bacteria, virus, parasite, fungi Flashcards
what are the 3 domains of life?
bacteria - prokaryote
archaea - prokaryote
Eucarya - eukaryote
what is the difference between sterile and non-sterile sites? give examples:
Sterile sites i.e. contain no microorganisms
Brain
Heart
Liver
Kidney
Non-sterile sites i.e. contain microbiomes
Mouth
Oesophagus
Lungs
Stomach
Intestine
what are the common specimen types of different bacterial cultures?
Mid stream specimen of urine (MSSU) – urinary tract infection.
Sputum – lower respiratory tract infection.
Throat swab – tonsillitis/pharyngitis.
Swabs – wound infection, genital tract infection.
Faeces – infectious diarrhoea.
Blood culture – septicaemia (sepsis).
Cerebrospinal fluid (CSF) – meningitis.
Aspirate of pus – abscess. (drainage of abscess)
Bone – osteomyelitis.
what is the role of microscopy in diagnosing bacterial infections where you don’t have to stain them?
1- to see white blood cells (in urine, CSF)
Lymphocytes in CSF → Viral meningitis
Polymorphs in CSF → Bacterial meningitis
what is the role of microscopy in diagnosing bacterial infections where you have to stain them?
to see parasites (in faeces)
Different parasites can be recognised according to size
- Gram stain - to visualise bacteria and yeasts/fungi
- Special stains
- Ziehl-Neelsen stain or auramine stain for Mycobacteria
why is light microscopy not used to identify viruses?
- Viruses are not visible in light microscopy
How do you interpret the results after culturing organisms and performing susceptibility tests?
i.e. the measurement of the susceptibility of bacteria to antibiotics
1- Knowledge of commensal flora
e.g. if you got a wound swab from the skin you should know the normal skin flora.
2- Knowledge of common pathogens
e.g. common pathogens in a site on the body
what is healthcare-associated infection?
infections that occur in a healthcare setting (such as a hospital) that a patient didn’t have before they came in.
ONSET - 48H
HIC - Most common bacteria:
* Staphylococcus aureus bacteraemia
* Clostridium difficile infection
HIC - Most common virus:
* Norovirus
HIC - Multi-drug resistant organisms:
* e.g. MRSA, VRE, ESBL, CPE
How are viruses detected from clinical samples?
Molecular methods i.e. real-time/multiplex PCR
PCR → only detects sections of viral RNA/DNA
Antigen detection
Serology to detect antibodies and determine immunity
Two classes of antibodies:
IgM → occurs initially at the start of viral infection
IgG → comes later & confers long-term immunity
what are the components that make up a bacteria’s surface?
Cytoplasmic membrane - is a very thin, elastic and semi-permeable membrane around the bacterial cell contents.
Cell wall - is a permeable, rigid wall, covering bacteria, it gives the cell strength and shape.
Outer membrane - a component of the Gram-negative cell wall.
what are the diagnostic principles in parasitology?
Microscopy of different life cycle stages e.g.
* parasites, cysts and ova in faeces
* blood films for malaria
Culture is rarely possible for parasites, mostly for bacteria.
Serology is sometimes useful & important for reference laboratories.
What is the appearance of the gram stain under light microscopy of gram-negative/ positive?
Gram Positive → Purple
Gram Negative → Red/Pink
what are the characteristics of the gram-positive/ negative cell wall?
Gram-positive cell wall contains a thick Peptidoglycan layer.
gram-negative cell wall contains a thin Peptidoglycan layer and an Outer membrane
what is the cell wall? what do antibiotics do to the cell wall?
made of peptidoglycans, it is strong and relatively rigid & maintains its shape.
Antibiotics interfere with the construction of cell wall peptidoglycans i.e. penicillin
→ penicillin binds to proteins on the cell wall to inhibit cell wall synthesis
what are the 3 bacterial shapes?
Spherical e.g. cocci
Rod-shaped e.g. bacilli
Spiral & corkscrew
what are peptidoglycans?
they are N-acetylglucosamine acid and N-acetylmuramic acid molecules linked alternately in a chain, with short peptides forming cross-links.
found on the cell wall
what is the lipopolysaccharide outer membrane?
It’s a structure that is only present in Gram-negative bacteria. It protects peptidoglycans from bile salts and lysozymes.
It blocks many antibiotics from getting into the bacterial cell.
what is lipid A?
one of the components of Lipopolysaccharide that forms endotoxin.
