Microbiology Flashcards
1
Q
what are the 2 ways which joints can become infected?
A
- haematogenous route
- directly following trauma or surgery
2
Q
how are viruses classified?
A
- molecular biology now permits classification by genetic sequence and biophysical structure
3
Q
what does taxonomy describe?
A
- virus order
- virus family
- subfamily
- type species
- morphology (what they look like)
- genetic material (DNA or RNA)
- envelope
4
Q
what are the 7 classes of viruses (Baltimore classification of viruses)?
A
Baltimore classification of viruses…
5
Q
how would you distinguish between bacterial and viral causes of infection?
A
- Symptoms of both: eg. fever, CNS, respiratory, GI symptoms
- bacterial infection symptoms: persist longer than the expected 10 days a virus tends to last, fever higher in bacterial infection
Have to rely on diagnostic tests to differentiate between the two…
- CRP: raised with bacterial infections
- FBC: neutrophils raised with bacterial infection (lymphocytes and monocytes raised in viral infections)
- blood cultures: can test for presence of bacteria
- PCR: can detect either viral or bacterial
- Cerebrospinal fluid (CSF) count: raised neutrophils points to bacterial (raised lymphocytes points to viral or TB)
6
Q
give an example of a rapid bedside PCR test
A
- PCR test for influenza A, influenza B, and respiratory syncytial virus (RSV)
- note: test takes 20-90 mins
7
Q
why would we use an enzyme immunoassay (EIA)?
A
- to detect antibodies against viruses
- or to detect viral antigens
8
Q
how does the standard enzyme immunoassay work?
A
- ‘capture’ antibody specific for the viral antigen is bound to the surface of the plastic wells
- when the sample is added, viral antigen present in the sample binds to the capture antibody
- when the second antibody is added (with enzyme label) colour change occurs
9
Q
who do you notify about a notifiable disease?
A
- the local health security agency (HSA)
- urgent cases should be reported by phone within 24 hrs
- the HSA then collects these notifications and publishes analyses of local and national trends every week
10
Q
what happens when you make a notification about a disease?
A
HSA undertakes a risk assessment…
- details of significant contacts who might have been exposed
- immunisation history
- epidemiologically linked cases
- factors that make contacts more vulnerable
- potential source of infection
- wider public context
note: the outcome can be isolation, exclusion, post-exposure prophylaxis, immunisation, further lab testing, control measures
11
Q
give some examples of notifiable viral infections
A
- acute poliomyelitis
- acute hepatitis A, acute hepatitis B
- measles
- MERS (Middle East Respiratory Syndrome)
- mumps
- rabies
- rubella
- SARS CoV-2 (Severe Acute Respiratory Syndrome)
- Viral haemorrhagic fever
- Yellow fever
12
Q
what is a needlestick injury?
A
- an incident in which the blood of a patient comes into contact with the blood of a health care worker
13
Q
what are the 3 types of exposure in health care settings associated with significant risk from blood or higher risk body fluids?
A
- Percutaneous injury (most common): (eg. from needles, sharp instruments, bone fragments, significant bites which break the skin)
- exposure of broken skin: eg. abrasions, cuts, eczema (ie. the skin barrier is broken)
- exposure of mucous membranes: eyes and mouth
14
Q
Which Blood Borne Viruses (BBV) could be transmitted in a hospital setting (needlestick injury)?
A
- Hepatitis B virus (HBV): most common
- Hepatitis C virus (HCV)
- Human Immunodeficiency virus (HIV)
- (HIV is the least common as viral load is not big enough)
15
Q
which 2 of the 3 blood borne viruses do we have post exposure prophylaxis (PEP) for?
A
- Hepatitis B
- HIV
- note: aim to give the PEP within 2 hrs
16
Q
what is the most common infectious material/body fluid? and name some other infectious materials.
A
- blood is most common infectious material
- others: semen, vaginal secretions, human breast milk, cerebrospinal fluid (CSF), synovial fluid
17
Q
what are some non-infectious body fluids?
A
- urine, vomit, saliva, faeces
- (which are not visibly blood stained)
18
Q
when is influenza season?
A
- Winter season (peaks December)
19
Q
what is influenza?
