Microbiology Flashcards
Define pathogen
Disease-causing organism
Define commensal
Organism which colonises the host but causes no disease in normal circumstances.
Define opportunist pathogen
Microbe that only causes disease if host defences are compromised
Define virulence/pathogenicity
The degree to which a given organism is pathogenic
Define asymptomatic carriage
When a pathogen is carried harmlessly at a tissue site where it causes no disease.
What are the 4 main types of bacteria?
Cocci - unicellular, spherical or elliptical shape and either remain single-cellular or aggregate in various configurations
Rods/Bacilli - rod-shaped bacteria which either remain singly or form chains.
Vibrio - curved, comma-shaped single bacteria
Spirochaete - spiral-shaped bacteria with terminal flagella
Define endotoxin
component of outer membrane of gram -ve bacteria - lipopolysaccharide.
Define exotoxin
secreted proteins of gram +ve and gram -ve bacteria. Can inhibit and stimulate the nervous system.
What are three ways bacteria mutate?
- base substitution
- deletion
- transfer
What are 3 ways bacteria undergo gene transfer?
- transformation
- transduction
- conjugation
What are the steps of performing a gram stain?
- Apply primary stain such as crystal violet (purple) to heat fixed bacteria
- Add iodine which binds to crystal violet and helps fix it to the cell wall
- Decolourise with ethanol or acetone
- Counterstain with safranin (pink)
What is the result of a gram stain on gram -ve bacteria?
Stains pink due to the thin layer of peptidoglycan (high lipid content) in the cell wall.
What is the result of a gram stain on gram +ve bacteria?
Gram + ve bacteria retain purple colour of crystal violet due to their cell wall composed of a thick layer of peptidoglycan.
What are the typical features of bacteria?
- outer membrane, inner membrane, chromosomes or nuclear membrane
What environment do bacteria survive in?
temp: < -80oC -> 80oC temp
pH: <4-9
water/dessication: 3 hours to 3 months (>50 years for spores)
Light: UV
What are 3 species groups of obligate intracellular bacteria?
- Rickettsia
- Chlamydia
- Coxiella
What are the mollicutes?
bacteria cultured on artificial media with no cell wall (e.g. mycoplasma pneumoniae, M. hominis, ureaplasma urealyticum)
What are 3 species groups of bacteria that can be grown on artificial media, have a cell wall and grow as filaments?
- Actinomyces
- Nocardia
- Streptomyces
What are 3 species groups of spirochaetes (can be grown on artificial media, have a cell wall and grow as single cells)?
- Leptospira
- Treponema
- Borrelia
Describe the characteristic features of gram positive bacteria
- single membrane
- large peptidoglycan area
Describe the charateristic features of gram negative bacteria
- Double membrane
- Small peptidoglycan area
What bacterial species are examples of gram negative cocci?
Aerobic = veillonella
Anaerobic = neisseria
What bacterial species are examples of aerobic gram positive cocci?
- Staphylococcus
- Streptococcus (beta-haemolytic, alpha-haemolytic, non-haemolytic, enterococcus)
What bacterial species are examples of anaerobic gram positive cocci?
Peptostreptococcus
What are Ziehl-Neelsen stain positive rods?
Mycobacteria
What are examples of anaerobic gram positive rods?
- Clostridium
- Propionibacterium
What species are aerobic gram positive rods?
- Corynebacterium
- Listeria
- Bacillus
What species are anaerobic gram negative rods?
Bacteriodes
Which species are aerobic gram negative rods?
Vibrio
Coliforms (Escherichia, Klebsiella, Enterobacter)
What is the difference between streptococci and staphylococci?
Streptococci are organised in chains of bacterial cells and staphylococci are arranged in clusters.
What is the main treatment for staphylococcus aureus infection?
Flucloxacillin
Give an example of a slow growing bacteria
TB
Give an example of a fast growing bacteria
E.coli and S.aureus
Name 5 infections caused by S.pyogenes?
- Tonsilitis
- Otitis media
- Impetigo
- Cellulitis
- Scarlet fever
Define nosocomial
Hospital-aquired
Describe the Ziehl-Neelson stain test.
Used to distinguish acid-fast bacilli (e.g. mycobacterium) from non acid-fast bacilli (e.g. E.coli).
Acid-fast bacteria will turn red with ZN stain whereas non acid-fast will turn blue.
Describe the catalase test
Used to differentiate between staphylococci and streptococci.
H2O2 is added to bacteria and a positive reaction results in bubbling.
Staphylococci are catalase positive and streptococci are catalase negative.
Describe the coagulase test.