When endotoxin is released into the bloodstream, it may give rise to endotoxic shock
It is a clinical state characterised by fever and low blood pressure
what are 2 types of capsules?
There are two types of capsules (polysaccharide layer):
- Rigid capsule → prevent phagocytosis
- Slimy capsule → forms biofilms and microcolonies
what is a flagellum? what are the 4 different types?
a long thin filament twisted spirally in an open regular waveform.
Provides motility to bacteria to move to an optimal environment
1- A-Monotrichous → one flagellum from one side
2- B-Lophotrichous → flagella from one side
3- C-Amphitrichous → flagella from both sides
4- D-Peritrichous → flagella all over
what are fimbriae?
they are short filaments that are far more numerous than flagella.
Important in mediating adhesion between bacterial cells and host cells.
Describe how bacteria replicates:
A bacterial cell has a single chromosome with no nucleus.
It replicates by binary fission to produce two daughter cells.
It may contain Plasmids which are DNA structures that replicate independently of the chromosome.
how does genetic variation occur in bacteria?
Genetic variation in bacteria occurs through:
1- Spontaneous mutation in the chromosome
2- Transfer of DNA through Plasmids
what is bacterial conjugation?
it’s a mechanism of gene transfer that requires direct contact between donor and recipient cells.
Steps:
F pilus forms a pathway between Donor cell F+ and Recipient cell F- through a receptor.
A single strand of the Plasmid enters the Recipient cell F-
Then synthesizes a complementary plasmid to the one in Donor cell F+
F- becomes F+
what are bacteriophages?
a type of virus that infects bacteria.
All of them are composed of a nucleic acid molecule that’s surronded by a protein structure.
It hijacks the cell machinery and makes it produce viral components until it bursts through lysis
what is sporulation?
is a highly resistant process whereby dormant bacteria are formed.
This process preserves the genetic material of bacteria when conditions are lethal and inhospitable.
Each normal (vegetative) cell forms one spore (dormant)
what are ribosomes? how are the divided?
they are structures in the bacterial cell cytoplasm, they consist of RNA and associated proteins.
Their role is to synthesize proteins.
They are divided into subunits, measured by the unit Svedberg.
70S ribosomes → made up of large (50S) and small (30S) subunits
30S subunit → made up of (16S) subunit - which is used for bacterial identification
how do you detect and culture bacteria from a patient? 4 steps
1- Get a specimen from a patient
2- Staining to determine whether it’s gram-positive or gram-negative infection to select the appropriate antibody
3- Incubation of a small amount of specimen onto agar plates at 37 C
4- Formation of bacterial colonies
Use a light microscope with an oil immersion lens (x1000) & staining to see the bacteria
what are the 2 bacteria classifications?
1- Phenotypically → i.e. relating to observable physical properties
e.g.
- Gram stain (gram + & gram -)
- Growth requirements
(aerobic & anaerobic & microaerophilic) - Serologic
- Mass spectrometry (protein profiling)
2- Genotypically → i.e. relating to DNA (used more in modern times)
e.g.
- Ribosomal RNA sequence analysis
- Whole genome sequencing
what is a parasite? how are they classified?
an organism that lives in or on another organism (host) and derives its nutrients at the expense of this host.
They are classified by:
- Cellular structure
- Life cycle - complex stages
An organism which acts as an intermediate host for a parasite is known as a Vector
what are the 3 classifications of parasites? give 3 examples of each:
Protozoa → malaria & amoebae & flagellates
- Helminths (worms) → roundworms & tapeworms & flukes
- Ectoparasites (outside of body) → lice & ticks & mites
what are protozoa? how do they replicate?
Protozoa are microscopic, single-celled organisms, that can be free-living or parasitic.
They can multiply in humans and they transmit through two routes:
1- Live in a human’s intestine → faecal-oral route
2- Live in the blood or tissue of humans → insect vector
what is malaria?
Malaria is a protozoan infection, the most common cause of death by parasitic infection globally, usually found in the tropics and subtropics.
It is a mosquito-borne preventable disease caused by a parasite called Plasmodium
Vector → Anopheles mosquito (female)
non-specific symptoms i.e. fever, chills, headache, sore throat
Blood films → parasitaemia
what is amoebic dysentery?
a protozoan infection that causes bloody diarrhoea.
It is caused by an invasion of Entamoeba histolytica in the gut wall.
