci
Staph aureus virulence factors
1 - Pore forming toxins
2 - Proteases
3 - Toxic shock syndrome toxin
4 - Protein A (binds antibodies in wrong direction)
How are beta haemolytic bacteria further classified
Lancefield grouping using Latex agglutination test used to group by antigens. 20 groups characterised by letter
What group is S. pyogenes. What infection does this cause?
Group A
throat, skin, post partum
(tonsilitis, pharyngitis, impetigo, scarlet fever, glomerulonephritis)
What group is S.aglactiae. What infection does this cause
Group B
Neonatal infections
S.pyogenes virulence factors with IMPORTANT examples
Enzymes (streptokinase)
Toxins (Streptolysins O&S, Ertyhtogenic toxin)
Surface factor (M protein - encourages complement degradation)
S. pneumoniae infections
Pneumonia, meningitis, otitis media, sinusitis
S. pneumoniae virulence factors
Capsule
Inflammatory wall constituents (peptidoglycan, teichoic acid)
Cyotoxin (pneumolysin)
Viridians streptococci properties, examples, infection
A-haemolytic and optochin resistant.
S. sanguinis, S. oralis
Found in mouth, cause deep organ abscesses (IE, brain, liver)
Clostridia properties, examples, infections
Anaerobic gram positive bacilli
C.tetani (tetanus - muscle contractions/spasms)
C. botulinum (botulism - paralysis from head to body)
C. difficile (diarrhoea or pseudomembranous colitis)
Main infections caused by Escherichia coli (6)
1 - Wound infections
2 - UTI
3 - Gastroenteritis
4 - Travellers’ diarrhoea
5 - Bacteraemia
6 - Meningitis in infants
Main infections caused by H. influenzae (4)
Opportunistic
1 - meningitis
2 - Pneumonia
3 - sinusitis, otitis media
4 - bronchopneumonia
What are the growth requirements for H influenzae
Factor X (haem) and factor Y (NAD) presence
Legionella infections
Man made aquatic environments
E.g. air conditioning, shower heads, humidifiers
Causes legionairres disease (legionaires pneumonia)
Neisseria properties
Non-flagellated diplococci
Fastidious requirements
Main ones are N meningitidis and N gonorrhoeae
What are the 7 sterile sites of the body?
Blood
CSF
Pleural fluid
Peritoneal cavity
Joints
Urinary tract
Lower respiratory tract
S. enterica infections
3 types of Salmonellosis
(Gastroenteritis, Enteric fever and Bacteraemia)
How does staph aureus appear on blood agar?
Golden/creamy yellow
How does staph epidermidis appear on blood agar?
Colourless/white
What are used in a gram stain
“Come In And Stain”
Crystal violet - purple dye that stains all bacteria
Iodine - Fixes crystal violet to cell wall
Acetone or Alcohol - Decolourising agent, removes it from some bacteria
Safranin - Counterstain that stains the decolourised bacteria a contrasting pink.
Why do gram stain results show as they do?
Gram positive - Have a thick peptidoglycan cell wall that retains crystal violet, appearing purple
Gram negative - Thinner peptidoglycan layer with outer membrane that is dissolved by the decolourising agent, making them colourless. This allows the Safranin to take effect, appearing pink
What is chocolate agar used for?
to detect bacteria with fastidious growth requirements (e.g. H. influenza, Bortadella pertussis, Legionella, Campylobacter jejuni, H pylori)
What is maconkey agar used for?
To differentiate lactose fermenting (pink) from non lactose fermenting (yellow/colourless)
Fermenting - E coli
Non lactose fermenting - Shigella, salmonella
How do E coli, shigella and salmonella appear on CLED agar?
E coli - yellow
Salmonella and shigella - Blue
What are the notable gram negative cocci
Neisseria e.g. N meningitidis
Moraxella
The rest are bacilli!
What are the notable gram positive bacilli
Clostridium e.g. C diff
Listeria
Cornybacterium
The rest are cocci!
What does XLD agar differentiate and how?
Differentiates salmonella and shigella
Salmonella - Red with black centres
Shigella - Red
What is Sabourard agar used for?
