Notes in 1- Intro to Microbiology

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Published	02/10/2024	The three domains of life:1- {{c1::Bacteria}} (Prokaryote)2- {{c1::Archaea}} (Prokaryote)3- {{c1::Eucarya}} (Eukaryote)
Published	02/10/2024	{{c1::Microbiology}} is the study of micro-organisms.Two types:- {{c1::Basic}} e.g. cellular microbiology- {{c1::Applied}} e.g. medical microbiology
Published	02/10/2024	What are the microbial causes of infection?• {{c1::Bacteria}} - “Chiefly round, spiral or rod shaped single celled prokaryotic organism that typi…
Published	02/10/2024	Microorganism size comparison:• {{c1::Parasites}} - microscopic to over 30 cm• {{c1::Fungi}} - 2 to 10 µm • {{c1::Bacteria}} - 0.2 to 0.5 µm&nbsp…
Published	02/10/2024	To tell if a patient has an infection:- {{c1::Clinical}} diagnosis- {{c1::Laboratory}} diagnosisBoth of the results should complement each other
Published	02/10/2024	Specimen types:1- {{c1::Sterile sites}} i.e. contain no microorganismsBrainHeartLiverKidney2- {{c1::Non-sterile sites}} i.e. contain microbiomesMouthO…
Published	02/10/2024	Common specimen types for bacterial culture• {{c1::Mid stream specimen of urine (MSSU)}} – urinary tract infection.• {{c1::Sputum}} – lower respirator…
Published	02/10/2024	Specimen → Microscope• Light microscopy (x1000 magnification)• Unstained             1- to see white blood cells (i…
Published	02/10/2024	Although microscopy is not {{c1::specific}}, it is rapid, and it assists provisional diagnosis and empiric antimicrobial therapy.
Published	02/10/2024	How do you interpret the results after culturing organism and performing susceptibility test?i.e. the measurement of the susceptibility of bacteria to…
Published	02/10/2024	{{c1::Healthcare Associated Infection}} are infections that occur in a healthcare setting (such as a hospital) that a patient didn't have before they …
Published	02/10/2024	How are viruses detected from clinical samples?- {{c1::Molecular methods}} i.e. real time / multiplex PCRPCR → only detects sections of viral RNA/DNA-…
Published	02/10/2024	Parasitology Classifications:
Published	02/10/2024	Diagnostic principles in parasitology: (shallow)• Microscopy of different life cycle stages e.g.     • parasites, cysts and ova in faec…
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Published	02/10/2024	Components that make up a bacteria's surface:{{c1::Cytoplasmic membrane}} - is a very thin, elastic and semi-permeable membrane around the bacterial c…
Published	02/10/2024	Gram Positive cell wall contains a {{c1::thick}} Peptidoglycan layer.Gram Negative cell wall contains a {{c1::thin}} Peptidoglycan layer and an Outer …
Published	02/10/2024	Gram stain appearance under light microscopy:Gram Positive → {{c1::Purple}}Gram Negative → {{c1::Red/Pink}}The first step to identify the bacteria is …
Published	02/10/2024	Bacteria shapes:- {{c1::Spherical}} e.g. cocci- {{c1::Rod shaped}} e.g. bacili- {{c1::Spiral & corkscrew}}Bacteria can exist as single cells, pair…
Published	02/10/2024	{{c1::Cytoplasmic membrane}} is a 5-10 nm thick structure, made of 40% phospholipids and 60% proteins.It allows passage of water and uncharged small m…
Published	02/10/2024	{{c1::Cell wall}} is a 10-25 nm thick structure, made of peptidoglycans, it is strong and relatively rigid & maintains shape.It plays an important…
Published	02/10/2024	{{c1::Peptidoglycans}} are N-acetylglucosamine acid and N-acetylmuramic acid molecules linked alternately in a chain, with short peptides forming cros…
Published	02/10/2024	{{c1::Lipopolysaccharide outer membrane}} is a structure that is only present in Gram negative bacteria, it protects peptidoglycans from bile salts an…
Published	02/10/2024	{{c1::Lipid A}} is one of the components of Lipopolysaccharide that forms endotoxin.When endotoxin is released into the bloodstream, it may give rise …
Published	02/10/2024	There are two types of capsules (polysaccharide layer):- {{c1::Rigid capsule}} → prevent phagocytosis- {{c1::Slimy capsule}} → forms biofilms and micr…
Published	02/10/2024	{{c1::Flagellum}} is a long thin filament twisted spirally in an open regular wave form.Provides motility to a bacteria to move to an optimal environm…
Published	02/10/2024	{{c1::Fimbriae}} are short filaments that are far more numerous than flagella.Important in mediating adhesion between bacterial cell and host cells.
