Microbiology Revision
Medical microbiology can be considered a subset of biomedicine
Biomedical ethics – protecting individuals with autonomy, justice, beneficence, and non-
maleficence
Communicable disease – Can be spread
- Infection can be important in the life cycle
- Infection cycles are linked to the tissues they infect; important in finding out diagnosis
and treatment
Non-communicable disease – Cannot be spread (genetics, diet)
Cyclic manner – occurring in circles, over and over
Understanding transmission – how contact occurred, how infection established, how
pathogen exists in host
External epithelia transmission
Pathogens tend to spread via mucosal epithelium instead of external epithelium, unless
transmitted via arthropods
Fungi that infect external epithelia are opportunistic, transmission via fomites and direct
contact. Only infect in the absence of a functioning immune system.
Arboviruses (arthropod borne viruses)
- Mosquitos, sandflies, ticks.
- Yellow fever – 17D vaccine available, transmission from humans -> monkeys through
mosquitos, tropical and subtropical regions
- Dengue fever – replicates in a range of host cells, general virus symptoms, dengue shock
syndrome.
- Chikungunya virus infection (CHICKV) – Togavirus in Africa and Asia, transmission through
mosquitos
- Zika virus – Flavivirus spread by mosquitos, can lead to congenital complications through
vertical transmission (i.e., foetal microcephaly), can also be sexually transmitted
Respiratory and GI tract transmission
Cleaning mechanisms - Mucus, ciliary action, and swallowing / peristaltic movements
Bile also possesses antibacterial activity because bile salts disrupt membranes, denature
proteins, and damage DNA
Firm attachment – attachment of microorganisms to epithelial cells, mainly through cellular
receptors. Evades cleaning mechanisms
- Influenza virus attaches to sialyloligosaccharides (oligos containing sialic acid) via the
viral haemagglutinin.
- Rhinoviruses attaches to ICAM-1 via the viral capsid protein.
- M. pneumoniae attaches to neuraminic acid.
- Strep. pneumoniae attaches to sequences within glycolipids.
Direct disruptions – evolved strategies to disrupt cleansing mechanisms (i.e., ciliostatic
substances are cytotoxins that some species use for this)
Helicobacter pylori is capable of counteracting stomach acid by releasing ‘large’ volumes of
urease. They produce ammonia from urea , which neutralises the acidic environment locally.
, Enteric infections of the GI tract almost always cause diarrhoea
Urogenital tract transmission
Women have an acidic pH of 5.0 , but no proper cleaning mechanism
Bartholin’s glands secrete vaginal mucus
Eye transmission
Mucus membrane is situated along the sclera (whites), where pathogens usually invade
Most invaders are adenoviruses , as well as strep pneumonia and staph aureus
Keratitis – inflammation of the cornea caused by herpes simplex or pseudomonas, can
sometimes be fungal (aspergillus, fusarium) – recent reports of acanthamoeba!
Horizontal transmission – occurs across individuals via any route (water, air, food, etc.)
Vertical transmission – occurs down a generation, like mother to offspring.
- Prenatal: typically, via the placenta (HBV, syphilis)
- Perinatal: via birth canal (conjunctivitis)
- Postnatal: via milk/blood (CMV, HIV, HBV).
Pathogenesis in transmission occurs directly or indirectly:
- Directly: the microorganism causes disease (i.e., to enhance transmission – causing
diarrhoea via cytolysis to spread oocyte)
- Indirectly: the immune system reacts to the pathogen, causing unintended damage
Eukarya – Animalia, Plantae, Fungi, Protists (which are unofficially their own kingdom,
but still officially eukaryotes)
- Identification of fungi via culturing typically involves visual analysis (colony colour,
analysis of structures, and/or biochemical tests).
Autotrophic protists - using pigments to harness solar energy and convert it into
simple carbohydrates (unicellular algae, mainly found in lakes and ponds?)
Heterotrophic protists – Consume other organisms for food (amoeba)
Diagnosis
When pathogens can’t be cultured, microscopy can be used – quicker, more efficient.