Coagulase is an enzyme produced by staphylococcus aureus that converts soluble fibrinogen in plasma to insoluble fibrin resulting in clumping. All other staphylococci are coagulase negative so do not demonstrate clumping.
Describe the haemolysis test.
Used to classify streptococci.
Haemolysis is the ability of bacteria to break down RBCs in blood agar.
Alpha haemolytic bacteria cause partial destruction of red blood cells so the blood agar around the colony becomes a green-brown colour. (e.g. strep. pneumoniae, strep. viridans)
Beta haemolytic bacteria cause complete lysis of RBCs resulting in the agar around the colony becoming clear and colourless. (e.g. strep pyogenes)
How can beta haemolytic bacteria be further distinguished?
Lancefield grouping (detection of surface antigens)
A, C, G - tonsilitis + skin infections
B - neonatal sepsis + meningitis
D - urinary tract infection
Describe the optochin test
Used to differentiate between streptococci.
Streptococcus pneumoniae is sensitive to optochin and so the test results in a clear zone around the optochin disc.
Viridans streptococci and other alpha haemolytic streptococci are optochin resistant and will grow around the disc.
Describe the oxidase test
Used to test whether the micro-organism contains a cytochrome oxidase (an enzyme of the bacterial electron transport chain).
All bacteria that are oxidase positive are aerobic and oxidase negative bacteria could be aerobic or anaerobic.
Oxidase positive bacteria turns blue and oxidase negative bacteria show no change.
Describe the Macconkey agar test.
Differentiates between lactose-fermenting and non-lactose fermenting gram negative bacilli.
Lactose-fermenting bacteria will produce lactic acid and turn the indicator in the agar from white/yellow to pink/red. (e.g. E. coli)
Non lactose-fermenting bacilli will not produce acid and appear white/transparent. (e.g. salmonella)
What are 6 infections caused by E.coli?
- Wound infections
- UTIs
- Gastroenteritis
- Traveller’s diarrhoea
- Bacteraemia
- Meningitis
Name 3 infections caused by salmonella
- Gastroenteritis
- Enteric fever (typhoid fever from drinking poor quality water)
- Bacteraemia
Describe the XLD test.
Xylose lysine deoxycholate agar is a very selective gorwth medium used to differentiate Salmonella and Shigella spp. Both colonies are red and can be differentiated by a hydrogen sulphide indicator. Salmonella spp. produce hydrogen sulphide and are initially yellow, then turn pink/red with black centres. Shigella spp. do not and therefore remain pink/red.
What is an API strip?
Analytic profile index strips consist of a series of 20 mini test-chambers containing dehydrated media which are used to distinguish enterobacteriaceae.
What are the sterile sites of the body? And examples of infections of these sites
Blood (sepsis)
CSF (meningitis)
Pleural fluid (pericarditis, pleural effusion)
Perineum (Spontaneous bacterial peritonitis)
Joints (septic arthritis)
Urinary tract (UTIs)
Lower respiratory tract (TB + pneumonia)
Define virus
An infectious, obligate intracellular (cell-dependent) parasite comprising genetic material (DNA or RNA) surrounded by a protein coat and/or a membrane.
Describe how viruses replicate.
- Receptor binding - virus binds to receptor on host cell
- Host cell invasion - viral core carrying nucleic acid and some associated proteins enters host cell
- Viral replication - virus interacts with host cell and uses its enzymes, amino acids and nucleotides to replicate and form new virus particles.
- New virus release - the new virus particles are then released from the cell causing the cell to die.
What is the humoral response to viruses?
- antibodies (IgG, A, M) - block binding and virus-host cell fusion, also involved in opsonisation
- IgM antibodies agglutinate viral particles
- Complement proteins cause opsonisation and lysis of infected cells
What is the cell-mediated response to viral infection?
- IFN from Th or Cytotoxic T cells - block virus replication
- Cytotoxic T cells can kill infected cells
- NK cells and macrophages are involved in antibody-dependent cellular cytotoxicity (ADCC)
- IFN induces anti-viral proteins for bystander cells
Which viruses cause direct cell cytotoxicity and to which cells?
- Influenza/RSV virus - respiratory epithelium
- Varicella Zoster virus - skin cells
- Yellow Fever virus - liver cells
- HIV – Th cells
How do viruses evade the immune system?
- Influenza - changes coat antigen
- Rhinovirus, HIV - show antigenic variation
- Mumps, measles, EBV, HIV, CMV - cause immune suppression by altering or destroying lymphocytes/macrophages
How does the influenza virus evade the immune system?
Changes in the glycoprotein projections haemagglutinin (HA) and neuraminidase (NA) result in coat variability
Define antigenic drift
spotaneous mutations which occur gradually resulting in minor changes in HA (haemagglutinin) and NA (neuraminidase). (epidemics)
Define antigenic shift
sudden emergence of a new subtype different to that of preceding virus (pandemics)
What are mycobacteria?
