9. Microbiology - Will Irving & Emma English Flashcards
State 3 things about virus size
Small
Filterable agents
20-250nm
Virus structure
- State 2 things about virus structure
- What does a virus contain?
- Simple / no organelles
2. Nucleic acid + proteins + sometimes lipid envelope
Virus metabolism
State 3 things about virus metabolism
Metabolically inert
Relies on host cell
Obligate Intracellular parasites
Virus replication
- How are component parts synthesised?
- Where will this happen?
- Control?
- What happens next?
- Independently
- May be in separate parts of cell
- Under separate control
- Subsequent assembly into new particles
Mature virus particle
- Also known as?
- What 2 things is it always made up of? Give the other names for these 2 things.
- What thing may or may not be present?
- Virion
- Nucleic acid = genome
Protein coat = capsid - Lipid envelope
Viral components: nucleic acid
- DNA: how stranded? Shape? Size?
- RNA: how stranded? Ss polarity? Shape? Size?
- DNA
Ds or ss / circular or linear / 3-200kb - RNA
ds or ss/ ss can be positive or negative polarity / linear or segmented / 5-10kb
Viral component: Proteins
- Capsid formation: discuss the shape
- Attachment: what determines viral tropism?
- Enzymes: what do they mainly do?
- Interference with cell function: give an example.
- Symmetrical
- There is a specific interaction between the viral ligand and the cellular receptor
- Macromolecular synthesis
- Stop apoptosis
Viral component: lipid envelope
- What is it derived from?
- What must it contain?
- What will stripping of envelope lead to?
- Enveloped viruses are generally more what?
- Host cell membranes
- External attachment proteins
- Loss of infectivity
- Fragile
Name the 6 steps of viral replication
- Attachment
- Entry
- Uncoating
- Macromolecular synthesis
- Assembly
- Release
Viral replication
1. Step 1 is attachment. What two things attach to each other?
2. Step 2 is entry. What 2 ways can a virus enter a cell?
Step 3 is coating
3. Step 4 is macromolecular synthesis. Multiple copies of which 2 things are made?
4. Macromolecular synthesis requires production of what type of RNA?
Step 5 is assembly
5. Step 6 is release. What process allows for release?
- Viral ligand to cellular receptor
- Endocytosis and fusion
- Viral genomes and viral proteins
- Positive ssRNA
- Budding
State the 4 effect of viruses on cells?
Acute cell death
Chronic infection
Latency
Transformation
Effect of viruses on cells - acute cell death
Give 2 ways the cell can die
Give an example
Cytolytic / cytocidal
Influenza virus on respiratory epithelial cells
Effect of viruses on cells - chronic infection
What happens in this case?
Give an example
Cell continually produces virus but survives
Hep B virus infection
Effect of viruses on cells - latency
- Replication?
- Is the viral genome present? Is viral protein made?
- Once infected…?
- Virus replication?
- Types of infection?
- Give an example
- No virus replication
- Viral genome present
No production of viral proteins - Once infected, always infected
- Virus replication can be reactivated
- Primary and secondary infections
- All herpes viruses eg. Herpes simplex
Effect of viruses on cells - transformation
What is meant by transformation?
Give an example
Immortalisation of the cell
Epstein Barr virus
Give 2 examples of viruses that cause cancer
Hep B - hepato cellular carcinoma
Epstein Barr virus - lymphomas
What are the 2 types of virus infections of the respiratory tract?
How serious are they?
URTI = upper respiratory tract infections
Common + relatively trivial
LRTI = lower respiratory tract infections
Potentially life-threatening
Name the infections in the following places:
- Nose
- Throat
- Sinuses
- Ear
- Epiglottis
- Larynx
- Rhinitis
- Pharyngitis
- Sinusitis
- Otitis media/ otitis externa
- Epiglottitis
- Laryngitis
URTI
- How common?
- Usual aetiology?
