Microbio Flashcards
What are the sterile areas in the body?
Lungs (lower resp tract)
Blood
Gallbladder
Kidneys
CSF
Joints
Bladder
Pleural fluid
Peritoneal cavity
What areas of the body are colonised with flora?
GI tract
Skin
Oral cavity
Vagina
Urethra
Examples of gram positive cocci
staphylococci
streptococci
enterococci
Examples of gram positive bacilli
b. anthracis
c. diptheria
clostrididia
Examples of gram negative cocci
neisseria
moraxella
Examples of gram negative bacilli
E.Coli
salmonella
shigella
pseudamonas
v.cholerae
Gram positive aerobic cocci in clusters
catalase positive
STAPHYLOCOCCUS
Coagulase positive: s. aureus
Coagulase negative: s. epidermis, s. soprophitious
Gram positive cocci aerobic in chains
catalase negative
STREPTOCOCCUS
alpha haemolytic strep
s. pneumoniae
viridans group strep
beta haemolytic strep
s. pyogenes (Group A)
Group B
Group G
Non-haemolytic strep
Group D (s. bovis)
Examples of spirochaetes
treponema
leptospira
borrelia
How does gram staining work?
differentiates bacteria by the chemical and physical properties of their cell walls through detecting peptidoglycan, which is present in the cell wall of gram-positive bacteria.
PURPLE POSITIVE PEPTIDOGLYCAN
Gram negative anaerobic bacilli
bacteroides
Gram negative aerobic lactose fermenting bacilli
E.Coli
Klebsiella
Gram negative aerobic non lactose fermenting bacilli
salmonella
shigella
proteus
pseudomonas
gram negative aerobic bacilli (lactose fermenting doesn’t apply)
vibrio
campylobacter
helicobacter
haemophilus
Gram positive aerobic bacilli
listeria
bacillus
corynebacterium
Gram positive anaerobic bacilli
Clostridium
Propionibacterium
Ziehl-neelsen/ acid fast positive bacilli
Mycobacteria
What is the process of gram staining?
Crystal violet
Iodine
Decolourisation (negative lose purple at this point)
Counter stain:
- positive stay purple
- negative are pink
How does staph aureus present on blood agar?
gold/yellow
aureus means gold
What is blood agar used for?
medium for lots of bacteria types to grow
description of chocolate agar
blood agar heated at 80 degrees for 5 mins to release nutrients and make growth easier
What is CLED agar used for?
non-inhibitory growth medium
differentiates microorganisms in urine
classification of lactose fermenting (yellow on CLED) and non LF (blue on CLED)
description of MacConkey agar
gram negative bacilli
bile salts inhibit gram positive
lactose fermenting are pink, NLF yellow
Description of gonococcus agar
growth factors for neisseria gonorrhoea
abx and antifungals inhibit growth of other organisms
description of XLD agar
selective to isolate salmonella (red and black) and shigella (red)
what is sabouraud’s agar used for?
culturing fungi
bacteria inhibited by abx in agar
What is the coagulase test used for?
differentiating between pathogenic and non-pathogenic strains of staph
bacteria that produce coagulase clot plasma around them to resist phagocytosis
What is strep pneumoniae sensitive to that other alpha haemolytic streps aren’t?
optochin test
How are beta-haemolytic strep differentiated?
Lancefield grouping
How do beta-haemolytic appear on agar?
completely haemolyse blood cells so have a clear zone
What is serology?
study of antibody responses in the serum
particulary IgG and IgM
What is meningitis?
inflammation of the pia and arachnoid mater
Micro-organisms infect the cerebrospinal fluid (CSF).
What are the 3 symptoms associated with meningism?
stiffness of the neck
photophobia
severe headache
What are common bacterial causes of meningitis?
neisseria meningitis (gram neg diplococci)
strep pneumoniae (gram positive diplococci)
also: e.coli in neonates and haemophilus influenza in infants
What is encephalitis?
inflammation of cerebral cortex
What are the symptoms of encephalitis?
lethargy
fatigue
decreased consciousness
fever
+ meningism = meningo-encephalitis
What virus normally causes encephalitis?
almost always Herpes simplex virus
occasionally Varicella zoster virus, Parvoviruses, primary HIV, Mumps virus, Measles virus
What is a pathogen?
Organism that causes or is capable of causing disease
What is a commensal?
Organism which colonises the host but causes no disease in normal circumstances
What is an opportunistic pathogen?
Microbe that only causes disease if host defences are compromised
What is virulence?
The degree to which a given organism is pathogenic
What is asymptomatic carriage?
When a pathogen is carried harmlessly at a tissue site where it causes no disease
What are some obligate intracellular bacteria?