Contraction of infection - through ingestion of faecal matter through contaminated food
i.e. Faecal-oral route
Clinical relevance:
- Intestinal and extra-intestinal infections
- Liver abscess in late disease
what are helminths? how do we diagnose?
To diagnose we look into stool samples of patients and check for worm eggs
Most are transmitted through the faecal-oral route but use an intermediate vector
Common in resource-poor / hygiene-poor areas
1- Nematodes → Roundworms
2- Cestodes → Tapeworms
3- Trematodes → Flatworms
describe nematodes (roundworms)
Enterobiasis (pinworm/threadworm) → 1cm, threadlike, very common in children
Causes anal itch
Diagnosis → sellotape on perianal region and check for eggs under a microscope
Treatment → anti-helminth tablets kill adult worms
[2] Ascaris lumbricoides/Ascaris Infection → 15-35 cm, largest nematode.
Often asymptomatic, may cause failure to thrive in children / blocking the small intestine & bile duct
→ Bowel obstruction
what are cestodes?
Cestodes are long, segmented tapeworms. e.g.
[1] Taenia saginata (beef)
[2] Taenia solium (pork)
Can migrate to the brain from the gut and make cysts causing → Neurocysticercosis
[3] Echinococcus
- carried by dogs, wolves, foxes (intermediate host)
- ## humans ingest eggs in dog faeces → eggs hatch and form cysts in the liver.
Eating larval cysts}} (intermediate host) that are found in raw or undercooked meat.
Adult tapeworms in humans (definitive host) → eggs excreted through human stool
Animals, e.g. pigs/cows, eat grass with human stool and the cycle continues.
The life cycle of worms can only keep going if animals are eating grass-containing eggs
i.e. poor sanitation/hygiene
what are trematodes?
Different species cause human infection in various body sites
i.e. Blood, Lung, Liver, Pancreas, Intestines
[1] Schistosomiasis, has three types:
- S. haematobium (bladder)
- S. mansoni (intestinal)
- S. japonicum (intestinal)
- endemic in tropical areas i.e. 200 million people affected annually
- Acquired by swimming in infected freshwater - development in snails (intermediate host)
- Swimmer’s itch is a common sign
- Can lead to liver failure & bladder cancer if untreated
what are ectoparasites?
they are parasites that live outside the body.
Usually insects with six legs or arachnids with eight legs.
how is malaria diagnosed?
Through blood microscopy
Thick and thin blood films under a microscope
Severity of malaria → number of red blood cells infected by Plasmodium parasites
We can then determine which type of treatment to use.
what diagnostic principles in parasitology?
Diagnostic principles in Parasitology: (deep)
[1] Definitive diagnosis → identify parasites in host tissue or faeces/urine
[2] Blood microscopy e.g. thick and thin blood films for malaria
[3] Stool microscopy is used to find enteric pathogens
e.g. Ova, cysts and parasites
[4] Helminth infection
- Eosinophilia → (high eosinophil levels)
- Elevated IgE → (high IgE levels to fight parasitic infections)
[5] Indirect testing (antibody & antigen testing)
- Serology → immune testing
- Rapid diagnostic tests
what is a fungus?
a chemo-organotrophic eukaryote that lacks chlorophyll and forms spores.
Cell wall → contains polysaccharides, often chitin or glucan, and it absorbs nutrients.
Membrane → contains ergosterol - major sterol
Classification is based on morphology
can infect plants and animals
what are the 3 main groups of the fungal kingdom?
Basidiomycetes
Ascomycetes
Zygomycetes
what are dermatophyte fungi?
cause skin infections
one main virulence factor - an enzyme that degrades and utilizes keratin as a nutrient source.
Diseases caused by these fungi - tinea, which are named according to the region they infect in the body.
Causative agents:
Epidermophyton - Microsporum - Trichophyton
describe the Malassezia species:
they are frequent colonisers and part of the normal skin microbiota, usually found in sebum-rich areas like the scalp and chest.
Their absence might be an indication of disease. but in certain conditions, they can cause superficial infections in immunocompromised individuals.
what are 3 host factors that contribute to the pathogenicity of fungal infections?
1- Favorable micro-environments e.g. (warm, moist areas) encourage the growth of fungi on skin and mucous membranes
2- Broad-spectrum antibacterial agents
reduce competition for epithelial colonization sites in the gut
3- Immunosuppression of all types
create a window of opportunity for fungal invasion
what forms can immunosuppression of host defences come in?