- What kind of secondary infections are common? (Name 2)
- Very common
- Viral
- Bacterial and fungal
Viral URTIs
- Name 3
- What may this predispose to? Give 2 examples
- Rhinoviruses/ parainfluenza viruses/ adenoviruses
- Secondary bacterial infection
Bronchitis/ pneumonia
Name 2 things that can cause pharyngitis/ tonsillitis and give an example for each
Viruses = adenoviruses Bacteria = strep pyogenes
Give an example of 4 viruses that cause LRTI
Influenza virus
Respiratory syncytial virus
Varicella zoster virus
Measles virus
Influenza viruses
- Shape / polarity / type of genome?
- How many segments? How many proteins do they encode?
- Name 2 viral proteins
- Name the types? What 2 things is this on the basis of?
- Name the subtype? What is this on the basis of?
- Segmented negative ssRNA
- 8 segments encode 11 proteins
- Haemagglutinin and neuraminidase
- A / B / C
Based on internal proteins and matrix - A only
Based on surface proteins (HA/NA)
What are the 2 major components to the influenza?
Respiratory tract symptoms
Systemic symptoms
Pathogenesis of influenza
- What is meant by pneumotropic virus?
- The infection strips of the respiratory epithelium- so the infection is what?
- Which 2 innate defence mechanisms does it remove?
- The virus doesn’t circulate in the blood but what is produced that does circulate in the blood?
- Infects cells lining the respiratory tract down to the alveoli
- Lytic
- Mucous secreting cells and cilia
- Interferons
Complications of influenza
- In the respiratory tract 2 types of pneumonia can occur. What are the 2 types and what kind of cell infiltrate is in each?
- What cardiovascular complication can occur?
- What CNS complication can occur?
- Primary viral pneumonia = mononuclear cell infiltrate
Secondary bacterial pneumonia = PMNL infiltrate - Myocarditis
- Encephalitis
Influenza: high risk patients
- Patients with pre-existing diseases. Name 3.
- Age?
- Other 2 categories?
- Lung disease / cardiac disease / renal disease
- Over 65 years old
- Pregnant women
Children
Influenza epidemiology
- Name 3 types of epidemics that cause influenza
- What 2 things cause these epidemics?
- Annual seasonal epidemics
Unpredictable worldwide epidemics
Pandemics and inter-pandemic epidemics - Antigenic drift and antigenic shift
Antigenic drift
- Which 2 influenza virus types does it occur in?
- Define antigenic drift including the percentage of amino acid sequence change
- What is this type of mutation responsible for?
- Influenza A and B viruses
- Random spontaneous mutations in viral genes encoding HA and NA
1-2% amino acid sequence change - Interpandemic epidemics
Antigenic shift
- Which influenza virus type does it occur in?
- Define antigenic shift, including percentage amino acid sequence change
- What is antigenic shift responsible for?
- Name 3 influenza A reservoirs.
- What is a mixing vessel for both human and avian viruses?
- Influenza A viruses only
- Genetic reassortment between human and non-human viruses leading to a new subtype
More then 20% amino acid difference - Emergence of new pandemic strains
- Wild aquatic shore birds / humans / other animals
- Pigs
Key measures to combat pandemic flu
- Medical treatment is one, what are the other 2?
- Explain 4 aspects of medical treatment
- Infection control and vaccination
2. Oxygen therapy / anti-viral drugs / antibiotics / ITU support
Respiratory syncytial virus
- What type of enveloped virus is it?
- Polarity and type of genome?
- How many polypeptides does it encode?
- Pattern of infection? Season?
- Popularity?
- Enveloped paramyxovirus
- Negative ssRNA
- 9 polypeptides
- Highly seasonal infection (winter)
- Extremely common
RSV (respiratory syncytial virus)
- What does it cause in infants? Give an example of 2
- Hospitalisation rates?
- Mortality? 3 exceptions?
- What 2 things does it require?