Published	02/10/2024	Bacterial cell has a single chromosome with no nucleus.It replicates by {{c1::binary fission}} to produce two daughter cells.It may contain {{c1::Plas…
Published	02/10/2024	How does genetic variation occur in bacteria?
Published	02/10/2024	{{c1::Bacterial conjugation}} is a mechanism of gene transfer that requires direct contact between donor and recipient cells.Steps:F pilus forms pathw…
Published	02/10/2024	{{c1::Bacteriophages}} are a type of virus that infects bacteria.All of them are composed of nucleic acid molecule that is surronded by a protein stru…
Published	02/10/2024	{{c1::Ribosomes}} are structures in the bacterial cell cytoplasm, they consist of RNA and associated proteins.Their role is to synthesize proteins.The…
Published	02/10/2024	{{c1::Sporulation}} is highly resistant process whereby dormant bacteria are formed.This process preserves genetic material of bacteria when condition…
Published	02/10/2024	Detection and Culture1- Get a specimen from patient2- Staining to determine whether it's gram positive or gram negative infection to select appropriat…
Published	02/10/2024	Bacterial Classification: 1- {{c1::Phenotypically}} → i.e. relating to observable physical propertiese.g.- Gram stain (gram + & gram -)- Grow…
Published	02/10/2024	Bacterial nomenclature is based on {{c1::genus}} and {{c1::species}}:- Strains of a species have similar characteristics- DNA typing techniques a…
Published	02/10/2024	A {{c1::Parasite}} is an organism that lives in or on another organism (host) and derives its nutrients at the expense of this host.Broadly classified…
Published	02/10/2024	{{c1::World Health Organisation (WHO)}} is a specialised agency of the United Nations concerned with international public health.
Published	02/10/2024	The {{c1::equator}} is the hottest part of the globe, and anything moving further north or south from there becomes generally colder.
Published	02/10/2024	Classification of parasites:
Published	02/10/2024	Classification of parasites:- {{c1::Protozoa}} → malaria & amoebae & flagellates- {{c1::Helminths}} (worms) → roundworms &…
Published	02/10/2024	{{c1::Protozoa}} are microscopic, single-celled organisms, can be free-living or parasitic in nature.They are able to multiply in humans and they tran…
Published	02/10/2024	{{c1::Malaria}} is a protozoan infection, the most common cause of death by parasitic infection globally, usually found in tropics and subtropics.It i…
Published	02/10/2024	Malaria is a protozoan infection that has a complex life cycle: (no need to know this)• Sporozoites injected by mosquito • Travel through blood and en…
Published	02/10/2024	Left-side → dark purple dots are genetic material of plasmodium falciparumRight-side → sexual form of plasmodium falciparum
Published	02/10/2024	Malaria prevention:A - {{c1::Awareness of the risk}} B - {{c1::Bite prevention}} C - {{c1::Chemoprophylaxis}} (appropriate choice …
Published	02/10/2024	{{c1::Amoebic Dysentery}} is a protozoan infection that causes bloody diarrhoea.It is caused by an invasion of Entamoeba histolytica in the gut wall.C…
Published	02/10/2024	Malaria vs Amoebic DysentryWhat are the similarities/differences?