A
- an acute viral infection of the respiratory tract
3 types (A, B, C)… - influenza A and influenza B are most common
- note: influenza is highly infectious and incubation period of 1-3 days
20
Q
what are the complications of influenza infection?
A
- lower respiratory tract infection (LRTI): or viral pneumonia
- admission to hospital
- death
21
Q
what defines somebody as ‘high risk’?
A
- any organ diseases
- any condition compromising respiratory functions (eg. morbid obesity, BMI > 40, age > 65)
- immunosuppressed people
- pregnant women
22
Q
what is the treatment for influenza and what is the mechanism for how they work?
A
Neuraminidase inhibitors:
- Oseltamivir (oral)
- Zanamivir (inhaled)
- they work on the surface of the virus’, they block neuraminidase enzymes and therefore the influenza virus cannot detach itself and infect the neighbouring respiratory cell
23
Q
what does quadrivalent mean in terms of vaccines?
A
- it protects against 4 strains
24
Q
which type of influenza vaccine are children given?
A
- quadrivalent live attenuated vaccine (LAIV)
25
Which type of influenza vaccine is given to over 65 yrs?
- trivalent adjuvanted inactivated vaccine
26
what is Respiratory Syncytial Virus (RSV) and which age groups are most commonly affected?
Respiratory Syncytial Virus (RSV) is the major cause of upper and lower respiratory tract infection in children and the elderly
- very infectious
- seasonal: peaks in December
- 2 subgroups: RSV/A, RSV/B
27
how might RSV (respiratory syncytial virus) be transmitted?
RSV is transmiited by repsiratory secretions:
- direct contact
- via fomites (the virus stays on objects for up to 6 hrs)
- by large droplets (entry can occur through contact with nasal mucosa or eyes)
note: the incubation period varies from 2-8 days
28
describe the pathology of bronchiolitis using the diagram
see diagram...
29
what is the characteristic illness caused by RSV and what are the clinical symptoms?
- characteristic illness caused by RSV is bronchiolitis
Clinical symptoms:
- expiratory wheezing
- cough and rhinitis (runny nose)
- cyanosis (blue skin or lips)
- fever only in 50% of infants requiring admission
30
how do you diagnose respiratory syncytial virus (RSV) from other respiratory viral infections?
- all respiratory viral infections present clinically similar
- therefore we need laboratory diagnosis
31
what is the line of management for RSV infection?
- treatment mainly supportive
- if hypoxemia (low blood oxygen), apnoea, and poor oral intake in children <1yr then require hospitalisation
- Antiviral treatment: Ribavirin has been licensed as an aerosol for treatment of RSV in immunocompromised patients
32
how is SARS-CoV-2 transmitted?
- Respiratory droplets
- Hand-to-mucus-membrane contact: eyes, nose, mouth are vulnerable
- Viable for 3 days on solids
- Airborne: cough, talking
- Faecal: viral shedding present in stool and diarrhoea is common
33
what are the symptoms of SARS-CoV-2?
**Normal symptoms...**
- fever, chills, cough, difficulty breathing, fatigue, muscle or body aches, headache, loss of taste or smell, sore throat, congestion or runny nose, nausea, diarrhoea
**More severe symptoms...**
- can develop severe dyspnoea (difficulty breathing) due to viral pneumonia requiring hospitilisation (oxygen needed and endotracheal intubation - tube to assist breathing)
- health can rapidly decline from mild hypoxia to ARDS (Acute Respiratory Distress Syndrome)
- ARDS can lead to multi-organ failure and death
34
how is SARS-CoV-2 diagnosed?
- Nose and throat swab for RT-PCR
- POCT (Point Of Care Testing) for RT-PCR
- LAMP (Loop-mediated isothermal amplification testing): genetic testing
- Antigen tests: lateral flow (not accurate at all)
- Blood tests: anti-N and anti-S antibody against SARS-CoV-2
(remember that early in infection, serological results can show negative results)
35
what is the treatment for SARS-CoV-2?
- asymptomatic and very mild symptoms (abscence of viral pneumonia and hypoxia): no treatment
Patients requiring hospital admission:
- Antiviral-therapy: Molnupiravir, Remdesivir
- Monoclonal antibodies (mAB): Ronapreve (work by coating the spike proteins and virus is then unable to latch onto the human cells in the respiratory system)
- Supportive treatment: low dose glucocorticosteroid, oxygen
36
is SARS-CoV-2 just a respiratory disease?