- Re-infection? How?
- LRTI
bronchiolitis / pneumonia - High hospitalisation rates
- Low mortality
Unless congenital heart disease / congenital lung disease / immunodeficiency - Rapid diagnosis and appropriate infection control measures
- Re-infection occurs throughout life - antigenic drift
Acute viral hepatitis - clinical features
- Name 4 preicteric features?
- Name 3 icteric features?
- Malaise / anorexia / nausea / abdominal discomfort
2. Pale stool / dark urine
Hep A virus
- Polarity and type of genome
- Route of transmission?
- Name 3 consequences of infection
- Name 3 methods of prevention
- Positive ssRNA
- Faecal-oral route
- Asymptomatic infection / acute icteric hepatitis / fulminant hepatitis
- Avoid uncooked foods / passive immunisation / active immunisation
Hep B virus
- Type of virus?
- State 3 modes of transmission
- Which Hep B marker shows a current infection?
- Which Hep B marker shows a recent infection?
- What are the 2 outcomes of an acute infection?
- Hepadnavirus
- Perinatal / sexual / parenteral
- HBsAg positive
- IgM anti-HBc positive
- Resolve or become chronic
Chronic HBV infection
- What is this defined as?
- Which marker would highlight high infectivity and increased risk of inflammatory liver disease?
- Which marker would highlight lower infectivity and lower risk of inflammatory liver disease?
- Persistent HBsAg for more than 6 months
- HBeAg positive
- Anti-HBe positive
State 3 ways the HBV infection can be prevented
- Simple precautions and education of carriers
- Passive immunisation
- Active immunisation
Apart from viruses, name 2 other types of microorganisms and give 2 examples for each
Prokaryotes = typical bacteria and atypical bacteria Eukaryotes = Protozoa and fungi
Viruses
- What are the 4 different types of RNA or DNA that it can contain?
- What is the size range?
- Describe the 2 basic components of a virus
- What can it be surrounded by that is derived from the host cell? What is on top of this?
- How is it metabolically
- Ss/ ds/ linear/ circular
- 30nm-400nm
- Nucleic acid in a protein capsid = nucleocapsid
- Lipid Envelope/ membrane with viral capsule proteins
- Metabolically inert
Name 9 things that are on a prokaryotic cell
Capsule Cell wall Plasma membrane Cytoplasm Ribosomes Plasmid Pili Bacterial flagellum Nucleoid
Prokaryotic cells
- Size?
- Nucleus?
- Membrane-enclosed organelles?
- Flagella?
- Glycocalyx?
- Cell wall?
- Plasma membrane?
- Cytoplasm?
- Ribosomes?
- Chromosome (DNA) arrangement?
- Sexual reproduction?
- Size = 0.2-2 mm
- Nucleus= no nuclear membrane or nucleoli - it has nucleoid
- Membrane-enclosed organelles = absent
- Flagella = made of 2 protein building blocks
- Glycocalyx= capsule/slime layer
- Cell wall= usually present and chemically complex
- Plasma membrane= no carbohydrates + usually lacks sterols
- Cytoplasm = no cytoskeleton
- Ribosomes = smaller size = 70s
- Chromosome (DNA) arrangement = single circular chromosome + lacks histones
- Sexual reproduction = conjugation only
Eukaryotic cells
- Size?
- Nucleus?
- Membrane-enclosed organelles?
- Flagella?
- Glycocalyx?
- Cell wall?
- Plasma membrane?
- Cytoplasm?
- Ribosomes?
- Chromosome (DNA) arrangement?
- Sexual reproduction?