Published	02/10/2024	Helminths (worms) are divided into three categories:To diagnose we look into stool samples of patients and check for worm eggsMost are transmitted thr…
Published	02/10/2024	Nematodes (Round worms)[1] {{c1::Enterobiasis}} (pinworm/threadworm) → 1cm, threadlike, very common in childrenCauses anal itchDiagnosis → sellotape o…
Published	02/10/2024	Cestodes are long, segmented tapeworms. e.g.[1] {{c1::Taenia saginata}} (beef)[2] {{c1::Taenia solium}} (pork)Can migrate to brain from gut and make c…
Published	02/10/2024	Trematodes (flukes) & (flatworms)Different species cause human infection in various body sitesi.e. Blood, Lung, Liver, Pancreas, Intestines[1] {{c…
Published	02/10/2024	{{c1::Ectoparasites}} are parasites that live outside the body.Usually insects with six legs or arachnids with eight legs.
Published	02/10/2024	How is malaria diagnosed?
Published	02/10/2024	Diagnostic principles in Parasitology: (deep)[1] {{c1::Definitive diagnosis}} → identify parasites in host tissue or faeces/urine[2] {{c1::Blood micro…
Published	02/10/2024	Describe some diagnostic principles in Parasitology
Published	02/10/2024	A {{c1::fungus}} is a chemo-organotrophic eukaryote that lacks chlorophyll and forms spores.{{c1::Cell wall}} → contains polysaccharides, often chitin…
Published	02/10/2024	The main groups of the fungal kingdom:1- {{c1::Basidiomycetes}}2- {{c1::Ascomycetes}}3- {{c1::Zygomycetes}}
Published	02/10/2024	{{c1::Dermatophyte fungi}} are fungi that cause skin infections, they have one main virulence factor which is an enzyme that degrades and utilizes ker…
Published	02/10/2024	{{c1::Malassezia}} species are frequent colonisers and part of the normal skin microbiota, usually found in sebum-rich areas like the scalp and chest.…
Published	02/10/2024	The host factors that contribute to the pathogenicity of fungal infections:1- {{c1::Favorable micro-environments}} e.g. (warm, moist areas)e…
Published	02/10/2024	Immunosuppression of host defenses can come in a number of forms:[1] {{c1::Iatrogenic}}: 'illness caused by medical examination or treatment'- Steroid…
Published	02/10/2024	{{c1::Candida infections, Candidiasis, Candidosis}} are fungal infections caused by yeastsC. Albicans can form hyphae (filamentous form of growth) → p…
Published	02/10/2024	Dissemination of Candidia species:1- Bacteria in competition with Candidia in the gut.2- Antibacterial added → bacteria ↓3- Candidia overgrowth & …
Published	02/10/2024	{{c1::Chronic mucocutaneous Candida infection}} is a type of candida infection that arises in individuals with an unusual combination of endocrine and…
Published	02/10/2024	{{c1::Aspergillosis}} is an infection caused by a type of fungus called aspergillusCausative species: Aspergillus fumigatus Aspergillus flavus Aspergi…
Published	02/10/2024	{{c1::Aspergillus fumigatus}} is transmitted to humans through inhalation of conidia, which germinate to hyphae (main mode of vegetative growth) …
Published	02/10/2024	{{c1::Cryptococcosis}} is an infection caused by a type of fungus called cryptococcusMain causative species: (yeasts with a thick extracellular capsul…
Published	02/10/2024	Damage-Response curve{{c1::Very weak}} immunity → invasion from pathogens and disseminationDiseases:Systemic candidosis Acute invasive Aspergillosis--…
Published	02/10/2024	Diagnostic methods of fungal infections:Direct detection:1 - {{c1::Histopathology}}Biopsy of lung tissue → A. fumigatus hyphaeSkin scraping treatment …
Published	02/10/2024	Mention some diagnostic methods of fungal infections
Published	02/10/2024	{{c1::Biopsy}} of lung tissue → A. fumigatus hyphaeA {{c1::biopsy}} is a sample of tissue taken from the body in order to examine it more closely
Published	02/10/2024	{{c1::Skin scraping}} treatment with KOH → visualise dermatophytes
Published	02/10/2024	{{c1::Direct smear}} with Periodic Acid Shiff (PAS) staining → fungi
Published	02/10/2024	{{c1::Vaginal smear}} with Calcofluor white stain → C. albicans hyphae
Published	02/10/2024	{{c1::Culture organism}} on selective medium and use ChromAgar Candida → detect species based on color.