- No, it is a systemic disease
- it affects all systems of the human body, including the CNS
37
what type of viruses are influenza, SARS-CoV-2, and HIV?
- RNA viruses
38
what makes HIV incurable?
- HIV reverse transcribe their genome to form double-stranded DNA which integrates into the host genomic DNA (genome)
39
which type of HIV dominates the current pandemic?
- HIV-1 group M viruses
40
how is HIV transmitted?
- blood, semen, vaginal secretions, breast milk
- (through vaginal, anal, or oral sex, contaminated needles, IV drug use)
41
what are the most frequent clinical symptoms of HIV?
- fever
- pharyngitis (inflammation of the back of the throat)
- headache
- myalgia (muscle pain)
- arthralgia (joint pain)
- malaise
- non-pruritic (non-itching) maculopapular rash on face and trunk
- generalised lymphadenopathy
- HIV also has systemic and organ-specific manifestations (CNS - HIV dementia complex, Peripheral NS - distal symmetrical polyneuropathy, Respiratory - interstitial pneumonitis, Blood - anaemia, neutropenia...)
42
how is HIV diagnosed?
- CD4 count: low (used to determine stage of HIV progression)
- Serology: HIV test
- HIV-1 viral load after serology: detects the amount of virus present, measured by HIV-1 RNA RT-PCR
43
what does CD4 count measure?
- CD4 count measures the state of a person's immune function
- normal values: 500-1300
- CD4 count determines risk of opportunistic infection (<200)
44
what are the WHO recommended principles for HIV testing (5Cs)?
- informed Consent for testing
- Confidentiality
- Counselling pre and post-testing
- Correct test results
- Connection (linkage to care, treatment, and other HIV services)
45
is there a cure for HIV infection?
- NO!
- However, effective antiretroviral drugs (AVRs) can control the virus and help prevent onward transmission to other people
46
what is the treatment for HIV infection?
- Pre-exposure prophylaxis (PrEP) of HIV is the daily use of ARVs (Antiretroviral drugs) by HIV-negative people to block the acquisition of HIV
- Post-exposure prophylaxis (PEP) is the use of ARVs within 72 hrs of exposure to HIV to prevent infection
( always use 3 or more different antiretroviral drugs in order for the therapy to be most effective )
47
how does somebody acquire AIDS?
- HIV infected patients develop Acquired Immunodeficiency Syndrome (AIDS) in the absence of treatment
48
how is AIDS diagnosed?
- when a HIV positive patient has a CD4 count of less than 200 or the patient is diagnosed with an AIDS-defining condition
49
What is meant by eukaryotic species, prokaryotic species, and viral species?
- eukaryotic species: a group of closely related organisms that breed among themselves
- prokaryotic species: a population of cells with similar characteristics
(clone = population of cells derived from a single cell)
(strain = genetically different cells within a clone)
- viral species: population of viruses with similar characteristics that occupies a particular ecological niche
50
Name 3 key functions of bacteria.
- soil and plant fertilising
- food digestion
- commensalism
51
What shape is E.coli (Escherichia coli)?
- rod-shaped bacterium that lives in the gut of warm-blooded animals
52
Do gram-positive bacteria retain the crystal violet dye?
- yes
53
Common bacteria seen in septic arthritis...
from left to right:
- Staph A (grapes)
- Strep (chains)
- Gram-negative rods (bacilli)
54
Gram positive bacteria (cocci and bacilli).
55
Gram negative bacteria (cocci and bacilli).
56
Examples of mycoses (fungi) (presentation on skin, under bright field light microscopy, on x-ray).
57
Name 2 living characteristics of viruses.
- they reproduce at a fast rate, but only in living host cells
- they can mutate
58
Name 3 non-living characteristics of viruses.
- they are acellular (they contain no cytoplasm or cellular organisms)
- they carry out no metabolism on their own and must replicate using the host cell's metabolic machinery (ie. viruses don't grow and divide, instead the new viral components are synthesised and assembled within the infected host cell)
- the vast majority of viruses possess either DNA or RNA but not both
59
Virus structure thing...
