Microbiology Flashcards
what are the 2 ways which joints can become infected?
- haematogenous route
- directly following trauma or surgery
how are viruses classified?
- molecular biology now permits classification by genetic sequence and biophysical structure
what does taxonomy describe?
- virus order
- virus family
- subfamily
- type species
- morphology (what they look like)
- genetic material (DNA or RNA)
- envelope
what are the 7 classes of viruses (Baltimore classification of viruses)?
Baltimore classification of viruses…
how would you distinguish between bacterial and viral causes of infection?
- 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)
give an example of a rapid bedside PCR test
- PCR test for influenza A, influenza B, and respiratory syncytial virus (RSV)
- note: test takes 20-90 mins
why would we use an enzyme immunoassay (EIA)?
- to detect antibodies against viruses
- or to detect viral antigens
how does the standard enzyme immunoassay work?
- ‘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
who do you notify about a notifiable disease?
- 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
what happens when you make a notification about a disease?
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
give some examples of notifiable viral infections
- 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
what is a needlestick injury?
- an incident in which the blood of a patient comes into contact with the blood of a health care worker
what are the 3 types of exposure in health care settings associated with significant risk from blood or higher risk body fluids?
- 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
Which Blood Borne Viruses (BBV) could be transmitted in a hospital setting (needlestick injury)?
- 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)
which 2 of the 3 blood borne viruses do we have post exposure prophylaxis (PEP) for?
- Hepatitis B
- HIV
- note: aim to give the PEP within 2 hrs
what is the most common infectious material/body fluid? and name some other infectious materials.
- blood is most common infectious material
- others: semen, vaginal secretions, human breast milk, cerebrospinal fluid (CSF), synovial fluid
what are some non-infectious body fluids?
- urine, vomit, saliva, faeces
- (which are not visibly blood stained)
when is influenza season?
- Winter season (peaks December)
what is influenza?
- 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
what are the complications of influenza infection?
- lower respiratory tract infection (LRTI): or viral pneumonia
- admission to hospital
- death
what defines somebody as ‘high risk’?
- any organ diseases
- any condition compromising respiratory functions (eg. morbid obesity, BMI > 40, age > 65)
- immunosuppressed people
- pregnant women
what is the treatment for influenza and what is the mechanism for how they work?
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
what does quadrivalent mean in terms of vaccines?
- it protects against 4 strains
which type of influenza vaccine are children given?
- quadrivalent live attenuated vaccine (LAIV)
Which type of influenza vaccine is given to over 65 yrs?
- trivalent adjuvanted inactivated vaccine
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
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
describe the pathology of bronchiolitis using the diagram
see diagram…
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
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
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
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
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
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)
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
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
what type of viruses are influenza, SARS-CoV-2, and HIV?
- RNA viruses
what makes HIV incurable?
- HIV reverse transcribe their genome to form double-stranded DNA which integrates into the host genomic DNA (genome)
which type of HIV dominates the current pandemic?
- HIV-1 group M viruses
how is HIV transmitted?
- blood, semen, vaginal secretions, breast milk
- (through vaginal, anal, or oral sex, contaminated needles, IV drug use)
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…)
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
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)
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)
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
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 )
how does somebody acquire AIDS?
- HIV infected patients develop Acquired Immunodeficiency Syndrome (AIDS) in the absence of treatment