For fungal cultures (e.g. candida. aspergillus etc)
What culture medium is used for Mycobacterium e.g. TB
Lowenstein-Jensen medium
What 2 ways can Staph aureus be differentiated from other Staphs
- Coagulase test: Coagulase positive
- Culture on blood agar. S aureus colonies are gold, the rest are colourless/white
What are the 2 methods of virus detection?
Viral detection e.g. PCR
Serology testing - detects immune response (Igs created in response to virus)
What virus causes shingles?
Varicella Zoster virus
What are the pros and cons for PCR
Pros
Cheap and quick
Sensitive
Can test for multiple viruses at once
Cons
Need to suspect virus beforehand
False positive
What swabs are used for bacterial and viral infections?
Bacterial - Black charcoal swab
Viral - Green viral swab
What is the main viral cause of infectious glandular fever, as well as the bacterial cause (less typical)
Viral: EBV
Bacterial: S. pyogenes
How does glandular fever typically present
White/yellow purulent lining over tonsils (both bacterial and viral, must differentiate using black charcoal swab)
What 3 features on investigation would indicate EBV rather than S pyogenes
FBC
- Atypical lymphocytes!
Serology (ELISA test)
- IgM active infection
- IgG previous/chronic
What antibody against S pyogenes can be detected for
Anti Streptolysin
What is CMV Colitis, and what is its characteristic histological sign
An “Aids-Defining” illness, causing inflammation of the colon. It is caused by cytomegalovirus.
Owl-eye inclusion bodies
What are 4 AIDS defining illnesses
Pneumocystis jirovecii (FUNGUS) pneumonia
CMV Colitis
Oral Candida
Lymphoma
What are the 3 main HIV markers in the blood
- HIV Igs
- HIV RNA
- P24 Antigen
What causes meningism in neonates
Bacteria that often colonise the maternal vagina/perianal region
- Group B Beta haemolytic Strep (S. agalactiae)
- E coli
- Listeria
What causes meningism in infants
S. pneumoniae
N meningitidis
H influenza
What causes Meningism in adults
N meningitidis
S pneumoniae
What causes Meningism in the elderly
N meningitidis
S pneumoniae
Listeria (gram positive bacillus, found in cheese, affects immunocompromised more)
What is group A streptococci and where are they found
Group A strep - S. pyogenes
Commonly found in healthy throat and on skin.
What can group A strep cause
Impetigo, cellulitis, toxic shock syndrome
What is the most common cause of meningitis
Viral
- Enteroviruses (coxsackievirus, echovirus)
What is the most common cause of Encephalitis
HSV-1
Herpes Simplex Virus - 1
How does CSF appear in meningitis
Bacterial: Yellow
Viral: Clear
TB/Fungal: Yellow/fibrous
What white cells appear in meningitis CSF
Bacterial - Neutrophils
Viral and fungal - Lymphocytes
How does glucose appear in meningitis CSF
Bacterial and fungal - <50% (low)
Viral - >=60% (normal)
How is H influenzae cultured
Using factor V and X on chocolate agar
S pneumoniae microscopy features
Gram Positive diplococci
Optochin sensitive and cultured on blood agar
Treatment of Encephalitis
IV aciclovir
Is C diff anaerobic or aerobic
Anaerobic
1st line antibiotic for Legionella pneumonia
Clarithromycin
What are 2 bacterial causes of acute COPD exacerbation
H influenzae
S pneumoniae
Treatment of H influenzae
B lactamase -ve (non resistant) - Amoxicillin
B lactamase +ve (resistant) - Co amoxiclav
Treatment of S pneumoniae
Amoxicillin
Causes of non caseating granuloma
Sarcoidosis
Leprosy
Crohns
What is the CD4 positive cell count in AIDS conditions?
<200
What is the cause of pneumocystis pneumonia, and what is its treatment
Pneumocystis jirovecii (fungus)
Co trimoxazole and prednisolone
What antibiotic is used against Pseudomonas aeruginosa
Piperacillin and Tazobactam
(Tazobactam is a beta lactamase inhibitor - prevents piperacillin breakdown)
Signs of cellulitis
Typical signs of inflammation (redness, heat, swelling, pain, loss of function).
Skin may be pitted with blisters
Main differential of cellulitis
DVT
Causative pathogens of cellulitis
S aureus
S pyogenes
If a child presents acutely with an itchy growing spot, what is this and how does it present?