60
What are prions (infectious proteins)?
- prions = protein-containing particles with no detectable nucleic acid
- (highly resistant infectious agent)
- (no inflammation or immune response in affected)
61
How do we measure antibiotic susceptibility?
- create a 'lawn' of bugs
- add filter paper disc with known quantity of antibiotic
- inhibition of growth around disc
- 'cut off' size of zone correlates to concentration of antibiotic in blood following normal dose
62
Name some drug-resistant super bugs.
- **MRSA (methicillin-resistant staphylococcus aureus):** a Staph. A that is methicilin (penicillin, flucloxacillin) resistant
- **Clostridium difficile:** anaerobic bacterium that lives in the gut (broad-spectrum antibiotics can cause it to overgrow)
- ESBL (extended spectrum beta-lactamases) bacteria: gram-negative enterobacteriacae that are resistant to all penicillin-based antibiotics (usually complicate urinary catheters)
- VRE (Vancomycin-resistant enterococcus)
63
What are the 6 main causes of antibiotic resistance?
- over-prescription of antibiotics
- patients not finishing the entire antibiotic course
- overuse of antibiotics in livestock and fish-farming
- poor infection control in healthcare settings
- poor hygiene and sanitation
- absence of new antibiotics being discovered
64
Name four viral infections that can be spread by mosquitoes.
- Yellow fever
- Dengue fever
- Zika
- Japanese encephalitis
65
Give two examples of methods of control for mosquito-borne viral infections and explain how these are effective
- Mosquito nets: act as barrier to prevent biting
- Use of insecticides: toxic to mosquitoes/kills them
- Genetic modification of mosquitoes: causes failure to reproduce
66
Patient has pyrexia, chills, and a sore throat, what is the most likely diagnosis?
- Upper respiratory tract infection
67
A 7 year old boy falls and has a deep scratch, pus is oozing out of it, what inflammatory cells are most likely to be present in the pus?
- Neutrophils
68
describe the process of tissue preparation for microscopy
- preserve the tissue using formalin
- tissue processing which removes water from the tissue by adding ethanol (to replace the water) and then adding xylene (which removes ethanol)
- embed in paraffin wax (removes xylene and solidifies into a paraffin block)
69
describe the process of light microscopy once the tissue has been prepared
- paraffin slice mounted on glass slide
- stained, easier to see under microscope
- most common stain is Hematoxylin and Eosin (H&E)
- note: Hematoxylin stains nuclei a purplish blue, Eosin stains cytoplasm pink
70
what is the most commonly used type of light microscopy?
- bright field microscopy
71
when would we use frozen sections of tissue and why?
- during surgery
- for urgent analysis (less accurate results however)
72
what is used to culture bacteria and fungi?
- solid nutrient media (agar-based)
73
why do we use PCR?
- to amplify a specific sequence of DNA from the genome of an organism
- eg. can be used to amplify known section of chlamydia genome from a swab or urine sample
74
explain the steps of PCR?
- denaturation: heat to 95ᵒϹ breaks hydrogen bonds between the two strands of DNA
- annealing: cool to 55ᵒϹ, allows primers to bind to their complementary sequences on the DNA
- extension: heat up to 70ᵒϹ and TAQ polymerase binds to primers and uses free nucleotides to assemble new strands of DNA
75
how does reverse-transcriptase PCR differ from normal PCR?
- uses RNA instead of DNA (Uracil instead of Thymine)
- uses reverse transcriptase to make a complementary DNA strand from the RNA, then normal PCR is carried out on the c-DNA strand
76
describe the gram stain and how it works
- the gram stain is used to study bacteria
- crystal violet dye and iodine bind to cell wall
- gram positive bacteria retain the stain when acetone is added and remain purple
- gram negative bacteria lose the purple stain when acetone is added and appear colourless until stained with a pink counterstain (safranin)
- this is due to gram positive bacteria having a thicker peptidoglycan cell wall so retains the stain
77
describe acid-fast stain and why it is used
- used for organisms that do not readily take up the gram stain (eg. mycobacteria ( TB ), have waxy cell walls)
- acid and alcohol are added to the cells after they have been stained through another method (Ziehl Neelson stain)
- if the cells withstand decolourisation from the acid and alcohol then they are known as acid and alcohol fast
78
what bacteria is commonly found on decaying meat?
