Medical Microbiology

Question 1

What is the reporting triangle?

Answer 1

Question 2

How many people does ARI’s diagnostic bacteriology lab serve? How many specimens per year?

Answer 2

530000 people, 700k specimens per year

Question 3

What do medical microbiologists do?

Answer 3

Advice on diagnosis of infection, supervision and review of lab tests, advice on test result interpretation, advice on treatment/management, infection control/prevention advice, antibiotic policy

Question 4

What are possible infecting agents? [5]

Answer 4

Bacteria, viruses, fungi, parasites, prions

Question 5

Taking specimens: what are sterile and non-sterile sites?

What’s the difference?

Answer 5

Sterile: blood, CSF, lung, bladder, Non-sterile: skin, nasopharynx, urethra, gut

Sterile: shouldn’t be any organisms in these sites, Non-sterile: commensal flora abounds (and can even cause problem)

Question 6

Microscopy: what can you do?

What can you definitely not see?

Answer 6

Unstained (see pus cells, parasites, etc), gram stain (see bacteria, yeast/fungi), ZN or auramine stain (see mycobacteria and other strains)

Can’t see viruses (only x1000 magnification)

Question 7

Bacterial culture: types of media?

How else could you identify bacteria?

Answer 7

Non-selective (eg: blood, chocolate), selective (eg: MacConkey - enteric gram negative microbes)

Genetic typing (Should be: Transferable, Reliable, Able to discriminate different strains, Cheap, Effort required low, Standardized lab methods/interpretation)

Question 8

Typing Methods Picture: What methods are there (phenotypic and genotypic)?

Answer 8

Question 9

Biochemical sugar fermentation strip: how does it work?

What about enzyme reaction plates?

Answer 9

Strip containing various kinds of sugar in separate compartments. Innoculate strip with microorganism. If it can use sugars, it will, and the colour will change from red to yellow/orange. Depending on the result, you get a different seven digit ID, which can then be used to ID strain.

Special plates where different microbes will grow with different appearance (eg: a chromogenic substrate which makes E coli grow purple, and other coliforms grow pink) [eg: to identify altered transgenic strains]

Question 10

How does serotyping work?

What about phage typing?

Answer 10

Targets antigenic variations on the cell surface with specific antibodies (eg: salmonella strain testing kit - different spots with different antibodies, will attach and be visible in appropriate spots)

Innoculate bacteriophage onto lawn of bacteria, and look for areas of lysis (if you know which bacteria the phage virus will attack, you can ID it based on what gets attacked) [old fashioned]

Question 11

How would you ID viruses nowadays?

Other methods?

Answer 11

real time PCR (RNA/DNA viruses)

Antigen detection, serology to determine immunity, cell/tissue culture, electron microscopy (not really anymore)

Question 12

Big issues relating to healthcare acquired infections?

Answer 12

MRSA, clostridium difficile, organisms with extended spectrum beta-lactamases (ESBLs), noroviruses

Question 13

What are the signs and symptoms of clinical infection? [7]

Answer 13

Inflammation, pain, pyrexia (raised temp), tachycardia (fast HR), rigors (cold shivering despite raised temp), increased white cell count, increased C Reactive Protein

Question 14

What’s the difference between a pathogen and a commensal?

What were Koch’s postulates in relation to whether something is a pathogen?

What is pathogenicity?

Answer 14

Pathogen is organism that can cause disease, commensals are part of natural flora (but can become pathogenic)

Organism must be found in all cases of disease, must be culturable outside of body for several generations, and should reproduce disease on inoculation

Capacity of microorganism to cause infection

Question 15

Pathogenicity = Capacity of microorganism to cause infection. What is needed for something to increase its pathogenicity?

Answer 15

Infectivity (ability to become established), virulence (ability to cause harmful effects once established)

Question 16

Give examples of things that increase the infectivity (ability to become established) of a microorganism

Answer 16

Attachment (eg: E Coli w/fimbriae that attach to receptors on uroepithelial cells), acid resistance (eg: heliobacter pylori produce urease that converts urea to ammonia, which is basic)

Question 17

Virulence (capacity to cause harm once established) is conferred by virulence factors. What are these? Give three examples

Answer 17

Genetically determined microbial components.

