Microbiology Flashcards
What is a pathogen?
An organism that causes disease
Define commensal. What is it also called?
- An organism that colonises the host but causes no disease under normal circumstances
- Also called colonisation
What is an opportunist pathogen?
A microbe that only causes disease if the host defence is compromised
Define virulence/pathogenicity.
The degree to which an organism is pathogenic
What are the categories for describing bacteria?
- Gram +ve or gram -ve
- Shape: cocci (circular) or bacilli (rods)
- Cocci can be individual, clusters or chains
- Bacilli can be chains, curved or spiral rods
What do we mean by gram positive and gram negative bacteria? What colours do these stain? Which dyes are responsible for these colours?
- Gram positive: has a thick layer of peptidoglycan, stains PURPLE. This is because it is stained by crystal violet
- Gram negative: has a thin layer of peptidoglycan (high lipid content), stains PINK. This is because it is stained by safranin
What are the stages for the gram staining method?
Mnemonic: Come In And Stain = Crystal violet, Iodine, Alcohol, Safranin
- Fixation of clinical materials to microscope slide (heat/methanol)
- Application of crystal violet. Wash off excess
- Application of iodine. Wash off excess
- Decolorisation step: use acetone or ethanol, this will distinguish between gram +ve and -ve bacteria. This is because gram +ve will be purple + rest will decolourise
- Application of safranin to stain gram -ve pink
What type of organism would you stain with Ziehl-Neelsen stain?
Used to identify acid-fast (resist decolorisation by acids during staining procedures) organisms, mainly mycobacteria, e.g. TB
What types of bacteria release endotoxin?
Gram negative bacteria. An example of endotoxins are lipopolysaccharides
What types of bacteria release exotoxins?
Gram positive and gram negative bacteria
What can gram positive cocci be split into? Which test can be used to distinguish between these?
- Gram +ve cocci can be split into staphylococcus (clusters) and streptococcus (chains)
- A CATALASE test can be used - this detects the presence of catalase enzyme using hydrogen peroxide (H2O2 + staphylococci = gas bubbles)
- +ve catalase test = staphylococcus, -ve catalase test = streptococcus
Which test can be performed to distinguish between staphylococci? What do positive and negative tests indicate?
- COAGULASE test. This looks at whether a fibrin clot is produced
- Coagulase +ve = staphylococcus aureus. This is because it produces coagulase that converts soluble fibrinogen to insoluble fibrin
- Coagulase -ve = all others (staphylococci epidermis, staphylococcus saprophyticus)
Which test can we perform to distinguish between streptococci?
Blood agar haemolytic. Blood agar can undergo 3 types of haemolysis depending on the organism: beta haemolysis = complete lysis (clear area), alpha haemolysis = partial lysis (green), gamma haemolysis = none
If alpha haemolysis is shown after haemolysis in blood agar, which test do we perform to differentiate? What do positive and negative results indicate?
- OPTOCHIN test
- Optochin +ve = STREPTOCOCCUS PNEUMONIAE (clear demarcated ring around optochin disc)
- Optochin -ve = streptococcus viridans
What is the appearance of strep pneumoniae under a microscope?
Gram positive diplococci
If beta haemolysis is shown after haemolysis on blood agar, which test is performed? What do the different groups indicate?
- LANCEFIELD TEST. This groups bacteria based on the carbohydrate composition of the bacterial antigen on their cell wall. Groups into A, B, C, D and G
- A: streptococcus pyogenes
- B: streptococcus agalactiae
- G: streptococcus dysgalactiae
If gamma haemolysis is shown after haemolysis on blood agar, which test is performed? What do the results indicate?
- Lancefield test
- D: streptococcus bovis, enterococcus
How does the haemolysis test work?
The haemolysis test uses hydrogen peroxide to test the reaction with haemoglobin
Useful table that summarises gram positive cocci. But learn microbiology by the condition, not the organism.
List some important gram positive bacilli.
- Listeria monocytogenes
- Propionibacterium acne - acne
- Clostridium difficile - diarrhoea from antibiotic overuse
What kind of bacteria is MacConkey agar used with? What does it contain? How does it work?