- Staphylococcus saprophyticus
79
is Staph. saprophyticus gram positive or negative
- gram positive
80
how can infectious agents be transmitted? (4 types)
- human to human spread (horizontal, and vertical transmission mother to foetus )
- animal to human
- environment to human (airborne, water, fomites)
- healthcare-acquired
81
what is meant by the term virulence?
- virulence is a measure of the pathogenicity of a microorganism
- an organism is considered highly virulent if a small number of microorganisms can cause disease
82
what are viruses and how do they work?
- viruses are intracellular parasites which depend on host proteins for replication
- they enter a cell, replicate, generate viral proteins, assemble the viruses, evade the host's defence, and disperse to continue in the environment
83
how are viruses classified?
- by the genome:
- single stranded RNA or double-stranded RNA
- single stranded DNA or double-stranded DNA
84
what is chicken pox caused by?
- the Varicella Zoster virus
85
how does shingles occur?
- the chicken pox virus (Varicella Zoster virus) causes shingles by becoming reactivated after being dormant in the nervous system for so long
- it can be triggered by a weakened immune system, stress, or by old age
86
what is the virus responsible for causing flu?
- influenza
87
what are some other common viruses?
- measles
- hepatitis
- human papilloma virus
- mumps
- ebola
- herpes
88
what are the key features of a virus?
- have genetic material (DNA or RNA)
- no cell membranes, cytoplasm, or organelles
- cannot independently synthesise macromolecules (depends on host cell)
- genetic material packed in capsules
89
what are prions, and what are the key features of a prion?
- infectious proteins
- no nucleic acids
- consist only of proteinacious infectious particles
90
what are Koch`s Postulates to establish pathogenicity of an organism ?
( four stages )
1. the microorganism found in abundance in diseased host (but not in healthy tissue)
2. the microorganism must be isolated from a diseased organism and grown in pure culture
3. the cultured microorganism should cause disease if introduced into a healthy host
4. the microorganism must be re-isolated from the inoculated diseased host and be identified as being identical to the original causative microorganism
91
name 2 common gram-positive bacteria
- staphlococcus aureus
- strep. pneumoniae
92
name 2 common gram-negative bacteria
- E. Coli
- Klebsiella
- Salmonella
- Pseudomonas
93
name 3 factors in a host that may predispose to infection
- extremes of age
- diabetes
- immune suppression eg steroids
- broken skin ( wound, post surgery, iv cannula )
- malnutririon
94
give 2 examples of hospital acquired infection
- UTI from catheter
- Clostridium difficile from excess antibiotic use
- MRSA post surgery or in central lines
95
describe basic infection prevention principles in healthcare
- hand hygiene
- appropriate PPE
- sterile technique eg for procedures ( ANTT )
- safe disposal of sharps
- isolating infected patients
96
what are the peri operative measures of safeguarding against infection ?
( name four )
- operating theatre air quality (eg. laminar flow for orthopaedic)
- sterile equipment
- sterile PPE
- antibiotic prophylaxis ( give before procedure )
- skin disinfection ( 5% chlorhexidine )
97
what organisms can be transmitted by needlestick injury ? name 3
- HIV
- Hepatitis B
- Hepatitis C
98
how do you manage a needlestick injury ?
- wash site with soap and water
- puncture wound should be allowed to bleed
- check immunisation status eg hep B
- blood tests for exposure
- consider post exposure prophylaxis eg immunoglobulin
99
name some mechanisms of action of antibiotics and an example for each
- **inhibit cell wall synthesis:** beta lactam eg penicillins, vancomycin
- **inhibit protein synthesis:** aminoglycosides (gentamicin), macrolides (erythromycin)
- **inhibit DNA replication:** quinolones
- **inhibit folic acid metabolism:** trimethoprim
100
how does antimicrobial resistance affect management of infection (4 things) and how can it be tackled (3 ways)?
- can make treating infections difficult, longer hospital stays, higher costs, increased deaths
- tackle : antibiotic stewardship ( careful use ), monitor organisms, develop new treatments
101
name some notifiable diseases ( 3 )
COVID-19
Monkeypox
Malaria
food poisoning : salmonella, campylobacter
TB
( + anything we immunise against : tetanus, measles, diptheria...)