- Size = 10-100mm
- Nucleus= true nucleus (nuclear membrane and nucleoli)
- Membrane-enclosed organelles = present
- Flagella = complex (made of multiple microtubules)
- Glycocalyx = present in some cells that don’t have a cell wall
- Cell wall = when present, chemically simple
- Plasma membrane = sterols and carbohydrates (receptors)
- Cytoplasm = cytoskeleton
- Ribosomes= larger size = 80s (and smaller 70s size in organelles)
- Chromosome (DNA) arrangement = multiple linear chromosomes with histones
- Sexual reproduction = meiosis
What is the difference between gram positive and gram negative bacterial cell wall?
Gram positive = 1 thick peptidoglycan cell wall with lipoteichoic acid and teichoic acid
Gram negative = 1 thin peptidoglycan cell wall with lipoproteins and porins as well as an outer membrane layer with lipopolysaccharides porins
Underneath both is the periplasmic space and then the cell membrane which has membrane proteins
- What are the 4 types of spherical bacteria (cocci)?
2. What are the other 2 types of bacteria called and what 2 extra characteristics can they have?
- Micrococci/ Diplococci / staphylococci/ streptococci
- Rod bacteria (bacilli) and spiral bacteria
With endospores / with flagella
Structural components - fimbriae or pili
- What are 2 things these protein structures are composed of?
- Size range?
- What kind of structures are they?
- What are sex pili involved in?
- Fimbrins/ pilins
- 10-25nm
- Attachment structures
- Gene transfer
Structural components - capsules
- What are the 2 things they can be made up of?
- What type of polymers are they?
- Polysaccharides / polypeptides
2. Loose extramural polymers
Structural components - endospores
- Which type of bacteria can make endospores?
- What can they survive and give 3 examples
- Water content?
- What kind of acid do they contain?
- Metabolically?
- How can dormant cells develop into vegetative cells?
- Give 2 examples of genera
- Some gram positive bacteria
- Environmental extremes = high heat/ radiation/ extreme pH
- Low
- Dipicolinic acid
- Metabolically inactive but not completely inert
- Activation, germination, and then outgrowth
- Clostridium/ bacillus
Atypical bacteria
- Give 3 examples
- Which one is the smallest bacteria at can grow on cell free media?
- Which 2 are obligate Intracellular organisms?
- Mycoplasmas / rickettsias / chlamydia
- Mycoplasmas
- Rickettsias / chlamydia
- Define infection
- Define pathogen
- Define opportunistic pathogen
- Presence of infectious organism in a person or population
- Agent of disease = disease producer
- Produces disease on an opportunistic basis rather than obligate
Colonisation
- Define the word colonisation
- What can colonisation lead to? What are 2 possible outcomes of this?
- What are the two ways colonisation can be mediated?
- Presence of microbe at an expected site
- Invasion = cellular damage / destruction
- Pathogen mediated or host mediated
What are the 6 stages of infection?
- Entry
- Spread
- Multiplication
- Evasion of host defence
- Transmission
- Host damage
- Name 3 endogenous sources of infection
2. Name 5 exogenous sources of infection
- GI tract / skin / genital tract
2. Direct (skin, saliva, sexual) / airborne / food / water / vertical
Name 4 physical host defences, giving some examples for each
1. Skin and mucous membrane Barrier / outward flow of mucus 2. Respiratory tract Coughing / sneezing / ciliary action 3. Urogenital Urination 4. Gut Commensal flora / defecation
What 3 issues can contribute to someone being immuno-compromised?
- Breakdown of host physical barriers
- Immune system failures (inherited / acquired)
- Immuno suppressed
Name 5 other bacterial actions aside from the following:
- Surface adhesins
- Anti-phagocytic agents
- Antibiotic resistance
- Ciliotoxic/ static molecules
- Sialylation
- Suppression of IFN-beta action
- Siderosphores
- Organotropism
H. Pylori
- What 2 things does the flagella allow?
- What 2 things does urease do?
- What 2 things do the lipopolysaccharides do?
- What do the outer proteins do?
- What do the exotoxins and secretory enzymes do?
- What does the type 4 secretion system allow for?
- What 2 things do the effectors do?