- MacConkey agar is used to differentiate gram negative bacilli
- MacConkey agar contains bile salts, lactose and neutral red (pH indicator)
- Identifies bacteria that can ferment lactose
- Ferment lactose -> produce acid -> pH drop < 6.8 = pink, pH>6.8 = normal colour
What can gram negative bacilli be split into? What is the appearance on MacConkey agar?
- Lactose fermenting and non-lactose fermenting
- Lactose fermenting = pink: E. coli, klebsiella
- Non-lactose fermenting = colourless/yellow: shigella, salmonella, pseudomonas, proteus
What is XLD agar used for?
It is a very selective growth medium used to isolate salmonella and shigella. Salmonella shows black dots.
The MacConkey agar appears yellow. Which test can be performed to decide which gram negative bacilli it is?
- OXIDASE test. This is used to determine if a bacterium produces certain Cytochrome C oxidases
- Positive result = black/purple = pseudomonas or neisseria (this is a COCCI and not a BACCILI)
- Negative result = colourless = shigella, salmonella, proteus
How do we know whether the positive result is pseudomona or neisseria?
Anti-pseudomonas sensitivity tests
How do we know if the negative result on the MacConkey agar is proteus or not?
The UREASE test. This would be positive if the gram negative bacilli was proteus mirabilis
Give 4 virulence factors of staphylococci.
- Toxins
- Proteases
- Toxic Shock Syndrome Toxin
- Protein A
Does salmonella have an H antigen?
Salmonella is motile and has a flagellum, therefore has an H antigen
Does E.coli have an H antigen?
E.coli is motile and has a flagellum, therefore has an H antigen
Whihc type of E.coli would you associate with causing traveller’s diarrhoea?
Enterotoxigenic E.coli (ETEC)
What are the symptoms of enteropathogenic E.coli infection?
Chronic watery diarrhoea
What are the symptoms of enterohaemorrhagic E.coli infection?
Bloody diarrhoea
What are the symptoms of shigella infection?
Severe bloody diarrhoea and frequent passage
What bacteria is responsible for salmonellosis?
S.enterica
What are some gram negative cocci?
Neisseria meningitidis, moraxella cartarrhalis
How does any neisseria appear under a microscope?
Gram negative diplococci
What is a comma/curbed shaped gram negative bacteria?
Vibrio cholera - rice water stool
Give examples of helical shaped gram negative bacteria.
- Campylobacter jejuni - bloody diarrhoea
- Helicobacter pylori - gastric and duodenal ulcer
Give an example of a coccobacilli.
Haemophilus influenza
What does haemophilus influenza require to grow?
Haemophilus influenza is a gram negative coccobacilli + requires factor X and V to grow
What is fastidious bacteria? In order to be able to grow, what does it require?
- Fastidious bacteria has complex or particular nutritional requirements
- It requires chocolate agar (which is blood agar but with lysed RBCs due to heating to 80 degrees Celsius)
What does neisseria meningitidis require to grow?
Chocolate agar as it requires haem and NAD
Useful table for gram negative bacteria.
What are the uses of these agar:
a) Blood
b) Chocolate
c) MacConkey
d) CLED
e) XLD agar?
How would you grow haemophilus influenzae?
On chocolate agar as it requires haem and NAD
What diseases can haemophilus influenzae cause?
Meningitis and pneumonia
What are mycobacteria? Give examples.
- Aerobic, non-spore forming, non-mobile bacilli
- Slow-growing causes gradual onset of disease
- Requires multi-antibiotic treatment for a prolonged period
- 2 main examples = TB + leprosy
Where can we get bovine TB from?
We can get bovine TB from m. bovis from cows
What is mycobacteria cultured with?
Mycobacteria take a long time to culture, so have to be cultured with Löwenstein-Jensen medium
Which stain is required to stain mycobacteria? Why?
- Ziehl-Neelsen stain is used to identify acid-fast bacilli
- This is because the mycolic acid in the cell wall does not absorb normal gram stain
Describe the process of Ziehl-Neelsen staining.
TOP EXAM QUESTION:
- Z-N staining involves HEATING the sample with CARBOL FUSCHIN (strong dye)
- Heat makes the bacteria resistant to decolourisation by acid = acid-fast (ACID-FASTNESS is a property of all Mycobacterium)
- So when the slide is then flooded with acid, Mycobacteria retain the pink dye. Meanwhile everything else is decolourised to blue
Are viruses self-dependent?