Invasiveness: streptococcus pyogenes causes necrotising fascitis, cellulitis, connective tissue breakdown, and fibrinolysis (helps microbe invade other tissues)

Toxins [exotoxins released by microorganism, called enterotoxins if they act on GI tract, endotoxin is part of gram negative cell wall]: vibrio cholerae causes cholera (increases cAMP, inhibits Na/Cl uptake, upregulates Cl/HCO secretion, causes loss of water in poops)

Evasion of immune system: exotoxins of strep pyogenes and staph aureus stimulate division of T cells -> overwhelming cytokine production causes toxic shock

Question 18

Gram positive: two important kinds? Different appearance?

Answer 18

Staphylococci (clusters of grapes), streptococci (chains of grapes)

Question 19

Staphylococci: what test is used to identify staph aureus in particular? What if it is negative (and can they also be a problem)?

Why is staph aureus commonly penicillin resistant? Does this also provide resistance to methicillin?

Answer 19

Coagulase test (Positive = MRSA/MSSA)(Negative = many species inc. skin commensals, can be pathogenic in presence of foreign bodies [eg: valves/wires piercing skin, implants, etc] or when immunocompromised

Has beta-lactamase enzyme (that cuts beta-lactam ring). No - resistance to methicillin is provided by a different mechanism

Question 20

How do you differentiate streptococci (3 possible types)?

Answer 20

Alpha-haemolytic (partial haemolysis - turns blood agar green), beta-haemolytic (complete haemolysis - turns blood agar clear), non-haemolytic (no change)

Question 21

Give some examples of alpha-haemolytic streptococci

Answer 21

Streptococcus pneumoniae (causes pneumonia, meningitis, septicaemia), viridans streptococci (many species, normal oral flora, cause of infective endocarditis [heart valves])

Question 22

How are beta-haemolytic (complete haemolysis - blood agar clear) streptococci further identified? Give examples from most clinically relevant groups.

Answer 22

Lancefield groupings (based on surface antigens): A-G (A, B, and D most clinically relevant)

A: strep pyogenes (sore throat, cellulitis, necrotising fasciitis)

B: strep agalactiae (neonatal sepsis, commonly (25%) carried in genital tract)

D: Enterococcus spp - e faecalis/faecium (gut commensal - causes UTIs)

Question 23

Gram positive bacilli can be _______ or _________

Give three clostridium species names, and details

Answer 23

aerobic, anaerobic

C. Perfringens (soil/gut commensal, can cause food poisoning/gangrene of wounds)

C. Difficile (can be carried asymptomatically, can also cause squits and toxin production, often invades after antibiotic use)

C. tetani (toxins cause tetanus [uncontrolled muscle spasm due to loss of inhibition at neuromuscular junction])

Question 24

What strains (gram positive bacilli) have been used for biological warfare?

Answer 24

Clostridium botulinum (also for botox), bacillus anthracis (anthrax- can also catch via exposure to infected animals/animal products)

Question 25

What are the important gram negative cocci? What do they do?

Answer 25

Neisseria spp (N. Meningitidis/meningococcus causes meningitis and septicaemia, N. gonorrhoeae causes urethritis in men and pelvic inflammatory disease in women)

Moraxella catarrhalis (doesn’t say in lectures)

Question 26

Gram negative bacilli - what test is used to identify lactose fermentation? What type of bacteria do ferment lactose?

What virulence mechanisms do they have?

How many serotypes (based on O antigen)? What are other antigen types?

What pathologies are they important in?

Answer 26

MacConkey agar (positive = coliforms, organisms within family enterobacteriaeceae, like e coli)

Pili, capsules, endotoxins and exotoxins

>160 (O = lipopolysaccharide, H = flagella, K = capsule … >700 in total)

UTIs and bacteraemia (presence in blood), enterotoxogenic/haemorrhagic E coli causes traveler’s/bloody diarrhoea

Question 27

What coliform doesn’t ferment lactose on MacConkey agar?

What other coliforms (gram negative bacilli) are there?