- Bacterial mobility and chemotaxis to colonise under mucosa
- Neutralise gastric acid + gastric mucosal injury
- Adhere to host cells + inflammation
- Adhere to host cells
- Gastric mucosal injury
- Injection of effectors
- Host cell growth + apoptosis inhibition
- What 2 ways can virulence factors be inherent?
- What 2 ways can virulence factors be acquired?
- What must be consider with regards to the virulence factors of a a particular microbe?
- Adhesion + invasion
- Mutated + horizontal transfer
- Pathogen life cycle (Intracellular or extracellular)
Swine flu influenza A H1N1
- What type of RNA?
- How many types of influenza are there and what are they called?
- What is H?
- What is N?
- Ss-RNA
- 3 types = influenza A, B and C
- Hemagglutinin
- Neuraminidase
- What is antigenic drift?
2. The new subtype can lead to what in a previously immune community?
- Small mutations causing changes in H and N
2. Re-infection
- What is antigenic shift?
- Which influenza only?
- What is antigenic shift caused by?
- What can it lead to?
- Sudden major change
- Influenza A only
- Caused by transfer of genetic information between 2 different viruses invading the same cell
- Pandemics
Respiratory tract
- Accessibility?
- Problem with URT?
- How is the LRT different?
- Give 3 examples of physical host defences
- Most accessible system in the body
- Continuously exposed to pathogens
- Essentially sterile
- Mucociliary escalator / alveolar macrophages / coughing
URTI’s
- Give 4 examples of URTI’s
- How common are they?
- Usual aetiology?
- What kind of secondary infections are common?
- Otitis media, sinusitis, pharyngitis, tracheitis
- Very common
- Often viral
- Secondary bacterial (or fungal) infections
LRTI’s
- Give 3 examples of LRTI’s
- Aetiology?
- What is important when determining likely pathogens?
- Bronchitis, bronchiolitis, pneumonia
- Bacterial, viral or fungal
- History
- What are the 4 aspects of the Centor criteria
2. How many need to be met?
- Tonsillar exudate / tender anterior cervical lymphadenopathy or lymphadenitis / history of fever / absence of cough
- 3 or 4
Streptococcus pyogenes
- Gram?
- Motile?
- Spore forming?
- Pathogenesis popularity in humans?
- Give one thing that it can cause
- What is another name for it?
- Gram positive
- Non motile
- Non sporeforming
- One of the most frequent pathogens of humans
- Pharyngitis
- Group A streptococci
Scarlet fever
- What is it caused by?
- What does it present with?
- Name 4 other symptoms
- Group A streptococci
- Rash over trunk and abdomen that then spreads to entire body
- Pyrexia, lymphadenopathy, aches and nausea
- Give 3 occasions when antibiotics should be given
- A patient that is 65 or 80 with an acute cough needs to have 2 or more (or 1 or more respectively) of what 4 criteria?
- Systemically very unwell, pre-existing co-morbidities and symptoms/signs suggestive of serious illness or complications
- Hospitalisation in previous year
Type 1/ type 2 diabetes
History of congestive heart failure
Current use of oral glucocorticoids
Pneumonia
- What is it?
- 4 general causes?
- What is the most common cause in adults? Give another example
- Name 2 common viral causes
- What is a common cause of pneumonia in young children?
- Lung tissue inflammation
- Bacterial/ viral/ chemical/ fungal
- Streptococcus pneumoniae / haemophilius influenzae
- Respiratory syncytial virus / influenza type A or B
- Viruses
Name as many factors predisposing to pneumonia as you can
Anatomic defects Immunosuppression Alcohol abuse Viral infection Advanced age Chronic lung disease Chronic renal disease Diabetes Nutritional status
Bacterial pneumonia
- What type of serious infection is this?
- Infection where in lung?
- Nosocomial: how many hours after admission? Name 2 causes. What can be a big issue?