Rickettsia
Chlamydia
Coxiella
How do beta-lactam abx work?
attack peptidoglycan in cell wall
good in gram positive
Examples of beta-lactams
Penicillins (fluclox is what MRSA is resistant to)
Cephalosporins
Carbapenems
Examples of cephalosporins
broad spectrum
Cefuroxime
Ceftriaxone
Cefotaxime
Example of a beta-lactamase inhibitor?
Co-amoxiclav (amoxicillin-clavulanate)
What can treat MRSA?
Vancomyocin
Examples of macrolide abx + uses
Clarithromycin
Erythromycin
gram positive and atypical pneumonia
When is clindamycin used?
gram positive
cellulitis (penicillin)
necrotising fasciitis
When are tetracyclines used?
e.g. doxycycline
covers staph aureus and strep
doxycycline: anti malaria
What is gentamicin used for?
an aminoglycoside
can be ototoxic and nephrotoxic so requires strict monitoring
used in UTIs and infective endocarditis
What is ciprofloxacin used for?
can be used for gram neg
UTIs
intra-abdo infections
side effects: lowering of seizure threshold, bad in AAA
What abx for UTIs?
Trimethoprim: not in pregnancy as targets folate synthesis
Nitrofurantoin
Examples of abx that affect nucleic acid synthesis
Rifampicin
Metronidazole
Fluroquinolones (cipro)
What abx inhibit folate synthesis?
Trimethoprine
Co-trimoxazole
What abx affect protein synthesis?
aminoglycosides (gentamicin)
Tetracyclines (doxycycline)
Macrolides (erythromycin)
What is C.difficile?
gram positive anaerobic bacilli
What is C.diff infection associated with?
associated with repeated use of antibiotics, proton-pump inhibitors (e.g., omeprazole) and healthcare settings
Which abx are associated with (lead to) c.diff?
Clindamycin
Ciprofloxacin (and other fluoroquinolones)
Cephalosporins
Carbapenems (e.g., meropenem)
How does a c.diff inection present?
diarrhoea, nausea and abdominal pain.
How is a c.diff infection treated?
Oral vancomycin (first-line)
Oral fidaxomicin (second-line)
What is dysentery?
An inflammatory disorder of the GI tract often associated with
- blood and pus in the faeces
- pain
- fever
- abdominal cramp
usually resulting from disease of the large intestine
Symptoms of gastroenteritis
nausea
vomiting
diarrhoea
abdo discomfort
What viruses can cause diarrhoea?
norovirus
rotavirus
What bacteria can cause bloody mucoid diarrhoea?
Clostridium difficile
E.Coli (EIEC, EHEC)
Campylobacter
Salmonella
Shigella
What can cause diarrhoea in a recent traveller?
Giardia
Cryptosporidium
Cyclospora
What are 2 food-borne diarrhoeal causes?
Campylobacter
Salmonella
What causes colonic or dysenteric diarrhoea?
bloody stools, fever, abdominal cramps, and tenesmus.
Shigella
What is HIV postive?
infected with the human immunodeficiency virus (HIV)
When does AIDs occur?
Acquired immunodeficiency syndrome (AIDS) occurs when HIV is not treated, the disease progresses, and the person becomes immunocompromised.
Immunodeficiency leads to opportunistic infections and AIDS-defining illnesses.
What key populations are affected by HIV?
commercial sex workers and their clients
gay men and other men who have sex with men
people who inject drugs
transgender people
Most new cases in sub-saharan africa
What is HIV-1 infection associated with?
progressive decrease in CD4 T-cell count and an increase in viral load leading to clinical AIDS
What is HIV-2 associated with?
more indolent course
largely limited to West Africa
How can HIV be transmitted?
blood
blood products
sexual fluids
other fluids containing blood
breast milk
How are most individuals infected with HIV?
sexual contact
before birth or during delivery
during breastfeeding
when sharing contaminated needles and syringes
How does HIV replicate?
Virus gains entry to cells by attaching to CD4 receptors of T-helper cells
Reverse transcriptase enzyme allows DNA copy from RNA
Virus integrated into cell DNA and replicated
What type of virus is HIV?
RNA retrovirus
What are the risk factors for HIV?
people who inject drugs
gay men and other men who have sex with men
commercial sex worker
transgender women
unprotected receptive intercourse
percutaneous needle stick injury
racial and ethnic minorities
high maternal viral load (mother to child transmission)
What are some symptoms of HIV?
immunodeficiency
fevers and night sweats
weight loss
skin rashes and post-inflammatory scars
oral ulcers
diarrhoea
weight loss
changes in mental status
generalised lymphadenopathy
How does the 4th gen HIV screening test work?
fourth-generation laboratory test for HIV checks for antibodies to HIV and the p24 antigen.
It has a window period of 45 days, meaning it can take up to 45 days after exposure to the virus for the test to turn positive.