Answer 27

Salmonella spp (eg: salmonella enterica = second commonest cause of bacterial diarrheoa in UK)(eg: salmonella typhi = cause of typhoid fever)

Shigella spp (diarrheoa), Klebsiella spp (UTI and pneumonia), Proteus spp (UTI and stones)

Question 28

Other Gram Negative bacilli (not coliforms). Say something about them:

Campylobacter spp.

Helicobacter pylori

Haemophilus influenzae

Pseudomonas spp

Anaerobe (bacteroides fragilis)

Answer 28

Camp: microaeophilic, source is domestic animals, fecal-oral route, commonest cause of bacterial diarrheoa in UK

Helico: curved rods, natural habitat is human stomach, damages mucosa and causes ulcers

Haemophilus: cocco-bacilli (mixed), causes respiratory infection secondary to strep pneumoniae

Pseudomonas: water and soil organism, hospital acquired cause of sepsis, sensitive to limited range of antibiotics

Bacteroides: part of colonic flora, causes intra-abdominal abcesses, may spread to other sites

Question 29

Cat Nasties. What is…

… Bartonella?

Which version is responsible for trench fever?

Answer 29

Bartonella: 40% of cats have been infected, transmitted between cats by fleas, transferred to humans by bite/claw, causes papule -> swollen lymph glands -> fever, fatigue, malaise, headache, poor appetite (can be fatal)

B. quinta (five day fever - now common in homeless and HIV patients), often transmitted via lice (faeces which is then scratched into skin)

Question 30

Mycobacterium are detected by which stain?

Which two conditions are they famous for causing?

Answer 30

Ziehl-Neelsen stain

Tuberculosis (M. Tuberculosis) and leprosy (M. Leprae)

Question 31

What are spirochaetes? How are they often diagnosed?

Common organisms and related diseases?

Answer 31

Long, spiral-shaped bacteria (not easily seen under microscope or via culture - needs dark ground microscopy, immunofluorescence, or serology)

Treponema pallidum (syphilis), borrelia burgdorferi (lyme disease), leptospira interrogans (leptospirosis)

Question 32

Treponema pallidum (spirochaete causing syphilis). What is syphilis?

Borellia burgdorfi (spirochaete causing lyme disease). Describe.

Leptospira interrogans (spirochaete causing leptospirosis). Describe.

Answer 32

Non-painful lesion at infection site (primary), generalised systemic illness and rash 6-8 weeks later (secondary), latent phases followed by tertiary (nervous symptom issues)

Transmitted by ticks. Stage 1: skin rash. Stage 2: systemic illness weeks/months later (cardiac, neurological, MSK). Stage 3: chronic reoccuring

Concentrates in kidneys. Spread via infected urine and other fluids. Causes Weil’s disease: febrile illness with systemic upset, liver and renal failure, and possible death

Question 33

Different types of chlamydia?

Answer 33

Rep infection ( C. pneumoniae, C. psittaci [from birds]), genital tract infection (C. trachomatis)

Question 34

Four different types of viral infection?

Answer 34

Question 35

Lay out what happens during an influenza A viral infection

What is the difference between antigenic drift and antigenic shift?

Answer 35

Virus infects cells of respiratory tract. This destroys epithelium (allowing for secondary bacterial infections), and alters cytokine expression leading to fever (interleukin-1 and interferon)

Drift: minor changes in genes of flu viruses (seasonal change), Shift: abrupt major changes (eg: Covid19 -> humans)

Question 36

Give examples of enteroviruses

Answer 36

Poliovirus (poliomyelitis), Coxsackie B (myocarditis and pancreatitis)

Question 37

Give example of latent viral infection

Give examples of viral induced tumors

Answer 37

Herpex Simplex (type 1: cold sores, type 2: genital lesions)

Papillomaviruses (cervical carcinoma), retroviruses (lymphomas, leukaemias)

Question 38

Active immunisation can be natural (through exposure) or via vaccination. What are the types of vaccines?

Answer 38

Live attenuated (lowered from pathogenic dose, repeated passage usually provides immunisation)

Killed/Inactivated (no chance of reversion to wild type organism, promotes weaker immune response [but often contains adjuvants to increase this])

Toxoid (modified toxin treated with formalin - retains antigenicity but no toxic activity - induces immunity against toxin instead of organism) [eg: tetanus, diptheria]