- Community acquired: name 2 causes. Name 4 symptoms.
- LRTI
- Lung parenchyma
- Nosocomial:
48 hours / S. Aureus + P. Aeruginosa / antibiotic resistance - Community acquired:
Streptococcus pneumoniae + pneumococcus sp
Lobar infection / fever / chest pain / purulent sputum
Signs and symptoms of pneumonia
- Cough: type? Colour?
- Breathing?
- Heart rate?
- Temperature?
- Name 4 other signs and symptoms
- Dry or productive + phlegm is yellow, green or blood stained
- Difficulty breathing = rapid and shallow
- Tachycardia
- Fever
- General malaise / sweating + shivering / loss of appetite / chest pain
Scoring systems - CPIS
- What does it stand for?
- Give 4 aspects of it
- Clinical pulmonary sepsis score
- Fever
Leukocytosis
Positive sputum culture
Worsening X-ray changes
Oxygenation levels
Scoring systems - CURB 65
- What does the age have to be?
- What are the 4 aspects of it?
- A score of 5 equals to what percentage of mortality?
- Older than 65 years
- Confusion
Uraemia
Respiratory rate
Blood pressure - 57% mortality
Streptococcus pneumoniae
- Gram?
- What shaped cocci?
- Seen in what formation usually?
- Give 3 examples of invasive pneumococcal disease
- Give 3 examples of non-invasive pneumococcal disease
- Gram positive
- Lancet-shaped cocci
- Diplococci
- Septicaemia / pneumonia / meningitis
- Otitis media / sinusitis / bronchitis
Mycobacterium tuberculosis
- Type of aerobe?
- What shaped bacillus?
- Acid?
- Spore forming?
- Why is it difficult to gram stain?
- Division time?
- What kind of tissue does it like?
- Obligate aerobe
- Rod shaped
- Acid fast
- Non spore forming
- Mycolic acid in cell wall
- Slow - 15-20 hours
- Highly oxygenated tissue
Name some risk factors for developing TB disease
Recent TB infection/exposure to people who have had it
Medical conditions that weaken the immune system
HIV infection
Substance abuse
Severe kidney disease
Low body weight
Organ transplants
Latent TB infection
- Signs / symptoms?
- What prevents growth of bacteria?
- Infectious?
- Skin / blood test result?
- Chest X-ray?
- What is required to prevent progression to TB disease?
- None
- Host defences
- Not infectious
- Positive
- Normal
- Treatment
TB disease
- Activation of what?
- Signs and symptoms?
- Infectious?
- Skin / blood test result?
- Chest X-ray? Sputum sample?
- What does it require to resolve it?
- Latent TB
- Present - patient feels sick
- Can spread
- Positive
- Abnormal
- Needs treatment
Name 4 sites of TB infection
Skin and soft tissues
bone and joints
genitourinary tract
disseminated disease
TB transmission
- Exposure to persons with what?
- What from coughs?
- Dust contaminated with what?
- What makes organism resistant to dessication?
- Active TB disease
- Aerosol droplets
- M. Tuberculosis from cough of person with active disease
- Waxy outer coating
TB signs and symptoms
- Temperature?
- Cough?
- Weight?
- Sputum
- Alertness?
- Appetite?
- Chest pain?
- Fever and night sweats
- Persistent cough lasting longer than 3 weeks
- Weight loss
- Blood in sputum
- Fatigue
- Loss of appetite
- Chest pain
What are the 4 methods to diagnose TB?
Skin test
Blood test
Chest X-ray
Microbiological sampling
TB diagnosis
- What is the skin test called?
- What is injected into the forearm in the skin test? The diameter of what is measured?
- What is the blood test called?
- In the blood test, interferon gamma is released upon exposure to what?
- TST = tuberculin skin test
- Tuberculin derived protein. Palpable, raised, hardened area/swelling measured
- Interferon gamma release assays
- Antigens derived from M. Tuberculosis