Iatrogenic: ‘illness caused by medical examination or treatment’
- Steroids
- Anti-cancer chemotherapy
- Solid-organ transplantation
Disease processes:
- AIDS
- Leukaemia
- Endocrinopathies
what are candida infections (candidiasis, candidosis)?
fungal infections caused by yeasts
C. Albicans can form hyphae (filamentous form of growth) → pleomorphic fungus
Clinical diseases:
- Superficial → mouth, vagina, penis, skin, nails
- Deep-seated → disseminated infections in immunocompromised hosts
describe the dissemination (spreading) of candida species
1- Bacteria in competition with Candida in the gut.
2- Antibacterial added → bacteria ↓
3- Candida overgrowth & might get access to epithelium.
4- Surgical insult → Candidia gets into the bloodstream & forms a biofilm on the catheter surface.
5- It then becomes resistant to anti-fungal treatments.
what is chronic mucocutaneous candida infection?
a type of candida infection that arises in individuals with an unusual combination of endocrine and immune dysfunction.
(autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy - APECED)
what is apergillosis?
an infection caused by a type of fungus called Aspergillus
Causative species:
Aspergillus fumigatus
Aspergillus flavus
Aspergillus nidulans (in CGD patients)
Aspergillus lentulus
other species on rare occasions
Types of disease:
simple asthma
asthma with eosinophilia
aspergilloma
(fungal ball in lungs - Farmer’s lung)
invasive bronchopulmonary aspergillosis
(associated with haematological malignancy - hyphae filaments penetrating lung tissue)
disseminated aspergillosis
Route of infection:
- inhalation of conidia (spores)
how is Aspergillus fumigatus transmitted?
transmitted to humans through inhalation of conidia, which germinate to hyphae (the main mode of vegetative growth) in the lung tissue.
It is angioinvasive i.e. invades the walls of blood vessels
what is cryptococcosis?
an infection caused by a type of fungus called cryptococcus
Main causative species: (yeasts with a thick extracellular capsule)
Cryptococcus neoformans
Cryptococcus gattii
Human diseases:
pulmonary cryptococcosis
meningitis (particularly in AIDS patients) → 1/2 million deaths each year
disseminated infection in severely compromised hosts
considering the damage response curve, why is it bad to have very weak immunity?
results in invasion from pathogens and dissemination
Diseases:
Systemic candidosis
Acute invasive Aspergillosis
considering the damage response curve, why is it bad to have very strong immunity?
results in a hyperinflammatory response
(damaged tissue)
Diseases:
Recurrent Candida vaginitis
Allergic bronchi pulmonary aspergillosis (ABPA)
Dermatophytosis
what are the diagnostic methods of fungal infections?
Direct detection:
1 - Histopathology
Biopsy of lung tissue → A. fumigatus hyphae
Skin scraping treatment with KOH → visualise dermatophytes
Direct smear with Periodic Acid Shiff (PAS) staining → fungi
Vaginal smear with Calcofluor white stain → C. albicans hyphae
Culture organisms and use ChromAgar Candida → detect species based on colour
Germ tube test in serum → C. albicans form hyphal germ tubes
2 - High-res CT scans
Liver → Candida infection
Pulmonary → Aspergillosis
Other methods:
- detection of circulating fungal antigens
- detection of circulating antibodies to fungi
- PCR for fungal DNA
- Culture of fungus from a normally sterile site
- MALDI-ToF Biotyping
what are 4 antifungal treatments? state what they target, route of administration and mechanism of action
Azoles (Triazoles) and Allylamines → Target sterols
Route of administration→ oral & IV & topical
Mechanism of action → inhibit the production of ergosterol
[2] Echinocandins → Target wall
Route of administration → IV only
Mechanism of action → inhibit the production of glucan
[3] Polyenes → Target membrane
Route of administration → oral & IV & topical
Mechanism of action → bind to ergosterol to make pores in the membrane
[4] Flucytosine → Target DNA synthesis
what are the 6 problems associated with antifungal treatments?
Spectrum of activity
Static or cidal
IV vs oral
Toxicity
Antifungal Resistance
Expensive Cost
what are viruses? what are the 3 structures?
small (20-400 nm) non-cellular organisms; their genetic element cannot replicate independently of a living (host) cell.
Virion: extracellular form of a virus
- Exists outside the host and facilitates transmission from one host cell to another
- Contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material
Structures:
[1] Icosahedral: 20 equilateral triangular faces, 12 vertices and 30 edges
[2] Helical: protein binds around DNA/RNA in a helical fashion
[3] Complex: neither of the above
what are obligate intracellular pathogens?
they are pathogens that can only replicate inside host cells.