( list on www.gov.uk )
102
how do you report a notifiable disease ?
send form to the `proper officer` when disease is suspected
( don`t wait for laboratory confirmation )
notification forms on www.gov.uk
103
name a cause of an STI in 4 different pathogen classifications and how you would test for them
- viral : herpes simplex 1 and 2 ( PCR ) , HIV ( serology ) , human papilloma virus
- bacterial : neisseiria gonnorhoea ( gm negative stain, culture ), syphilis / treponema pallidum ( serology ), chalmydia
- fungal : candida albicans ( culture )
- protozoa : trichromonas vaginilis ( microscopy, culture )
104
discuss consent framework for notifying STDs and legal requirements
- legal duty to notify disease confidentially
- duty to inform partners of index case ( in public interest )
- should inform index case that going to do it, their consent not required
( GMC backs this , has guidance eg you may protect unborn baby )
105
what are the mechanisms for haematogenous spread of organisms and what infections can be caused ?
spread of organism to distant site eg osteomyelitis, can be vertebral or intervetebral
106
Cellulitis image...
107
How is a bacterial infection usually acquired in a UTI, what are the 3 typical symptoms of a UTI, and what is the most common causative organism of a UTI, and what is the laboratory confirmation of a UTI?
- bacterial infection is usually acquired by the ascending rute from the urethra to the bladder (infection may then proceed to the kidney)
- symptoms: dysuria, urgency, frequency
- most common causative organism: gram-negative rod Escherichia coli
- lab confirmation: MSU sample (midstream)
108
What is pneumonia and what are the symptoms of pneumonia?
- pneumonia is a lower respiratory tract infection (LRTI)
- symptoms: fever/sweating/chills, productive cough, shortness of breath, difficulty breathing
109
What is the most common outcome of gastrointestinal tract infections and what is the most common cause of food-associated diarrhoea?
- Diarrhoea is the most common outcome of GI infections
- Salmonellae (Campylobacter close second)
110
What is the most common causative organism of hospital diarrhoea, and what is the most common cause of diarrhoea worldwide?
- Hospital diarrhoea: Clostridium difficile
- Worldwide: Noroviruses (causes diarrhoea and vomiting)
111
Chain of infection diagram...
112
What is the causative organism of malaria?
- Plasmodium
113
What is the most dangerous complication of malaria?
- cerebral malaria: convulsions, reduced consciousness, then coma
- can also get severe anaemia
114
What is the treatment for malaria?
- IV artesunate (in combination with other antimalarials)
115
Are these vaccines 'Active bacterial', 'Active viral', or 'Passive' (pneumococcal, pertussis, HiB vaccines, meningococci, MMR, hep B, use of immunoglobulins).
- **Active bacterial:** pneumococcal, pertussis, HiB vaccines, Meningococci
- **Active viral:** MMR, hep B
- **Passive:** use of immunoglobulins
116
The childhood vaccination schedule...
- **primary immunisations (8, 12, 16 weeks):** 6 in 1 (tetanus, diphtheria, polio, pertussis (whooping cough), HiB, hep B)
- **8, 12 weeks:** oral rotavirus
- **8,16 weeks:** men B
- **12 weeks:** pneumococcal
- **BCG (for TB):** for at risk babies
- **RSV:** for premature and at risk babies
- **12 and 13 months:** MMR, men B, men C, pneumococcal, HiB
- **from 2 yrs:** nasal influenza
- **pre-school (3 yrs 3 months):** second MMR, 4 in 1 (tetanus, diphtheria, polio, pertussis)
- **year 8:** HPV (2 doses 6 months apart)
- **year 9:** 3 in 1 (dip, tet, polio), meningitis A C W Y
- **note:** live vaccines are rotavirus, nasal influenza, BCG, MMR
(note: varicella zoster virus is live)
(RSV, rabies, tetanus: post-exposure IgG)
(live: yellow fever, oral typhoid)
117
Prokaryotic cells vs eukaryotic cells...
118
Viral structure...
119
Prokaryotic vs eukaryotic cells diagram...