What investigations should be run for HIV?
HIV enzyme-linked immunosorbent assay (ELISA): positive
HIV rapid test: positive
HIV PCR: positive
Serum p24 antigen: positive
CD4 count
Genotypic resistance testing
Hepatitis B and C screening
What is an AIDS defining illness?
AIDS defining illnesses associated with end-stage HIV
(CD4 count has dropped to a level that allows for unusual opportunistic infections and malignancies to appear)
What are some examples of AIDS defining illnesses?
- Kaposi’s sarcoma
- Pneumocystis jirovecii pneumonia (PCP)
- Cytomegalovirus infection
- Candidiasis (oesophageal or bronchial)
- Lymphomas
- Tuberculosis
What are the classes of antiretroviral therapy medications?
Protease inhibitors (PI)
Integrase inhibitors (II)
Nucleoside reverse transcriptase inhibitors (NRTI)
Non-nucleoside reverse transcriptase inhibitors (NNRTI)
Entry inhibitors (EI)
How can HIV be monitored?
CD4 count (<200ml more at risk of opportunistic infection)
HIV viral load
What is the usual starting ART for HIV?
two NRTIs (e.g., tenofovir plus emtricitabine) plus a third agent (e.g., bictegravir)
What does treatment in HIV aim for?
Treatment aims to achieve a normal CD4 count and undetectable viral load
Apart from ARTs, what additional management is offered to HIV patients?
- Prophylactic co-trimoxazole is given to all HIV positive patients with a CD4 count under 200/mm3 to protect against pneumocystis jirovecii pneumonia (PCP)
- Vaccinations (not live)
- Yearly cervical smears
- CVD risk management
How can reproductive health be maintained in HIV?
Correct use of condoms protects against spreading HIV.
Effective treatment combined with an undetectable viral load appears to prevent the spread of HIV, even during unprotected sex
What is used in post-exposure prophylaxis for HIV?
- emtricitabine/tenofovir (Truvada) and raltegravir for 28 days. (ARTs)
- given within 72 hours
What is used as pre-exposure prophylaxis in HIV?
emtricitabine/tenofovir (Truvada).
What are the basic BHIVA guidelines for reducing HIV transmission in pregnancy?
Viral load depends on method of brith
- Under 50: normal vaginal
- Over 50: consider pre-labour C section
- Over 400: pre-labour C section
IV zidovudine is given as an infusion during labour and delivery if the viral load is unknown or above 1000 copies/ml
What prophylaxis can be given to babies at risk of HIV from mother?
- Low-risk babies (mother’s viral load is under 50 copies per ml) are given zidovudine for 2-4 weeks
- High-risk babies are given zidovudine, lamivudine and nevirapine for four weeks
What bacteria causes chlamydia?
- Chlamydia trachomatis is a gram-negative bacteria
- Intracellular organism
How is chlamydia diagnosed?
Nucleic acid amplification tests from swab
How is chlamydia treated?
- First line doxycycline 100mg a day
- In pregnancy and breastfeeding: Azithromycin (or other macrolides)
What bacteria causes gonorrhoea?
Neisseria gonorrhoeae is a gram-negative diplococcus bacteria.
Where does gonorrhoea infect and how does it spread?
It infects mucous membranes with a columnar epithelium
- endocervix in women
- urethra
- rectum
- conjunctiva
- pharynx
It spreads via contact with mucous secretions from infected areas
What symptoms may be present in gonorrhoea?
- Odourless purulent discharge, possibly green or yellow
- Dysuria
- Pelvic pain
- testicular pain
How is gonorrhoea diagnosed?
Nucleic acid amplification testing (NAAT) is used to detect the RNA or DNA of gonorrhoea.
Genital infection can be diagnosed with endocervical, vulvovaginal or urethral swabs, or in a first-catch urine sample
What is the management for gonorrhoea?
A single dose of intramuscular ceftriaxone 1g if the sensitivities are NOT known
A single dose of oral ciprofloxacin 500mg if the sensitivities ARE known
What bacteria causes syphilis?
Treponema pallidum
Spirochete (spiral-shaped bacteria)
How does syphilis enter body?
gets in through skin or mucous membranes, replicates and then disseminates throughout the body
How can syphilis be transmitted?
Oral, vaginal or anal sex involving direct contact with an infected area
Vertical transmission from mother to baby during pregnancy
Intravenous drug use
Blood transfusions and other transplants
How does primary syphilis present?
A painless genital ulcer (chancre). This tends to resolve over 3-8 weeks.
Local lymphadenopathy
What can be used to screen for syphilis?
Antibody testing for antibodies to the T. pallidum bacteria
How is syphilis treated?
single deep IM dose of benzathine benzylpenicillin