No, they rely on the host cells for living - they have no organelles or cell walls
What are some ways that viruses cause disease?
- Direct destruction (polio)
- Modification (rotavirus)
- Over-reactivity of the immune system (hepatitis B)
- Damage through cell proliferation (HPV)
- Evasion of host cell defences (VZV)
Do viruses have a cell wall?
NO! Viruses have an outer protein coat that is sometimes surrounded by a lipid envelope but they do not have a cell wall
What are the 6 stages of viral replication?
- Attachment.
- Cell entry.
- Interaction with host cell.
- Replication.
- Assembly.
- Release.
How do viruses attach to a host cell?
Viruses have proteins on their surface that interact with receptors on host cell membranes
What part of the virus will enter the host cell?
Only the viral core carrying the nucleic acids will enter the host cell cytoplasm. Sometimes proteins that act as enzymes may enter too
How do viruses interact with host cells?
Viruses use cell materials, e.g. enzymes, amino acids and nucleotides, for their replication and they evade host defence mechanisms
Where in a cell does viral replication occur?
In the nucleus, cytoplasm or both
How can viruses be released from a cell?
- Bursting open; lysis of cell.
- ‘Leaking’ from the cell over a period of time; exocytosis
What are the 5 ways by which viruses can cause disease?
- Damage by direct destruction: cell lysis
- Damage by modification of cell structure
- ‘Over-reactivity’ of the host as a response to infection: immuno-pathological damage
- Damage via cell proliferation and immortalisation
- Evasion of host defences
How can we detect viruses?
- Not visible in light microscopy, can’t culture as only reproduce inside live cells
- PCR + nucleic acid amplification tests (NAAT) used, also can do serology (look for antibodies in response to virus)
What can qPCR detect?
- The presence or absence of DNA/RNA
- It can quantify the level of virus in a tissue
What virus can cause shingles?
Varicella Zoster Virus
What are the 3 groups of worms/helminths?
- Nematodes (roundworms)
- Trematodes (flatworms)
- Cestodes (tapeworms)
Define pre-patent period.
Pre-patent period = the interval between infection and appearance of eggs/larvae in the stool
Which immunoglobulins are mainly involved with worms?
IgG and IgE
What is hookworm the leading cause of? What are the clinical features of hookworm? What is the treatment for hookworm?
- Hookworm is the leading cause of iron-deficiency anaemia
- Clinical features: ground itch (papules at the site of entry, e.g. on feet) + pulmonary symptoms
- Treatment: normally mebendazole
Which helminth is very common in the UK, usually affects whole households and causes an itchy bum?
Enterobius vermicularis
What symptoms does Wucheria bancroftii cause?
Filiriasis causing lymphoedema
What does Schistosomiasis cause?
Squamous cell bladder cancer
What are protozoa?
Microscopic unicellular eukaryotes
Protozoa are classified based on what? What are the 5 categories of protozoa?
- Protozoa are classified based on their movement
- 5 types:
1. Flagellates
2. Amoebae
3. Sporozoa
4. Ciliates
5. Microsporidia
What is giardiasis caused by? What are the symptoms? How is it treated?
- Giardiasis is caused by giardia
- Diarrhoea due to the alteration of intestinal villi, reducing absorption
- Treatment: metronidazole
What are the symptoms of Entmoeba histolytica? What is the treatment?
- Bloody diarrhoea, liver abcess
- Treatment: metronidazole
How is malaria transmitted?
Malaria is transmitted by the bite of a FEMALE ANOPHELES mosquito. The mosquito carries plasmodium (5 types)
What are the 5 species of malaria?
- Plasmodium falciparum (most important)
- Plasmodium ovale
- Plasmodium vivax
- Plasmodium malariae
- Plasmodium knowlesi
What are the signs and symptoms of malaria?
- Signs: anaemia, jaundice, hepatosplenomegaly, ‘Black Water Fever’
- Symptoms: FEVER, chills, headache, myalgia, fatigue, diarrhoea, vomiting, abdominal pain
What are the stages of the plasmodia life cycle in the human called?
Exo-erythrocytic and endo-erythrocytic stages
Describe the life cycle of malaria.