However, you need extra techniques (gram staining, urinalysis)
Some helminth eggs can be identified in the faeces itself
Protozoa (includes protists) don’t really need culturing; they can be observed based on
morphology and light microscopy
Acid-fastness is a physical property of certain bacterial and eukaryotic cells, as well as some
sub-cellular structures, specifically their resistance to decolorization by acids during
laboratory staining procedures. This trait is mostly found on mycobacterium
Acid-fast stains used for mycobacterium (the ziehl-neelson stain), staining cells with
carbolfuchsin and then treating with acid (non-acid-fast cells don’t retain colour.
, Gram staining used for morphological analysis and getting information on the bacterial cell
wall
- Gram positive has a cell wall (lipoteichoic acid)
- Gram negative has a lipopolysaccharide layer (O antigen)
Fluorochrome stains – used for some acid-fast bacilli and mycobacterium , fluorescing under
ultraviolet light. Antibodies can be conjugated with fluorophores, so they bind and indicate
the presence of microorganisms
Molecular methods can be used to detect microbial antigen
- Latex agglutination (latex particles bind to specific antibodies)
- Latex is a carrier molecule, but can be changed along with the antibodies depending on
the microorganism
- Streptococcus pneumoniae in CSF and urine - detection of capsular antigen.
- Cryptococcus neoformans in CSF and urine - again, detection of capsular antigen.
Immunoassays: quantifying antigen concentrations
Western blotting: detects specific proteins (i.e., prions) , sometimes using enzymes
- Can be used to detect BSE (mad cow disease) prion
- Can detect E6 and E7 oncoproteins in HPV
PCR: detects microbials at low concentrations, as well as viruses which cannot be cultured.
Can include serotyping (detailed analysis of the microorganism).
Real-time PCR: same as regular PCR, but uses a florescent probe. The probe contains a
quencher and a reporter, and when separated from the quencher, the reporter will
fluorescence. This fluorescence provides a quantitative measure.
Detection of specific antibodies can be flawed, as they’re not usually shown straight away,
making it likely for false negatives to occur
Medical microbiology can be considered a subset of biomedicine
Biomedical ethics – protecting individuals with autonomy, justice, beneficence, and non-
maleficence
Communicable disease – Can be spread
- Infection can be important in the life cycle
- Infection cycles are linked to the tissues they infect; important in finding out diagnosis
and treatment
Non-communicable disease – Cannot be spread (genetics, diet)
Cyclic manner – occurring in circles, over and over
Understanding transmission – how contact occurred, how infection established, how
pathogen exists in host
External epithelia transmission
Pathogens tend to spread via mucosal epithelium instead of external epithelium, unless
transmitted via arthropods
Fungi that infect external epithelia are opportunistic, transmission via fomites and direct
contact. Only infect in the absence of a functioning immune system.
Arboviruses (arthropod borne viruses)
- Mosquitos, sandflies, ticks.
- Yellow fever – 17D vaccine available, transmission from humans -> monkeys through
mosquitos, tropical and subtropical regions
- Dengue fever – replicates in a range of host cells, general virus symptoms, dengue shock
syndrome.
- Chikungunya virus infection (CHICKV) – Togavirus in Africa and Asia, transmission through
mosquitos
- Zika virus – Flavivirus spread by mosquitos, can lead to congenital complications through
vertical transmission (i.e., foetal microcephaly), can also be sexually transmitted
Respiratory and GI tract transmission
Cleaning mechanisms - Mucus, ciliary action, and swallowing / peristaltic movements
Bile also possesses antibacterial activity because bile salts disrupt membranes, denature
proteins, and damage DNA
Firm attachment – attachment of microorganisms to epithelial cells, mainly through cellular
receptors. Evades cleaning mechanisms
- Influenza virus attaches to sialyloligosaccharides (oligos containing sialic acid) via the
viral haemagglutinin.
- Rhinoviruses attaches to ICAM-1 via the viral capsid protein.
- M. pneumoniae attaches to neuraminic acid.
- Strep. pneumoniae attaches to sequences within glycolipids.