Published	02/10/2024	{{c1::Germ tube test}} in serum → C. albicans forms hyphal germ tubes
Published	02/10/2024	This is a CT scan of → {{c1::Hepatic/Liver Candida infection}}
Published	02/10/2024	This is a CT scan of → {{c1::Pulmonary development of aspergillosis}}
Published	02/10/2024	Antifungal treatments:[1] Azoles (Triazoles) and Allylamines → Target {{c1::sterols}} Route of administration→ oral & IV &…
Published	02/10/2024	Problems associated with antifungal treatments:[1] {{c1::Spectrum of activity}}[2] {{c1::Static or cidal}}[3] {{c1::IV vs&nbs…
Published	02/10/2024	Mention some problems associated with antifungal treatments:
Published	02/10/2024	{{c1::Viruses}} are small (20-400 nm) non-cellular organisms; their genetic element cannot replicate independently of a living (host) cell.Structures:…
Published	02/10/2024	{{c1::Obligate intracellular pathogens}} are pathogens that can only replicate inside host cells.Most viruses have a specific host range and only infe…
Published	02/10/2024	{{c1::Virus}}: genetic element that cannot replicate independently of a living (host) cell {{c1::Virology}}: the study of viruses {{c1::Virion}}: ext…
Published	02/10/2024	TaxamomyOrder → Family → Genus → SpeciesVirus families can be classified according to: 1- {{c1::Virion shape / symmetry}} 2- {{c1::Presence / absence …
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Published	02/10/2024	Virus replication process:1- Attachment to host cell2- Uncoating of envelope3- Replication of Genomic nucleic acid in nucleus4- Nucleic acid + Protein…
Published	02/10/2024	Describe the virus replication process:
Published	02/10/2024	Transmission of viruses
Published	02/10/2024	The concept of host range:Some viruses may only infect humans, e.g. smallpox, measles, Some may also infect other animals / birds • Transmission of a…
Published	02/10/2024	Syndromes of a viral infection:
Published	02/10/2024	Consequences of viral infection:[1] {{c1::Clearance of virus}} i.e. with no, short or long term immunity     • Hepatitis C (no lasting immun…
Published	02/10/2024	What are the consequences of viral infection?
Published	02/10/2024	{{c1::Viral latency}} is when a virus lies dormant (latent) in the cell after primary infection.The full viral genome is retained in the host cell, bu…
Published	02/10/2024	A number of viral infections can lead to cancer (often requires another of event to occur)Mechanisms: 1- Modulation of {{c1::cell cycle control}} (dri…
Published	02/10/2024	Detection methods of viruses:[1] {{c1::Whole organism}} - i.e. virus→ electron microscopy → culture using light microscopy to see (uninfected / i…
Published	02/10/2024	All antiviral agents are {{c1::virustatic}}, none are {{c1::virucidal}}Only a minority of antiviral agents are used against infections because they co…
Published	02/10/2024	Why are antiviral drugs much more limited than antibiotics?
Published	02/10/2024	How can Antivirals be used?
Published	02/10/2024	Ways to prevent Viral Infection:[1] {{c1::Immunisation}} • Vaccination • Passive immunisation with immunoglobulin----------------- [2] {{c1::Prophylac…
Published	02/10/2024	What are the methods done to prevent Viral Infections:
Published	02/10/2024	Eradication of viruses:• No animal reservoir or ability to amplify in the environment • Clearly identifiable, with accurate diagnostic tool • No chron…
Published	02/10/2024	Explain how viruses can be eradicated:
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