Impetigo
- Honey coloured, clustered lesions on the chin and cheeks of a young person.
- Otherwise well with no allergies
Investigations of impetigo
Black charcoal swab
- catalase/coagulase test
- Culture on blood agar (golden colonies = S aureus, haemolysis = S pyogenes)
What is MRSA and what should be used against it
Methicillin Resistant Staphylococcus aureus
Vancomycin for 2 weeks
How should a cellulitis blood culture be taken
More than 1 site, more than once. High volume sample
Microscopy of strep pyogenes
Catalase negative cocci, full haemolysis (pale yellow/transparent on blood agar)
If a cannula becomes infected, what 3 samples must be taken?
- Infected cannula tip (4cm)
- Blood culture (at least 2)
- Black charcoal swab of exudated/inflamed/infected area
What are the main symptoms of upper and lower UTI
Upper (pyelonephritis) - Loin pain, fever, nausea/vomiting
Lower - LUTs
Investigations in cases of UTI
- Urine dipstick (leukocytes, nitrites, protein)
- Midstrearm urine sample MC+S
- Blood culture if bacteraemia suspected
What antibiotics are used for uncomplicated UTI
Trimethoprim 200mg (2 a day) (teratogen!) and nitrofurantoin 50mg (4 a day)
both for 3 days
Most commonly causative pathogen of pyelonephritis
E coli
Risk factors of UTI
BPH
Renal stones
Renal tumours
Catheterisation
Unprotected sex
Why should urinalysis never be done from a catheterised urine sample
There is likely to be bacteria present in all CSU samples regardless of infection, whereas midstream urine is normally sterile so all bacteria is abnormal.
Why can microscopy not be done on catheterised patients
Catheterisation irritates the bladder, causing an inflammatory response. Neutrophils will be positive regardless of infection
Why are urine samples taken from pregnant women
Check for preeclampsia
Immunological signs of Endocarditis
- Oslers nodes
- Janeway lesions
- Splinter haemorrhages
- Septic emboli
- Petechiae
- Roth spots
What differentiates S pneumoniae from other a haemolytic streps
Optochin sensitivity test.
Optochin sensitive - S. pneumoniae
Optochin resistant - Viridians streptococci
What 2 streptococci are known as viridans streptococci, and where are they normally found?
- S oralis
- S sanguis
Normally found in mouth, throat, GI tract
Treatment of viridans streptococci Endocarditis
IV Benzylpenicillin +- Gentamicin
What is the most common cause of IE and how does this come about?
Staph aureus - IV drug use
What are other causes of IE
Staph epidermidis
Candida albicans (Fungal)
How does candida albicans appear on gram staining
Stains positive, but is larger than bacteria and shows “budding”.
Grows as creamy colonies on sabourard agar
What complication can arise from candida IE
Candida ophthalmitis
- Septic embolus of fungus causes infection of eye
What do the b haemolytic streptococci groups cause?
a haemolytic
A - pyogenes - Cellulitis, pharyngitis, glomerulonephritis, septicaemia
B - agalactiae - neonatal meningitis, septicaemia
C - Pharyngitis, cellulitis
G - Cellulitis
What do alpha haemolytic streptococci cause?
Viridans - dental abscesses, IE
S. pneumoniae - Otitis media/sinusitis, pneumonia, meningitis,
Define gastroenteritis
Syndrome of nausea/vomiting, diarrhoea and abdominal pain
Define dysentry
Inflammatory, bloody diarrhoea
Define diarrhoea
Frequent, loose stools, associated with water and electrolyte loss
Usually 5-7 on bristol stool chart
Bacterial causes of diarrhoea
E coli
Salmonella
Shigella
Campylobacter jejuni
Clostridium difficile
Viral causes of diarrhoea
Norovirus
Rotavirus
Adenovirus
Astrovirus
Treatments for the bacterial causes of diarrhoea
Ecoli - Usually self limiting, but Abx = ciprofloxacin
Salmonella - Self limiting, but ciprofloxacin or azithromycin
Shigella - Ciprofloxacin or azithromycin
Campylobacter jejuni - usually self limiting but can use ciprofloxacin
C diff - vancomycin or metronidazole if severe
What bacteria causes cholera
Vibrio cholerae
What are some possible stool tests
Stool culture
Faecal calprotectin
Faecal occult blood
Faecal immunochemical test (FIT)
How are diarrhoea causing bacteria cultured
On MacConkey agar
Lactose fermenters (pink)
- E coli
(Klebsiella also)
Non lactose fermenters (pale yellow/ colourless)
- Shigella
- Salmonella
(Proteus also)
All aerobic, gram negative, bacilli.