Aerobic, non-spore forming, non-motile bacilli with high lipid content and myolic acids in cell wall which makes them gram stain resistant.
What are 5 diseases and the mycobacterial species that cause them?
Tuberculosis (TB) - M. tuberculosis
Leprosy - M. leprae
Chronic lung infection - M. kansasii
Disseminated infection in AIDS, chronic lung infection - M. avium complex (MAC)
Buruli ulcer - M. ulcerans
Why are mycobacteria difficult to treat with antibiotics?
They are slow growing and have lipid rich cell walls and have multiple drug resistance mechanisms.
What are the 5 stages of rash evolution in chickenpox?
Macule - flat reddened area of skin
Papule - raised area of skin
Vesicle - raised spot filled with blister fluid
Pustule - pus filled spot
Crust - spot covered with hardened layer
What are the 2 main approaches to viral diagnosis?
- Viral detection (e- microscopy, PCR)
- Serology (ELISA, immunofluorescence, complement fixation test)
What is shingles (herpes zoster)?
Red, painful rash that is confined to a single dermatome. Caused by reactivation of the varicocella-zoster virus (chickenpox virus)
What is EBV?
Epstein-Barr virus is the cause of infectious mononucleosis (glandular fever).
Presents with white/yellowish purulent lining over the tonsils (DDx = s.pyogenes throat infection), cough, fever and splenomegaly.
Diagnosed using blood test (atypical lymphocytes), serology (ELISA test)
How is Eptein Barr virus treated?
Fluids and analgesia, avoid contact sports for 6 weeks to prevent splenic rupture.
What is CMV?
Cytomegalovirus causes CMV colitis which is gastrointestinal inflammation. It can also cause eye and lung infections or infect the foetus while it’s in the womb.
It is an AIDS defining virus and presents with characteristic owl eye inclusion under the microscope.
Treated with IV ganciclovir (antiviral)
What are protozoa?
Single-celled, nucleated organisms of over 30000 species.
What are the 5 major groups of protozoa?
- Flagellates (e.g. Trypanosoma spp)
- Amoebae (e.g. Entamoeba histolytica)
- Sporozoa (Toxoplasma gondii)
- Cilliates (Balantidium coli)
- Microsporidia
What is malaria?
A potentially life-threatening parasitic infection transmitted by female anopheles mosquitos which causes a variety of symptoms.
What are the 5 sporozoite species that cause malaria?
- Plasmodium falciparum (most common, high mortality)
- Plamodium ovale
- Plasmodium vivax
- Plasmodium malariae
- Plasmodium knowlesi
What are the symptoms of malaria?
FEVER
Chills
Headaches
Myalgia
Fatigue
D+V
Abdo pain
What are signs of malaria
Anaemia, Jaundice, Hepatosplenomegaly, ‘Black Water Fever’(very dark urine)
*patients will not always “look sick”
What are the steps in the development of malarial infection? (Exo-erythrocytic and erythrocytic cycles)
- Mosquito bite
- Sporozoites are injected into blood as mosquito takes up blood - Abdo pain
- The sporozoites are carried in the blood to liver cells where they enter and form schizonts which rupture forming merozoites which enter the blood stream . - Cyclical fever
- Merozoites infect erythrocytes and multiply forming schizonts again so the process repeats.
- This causes death of erthyrocytes and anaemia, jaundice and haemoglobinuria as a result.
How does malaria spread? (sporogonic cycle)
- When an Anopheles mosquito takes a blood meal from a person infected with malaria, gametocytes formed from sporozoites will be ingested.
- Once in the mosquito’s stomach, the microgametes (male gametocytes) penetrate the macrogametes (female gametocytes) generating zygotes.
- The zygotes in turn become motile and elongated (ookinetes) which invade the midgut wall of the mosquito where they develop into oocysts.
- The oocysts grow, rupture, and release sporozoites, which make their way to the mosquito’s salivary glands.
- These are then injected into the blood of humans bitten by the mosquito.
What are the symptoms of complicated malaria?
- Cerebral - drowsiness, increased ICP, seizures and coma
- ARDS/Pulmonary oedema - SOB, hypoxia and pulmonary oedema
- Renal failure - proteinuria, fatigue and haematuria
- Sepsis
- Bleeding/Anaemia - epitaxis, abnormal bleeding and worsening anaemia
How is P.falciparum malarial infection different?
It causes red blood cells to become more “sticky” and adhere to capillary endothelial walls - this causes obstructed microcirculation which leads to “complicated malaria”