Most viruses have a specific host range and only infect specific host cell types, this is known as tissue tropism
what is the taxonomy of viruses? what are 4 ways they’re classified?
Order → Family → Genus → Species
Virus families can be classified according to:
1- Virion shape/symmetry
2- Presence/absence of envelope
3- Genome structure
4- Mode of replication
what is the virus transmission replication process?
Virus replication process:
1- Attachment to the host cell
2- Uncoating of envelope
3- Replication of Genomic nucleic acid in the nucleus
4- Nucleic acid + Proteins Insertion into membrane
5- Assembly of Virion
6- Release of Virion outside of cell
what are the 4 consequences of viral infection?
[1] Clearance of virus}} i.e. with no, short or long-term immunity
* Hepatitis C (no lasting immunity) * Measles (long-term immunity)
[2] Chronic infection
* HIV, hepatitis B, hepatitis C
[3] Latent infection:
* Herpes Virus
[4] Transformation i.e. long-term infection with altered cellular gene expression
* Epstein-Barr Virus, Human Papilloma Virus
what is viral latency?
when a virus lies dormant (latent) in the cell after primary infection.
The full viral genome is retained in the host cell, but its expression is restricted, so that few viral antigens and no viral particles are produced.
This allows the reactivation of viral replication, which may or may not cause apparent disease.
Reactivation is more likely to occur in immunocompromised individuals.
Examples:
1- Herpes Simplex Virus
2- Varicella Zoster Virus
what are the mechanisms of viral infections that can lead to cancer? give examples
1- Modulation of cell cycle control (driving cell proliferation)
2- Modulation of apoptosis (prevention of programmed cell death)
3- Reactive oxygen species-mediated damage
(some persistent viral infections can cause persistent inflammatory processes which lead to cancer via reactive oxygen species)
e.g. Virus & Cancer diseases
- EBV: Burkitt’s lymphoma, Hodgkin’s lymphoma, nasopharyngeal carcinoma, post-transplant lymphoproliferative disease (PTLD)
- Human herpes virus 8: Kaposi’s sarcoma, primary effusion lymphoma, Castleman’s disease
- Human T-cell Lymphotropic Virus (HTLV): Adult T-cell leukaemia/lymphoma
- Human Papillomavirus (HPV): cervical, anal, oropharyngeal cancers
- Hepatitis B and Hepatitis C: hepatocellular carcinoma
what are 3 detection methods of viruses?
[1] Whole organism - i.e. virus
→ electron microscopy
→ culture using light microscopy to see (uninfected/infected cells)
[2] Part of organism – e.g. antigen, nucleic acid
→ antigen detection
→ nucleic acid detection from the sample then amplify a region of the target organism genome
[3] Immune response to a pathogen – i.e. antibodies
→ antibody detection
- determines acute/recent infection - determines prior infection/response to vaccination
what can antivirals be used for?
[1] Prophylaxis
(to prevent infection)
[2] Pre-emptive therapy
(when evidence of infection/replication is detected, but before symptoms are apparent)
[3] Overt disease
[4] Suppressive therapy
(to keep viral replication below the rate that causes tissue damage in an asymptomatic infected patient)
Why are antiviral drugs much more limited than antibiotics?
Because there are limited viral proteins that are potential targets for antiviral drugs
what are 5 ways to prevent viral infections?
immunisation
- Vaccination
- Passive immunisation with immunoglobulin
Prophylactic treatment post-exposure
- Post-exposure prophylaxis in HIV
Infection prevention and control (IPC) measures
- Isolation of symptomatic patients
- Personal protective equipment (PPE)
- Safe use and disposal of sharps
Blood/tissue / organ screening
Antenatal screening - identifying those at high risk of a disorder for prenatal diagnosis
what are 5 ways to eradicate viruses?
- No animal reservoir or ability to amplify in the environment
- clearly identifiable, with accurate diagnostic tool
- No chronic carrier state
- Efficient and practical intervention, e.g. vaccination
- Political & social support
Examples: Smallpox (eradicated in 1979)
- Measles
- Polio
All antiviral agents are virustatic (inhibit viral infection via a reversible extracellular mechanism), and none are virucidal (can kill viruses).
Only a minority of antiviral agents are used against infections because they commonly cause Toxicity to host cells which has nasty side effects.