What is the diarrhoea causing pathogen that is gram positive and anaerobic
Clostridium difficile
After MacConkey, how can salmonella and shigella be further differentiated?
XLD agar culture
Shigella - Red
Salmonella - Red with black centres
What 2 problems do salmonella cause
- Diarrhoea
- Typhoid fever
What is the main type of diarrhoeal salmonella. How does this arise, what is its incubation period and how is it treated?
S. enteriditis
- Caused by undercooked poultry and eggs
- Incubation 12-36 hours
- Self limiting, supportive treatment
What salmonella species can cause typhoid fever
S. typhi, S. paratyphi
Waterborne, found in canned meat and shellfish
How is salmonella typhoid treated
- Fluoroquinolones (ciprofloxacin)
- 3rd gen cephalosporin (ceftriaxone)
- Azithromycin
Is there a vaccine for salmonella typhoid
Yes
What organ does salmonella typhoid damage most
Gallbladder (Especially with relapse, which is common)
What does shigella cause and what does it do that aids its virulence
Causes shigellosis dysentry
Produces shiga toxin
What is usually a preceding case in Campylobacter infection
Patient eats shellfish/ BBQ chicken the DAY before. Patient now presents acutely unwell with diarrhoea
How does campylobacter present on microscopy
Gram negative bacillus
What neurological disease is Campylobacter strongly implicated in
Guillain barre syndrome
What agar is Campylobacter cultured on
- CCDA agar (charcoal based, no blood)
What must be done immediately if a norovirus diarrhoea case is found
Notify UKHSA (formerly Public Health England)
What virus normally causes diarrhoea in children
Rotavirus
What antibiotics increase risk of C diff
“C” antibiotics - kill normal gut flora, allowing colonisation of C diff
- Co amoxiclav
- Ciprofloxacin
- Clarithromycin
- Cephalosporins
How should C diff be treated
Stop “C” antibiotics immediately and start vancomycin 4 daily for 10 days.
Patient should be isolated for 48 hours
Ruptured appendicitis causes intraabdominal infection. What bacteria are implicated in this?
G- - Colliforms: E coli, Klebsiella, Enterobacter
G+ - Entercocci
Anaerobe: Bacteroides fragills
Empirical treatment of apprendix rupture
Cefuroxime (covers G- and enterococcus)
or Metronidazole for Bacteroides
What bacteria are implicated in ascending cholangitis
E coli
Klebsiella
Enterococcus
Bacteroides fragillis
Treatment of ascending cholangitis
Co Amoxiclav
Structure of gram positive bacteria
Single thick peptidoglycan wall. Produce Exotoxin (produced inside and secreted)
Structure of gram negative bacteria
Double, thinner cell walls. Less peptidoglycan. Produce endotoxins. Action is non specific
What are the 2 main classes of beta lactam, what are they good at treating?
Penicillins, cephalosporins
Good at treating gram +ves (streps and staphs)
What is used in penicillin allergy
Vancomycin
What antibiotics largely cover gram positives?
Beta lactams
- S aureus, Group ABCG strep - Flucloxacillin
- S pneumoniae - Amoxicillin or Benzylpenicillin (can also be used for ACG)
What antibiotic is used for Listeria
Amoxicillin
What does vancomycin treat
C diff and MRSA
What antibiotics largely cover gram negatives?
Fluoroquinolones (Ciprofloxacin! (2nd gen))
What antibiotic is used for UTIs, and what bacteria does this cover?
Trimethoprim
- Klebsiella
- E coli
- Enterococcus
- Proteus
Who are at risk of fungal infection
The immunocompromised (old/young, HIV, long term steroids)
What are 2 antifungal medications used to treat fungal infection
Azoles
Amphotericin