Direct disruptions – evolved strategies to disrupt cleansing mechanisms (i.e., ciliostatic
substances are cytotoxins that some species use for this)
Helicobacter pylori is capable of counteracting stomach acid by releasing ‘large’ volumes of
urease. They produce ammonia from urea , which neutralises the acidic environment locally.
, Enteric infections of the GI tract almost always cause diarrhoea
Urogenital tract transmission
Women have an acidic pH of 5.0 , but no proper cleaning mechanism
Bartholin’s glands secrete vaginal mucus
Eye transmission
Mucus membrane is situated along the sclera (whites), where pathogens usually invade
Most invaders are adenoviruses , as well as strep pneumonia and staph aureus
Keratitis – inflammation of the cornea caused by herpes simplex or pseudomonas, can
sometimes be fungal (aspergillus, fusarium) – recent reports of acanthamoeba!
Horizontal transmission – occurs across individuals via any route (water, air, food, etc.)
Vertical transmission – occurs down a generation, like mother to offspring.
- Prenatal: typically, via the placenta (HBV, syphilis)
- Perinatal: via birth canal (conjunctivitis)
- Postnatal: via milk/blood (CMV, HIV, HBV).
Pathogenesis in transmission occurs directly or indirectly:
- Directly: the microorganism causes disease (i.e., to enhance transmission – causing
diarrhoea via cytolysis to spread oocyte)
- Indirectly: the immune system reacts to the pathogen, causing unintended damage
Eukarya – Animalia, Plantae, Fungi, Protists (which are unofficially their own kingdom,
but still officially eukaryotes)
- Identification of fungi via culturing typically involves visual analysis (colony colour,
analysis of structures, and/or biochemical tests).
Autotrophic protists - using pigments to harness solar energy and convert it into
simple carbohydrates (unicellular algae, mainly found in lakes and ponds?)
Heterotrophic protists – Consume other organisms for food (amoeba)
Diagnosis
When pathogens can’t be cultured, microscopy can be used – quicker, more efficient.
However, you need extra techniques (gram staining, urinalysis)
Some helminth eggs can be identified in the faeces itself
Protozoa (includes protists) don’t really need culturing; they can be observed based on
morphology and light microscopy
Acid-fastness is a physical property of certain bacterial and eukaryotic cells, as well as some
sub-cellular structures, specifically their resistance to decolorization by acids during
laboratory staining procedures. This trait is mostly found on mycobacterium
Acid-fast stains used for mycobacterium (the ziehl-neelson stain), staining cells with
carbolfuchsin and then treating with acid (non-acid-fast cells don’t retain colour.
, Gram staining used for morphological analysis and getting information on the bacterial cell
wall
- Gram positive has a cell wall (lipoteichoic acid)
- Gram negative has a lipopolysaccharide layer (O antigen)
Fluorochrome stains – used for some acid-fast bacilli and mycobacterium , fluorescing under
ultraviolet light. Antibodies can be conjugated with fluorophores, so they bind and indicate
the presence of microorganisms
Molecular methods can be used to detect microbial antigen
- Latex agglutination (latex particles bind to specific antibodies)
- Latex is a carrier molecule, but can be changed along with the antibodies depending on
the microorganism
- Streptococcus pneumoniae in CSF and urine - detection of capsular antigen.
- Cryptococcus neoformans in CSF and urine - again, detection of capsular antigen.
Immunoassays: quantifying antigen concentrations
Western blotting: detects specific proteins (i.e., prions) , sometimes using enzymes
- Can be used to detect BSE (mad cow disease) prion
- Can detect E6 and E7 oncoproteins in HPV
PCR: detects microbials at low concentrations, as well as viruses which cannot be cultured.
Can include serotyping (detailed analysis of the microorganism).
Real-time PCR: same as regular PCR, but uses a florescent probe. The probe contains a
quencher and a reporter, and when separated from the quencher, the reporter will
fluorescence. This fluorescence provides a quantitative measure.
Detection of specific antibodies can be flawed, as they’re not usually shown straight away,
making it likely for false negatives to occur