- Infected mosquito injects parasite (sporozoite) when it bites human
- Sporozoites travel to liver via blood and take up residence in hepatocytes
- In the liver, the sporozoites multiply and become merozoites. The hepatocytes then burst, releasing it into the blood
- In the blood, these merozoites invade erythrocytes and multiply again until the cell bursts
- The cycle repeats itself, the merozoites invade RBCs and multiply and then burst out. This causes chills, fever and sweating
- After several asexual cycles, merozoites can invade RBCs + instead of replicating, they develop into sexual form of the parasite (gametocytes)
- Mosquito bites the infected human. It digests the gametocytes which will allows it to develop into mature sex cells (gametes)
- Male and female gametes enter sporogenic cycle producing more pathogenic sporozoites
- Mosquito (female) can infect another human causing malaria
What 2 species of the plasmodia genus lie dormant and cause late relapse of malaria?
P.ovale and P.vivax
What is the treatment for malaria?
- Uncomplicated malaria:
- ORAL CHLOROQUINE
- QUININE SULPHATE
- DOXYCYCLINE
- Severe or complicated malaria:
- IV ARTESUNATE. This is the most effective treatment but is not licensed
- QUININE DIHYDROCHLORIDE
What is an antibiotic?
Antibiotics are molecules that work by binding to a target site on a bacteria
What varies with antibiotic class?
The binding site will vary with antibiotic class
What are the two groups of antibiotics that inhibit cell wall synthesis?
- Beta lactams
- Glycopeptides
What are the categories of beta lactam antibiotics? Name the important antibiotics within these categories.
- Penicillins: Flucloxacillin, Amoxicillin/Ampicillin, Benzylpenicillin (Penicillin G), Penicillin V, Pipericillin
- Cephalosporins: Cefuroxime, Cefotaxime, Ceftriaxone
- Carbapenems: Meropenem
What are the glycopeptides we need to know?
Glycopeptides: vancomycin, teicoplanin
What are beta lactams effective against?
Gram positive bacteria (because they inhibit cell wall synthesis + gram positive have a large cell wall)
What is the mechanism of beta lactams?
- They disrupt peptidoglycan production by irreversibly binding to Pencillin Binding Proteins (PBPs)
- Cell wall is disrupted and lysis occurs. This results in a hypo-osmotic or iso-osmotic environment
In order to bind to the PBPs, what must beta lactams first diffuse through? Which bacteria are usually more susceptible to beta lactams? Why?
- To bind to the PBPs, the β-lactam antibiotic must first diffuse through the bacterial cell wall
- Gram-positive usually more susceptible to β-lactams than gram-negative bacteria. Gram-negative organisms have an additional lipopolysaccharide layer that decreases antibiotic penetration
Why do beta lactams differ in their activity? Are they effective at treating intracellular pathogens? Why?
- Due to their relative affinity for different PBPs
- Because the penicillins poorly penetrate mammalian cells, they are ineffective in the treatment of intracellular pathogens
Name a few antibiotics that inhibit nucleic acid synthesis.
- DNA strand breaks: Metronidazole (Nitroidimazoles)
- Inhibit DNA gyrase: Ciprofloxacin, Levofloxacin (Fluoroquinolones)
- Binds to RNA polymerase: Rifampicin
Name a few antibiotics that inhibit protein synthesis.
- Aminoglycosides: Gentamycin, Streptomycin
- Tetracyclines: Tetracycline, Doxycycline
- Macrolides: Clarythromycin, Erythromycin
- Chloraphemnicol
Name a couple of antibiotics that inhibit folate synthesis.
- Trimethoprim
- Sulfonamides: Sulphamethoxazole
- Co-trimaxazole (Trimethoprim and Sulphamethoxazole)
What do bacteriocidal antibiotics do?
They kill the bacteria, e.g. antibiotics that inhibit cell wall synthesis
What do bacteriostatic antibiotics do?
They prevent the growth of bacteria - ‘inhibitory to growth’, e.g. antibiotics that inhibit protein synthesis, DNA replication or metabolism
Name 6 sterile sites in the body.
- Urinary tract.
- CSF.
- Pleural fluid.
- Peritoneal cavity.
- Blood.
- Lower respiratory tract.