Medical Microbiology Past Lectures (BO101) PDF

BO101 Medical Microbiology Prof. Gerard Wall [email protected] Topic 1: Disease-causing micro-organisms Course content: Topic 1: Disease-causing micro-organisms Topic 2: Diagnosis, control, therapy Topic 1: Disease-causing micro-organisms...

BO101 Medical Microbiology Prof. Gerard Wall [email protected] Topic 1: Disease-causing micro-organisms Course content: Topic 1: Disease-causing micro-organisms Topic 2: Diagnosis, control, therapy Topic 1: Disease-causing micro-organisms Phylogenetic tree: Baker’s yeast Mycobacterium tuberculosis Topic 1: Disease-causing micro-organisms Disease-causing microbes Bacteria Gram + Gram - Viruses Yeasts Others What size / scale are we talking about? Topic 1: Disease-causing micro-organisms Disease-causing microbes Bacteria Gram + Gram - Viruses Yeasts Others What size / scale are we talking about? Topic 1: Disease-causing micro-organisms Gram + bacteria: Cocci : Staphylococcus (aureus, epidermis) Streptococcus (pnuemoniae, pyogenes) Rods : Clostridium (difficile, perfringens, botulinum, tetani) Bacillus (cereus, anthracis) Mycobacterium (leprae, tuberculosis) Gram – bacteria: Rods : Escherichia (coli) Salmonella (enterica, typhi) Vibrio (cholerae) Neisseria (mengitidis, gonorrhoeae) Fungi : Candida (albicans) Plasmodium : Plasmodium (falciparum) Viruses : Smallpox, Herpes, Influenza, HIV Prions: CJD Topic 1: Disease-causing micro-organisms Topic 1: Disease-causing micro-organisms Topic 1: Disease-causing micro-organisms Gram + bacteria: Staphylococcus aureus “Staphyle” – bunch of grapes * Staphylococcus aureus: commonly found on the skin; normal flora of the nose (30% of people) * produces cell-associated and secreted factors to survive and colonise; these include a number of toxins / virulence factors Topic 1: Disease-causing micro-organisms Gram + bacteria: Staphylococcus aureus Symptoms: mostly cutaneous - pimples, boils, abscesses - scalded skin syndrome, impetigo sometimes systemic – toxic shock Treatment: can survive dried conditions (bed clothes, dust) for months but easily killed by heat (65°C for 30 mins); also inherently sensitive to many antibiotics Topic 1: Disease-causing micro-organisms So if it’s easy to kill, why is Staph. aureus such a problem? MRSA = methicillin-resistant Staph. aureus * MRSA is endemic in many hospitals; particular problem in immunocompromised patients; also wounds / operations * good hospital hygiene programmes, patient isolation, sensible use of antibiotics … Staphylococcus: also Staph. epidermis: opportunistic pathogen; no virulence factors Topic 1: Disease-causing micro-organisms Gram + bacteria: Clostridium difficile * motile, G+, toxin-producing, spore-forming rod * normally found in human bowel * problems upon mutation / reaction to antibiotics * most common cause of hospital-acquired diarrhoea * resistant to heat, chemicals * usually mild but can be serious, kill – usually elderly patients Topic 1: Disease-causing micro-organisms Clostridium – many obligate anaerobes (C. difficile: gastroenteritis) C. tetani: tetanus: stiffness, lockjaw, spasms C. perfringens: food poisioning, gas gangrene Opisthotonous in a patient suffering from tetanus; Sir Charles Bell, 1809 Topic 1: Disease-causing micro-organisms Clostridium – many obligate anaerobes (C. difficile: gastroenteritis) C. tetani: tetanus: stiffness, lockjaw, spasms C. perfringens: food poisioning, gas gangrene C. botulinum: botulism – most potent toxin known (botox); specific for nerve endings; blocks nerve impulses! Topic 1: Disease-causing micro-organisms Gram + bacteria: Mycobacterium tuberculosis * > 100 sp.; non-motile, non-sporing, obligate aerobes * leading cause of death from a single microbe – affects 1.7 billion people / yr; causes tubercles in lungs, bones * poor health, crowding play a role (communicable) * 90% of infected have asymptomatic TB; death rate for active + untreated TB is 50% Merlin Park Hospital: built as Western Regional Sanatorium under the Tuberculosis Act of 1945; by 1960, blocks were already being converted to, e.g., geriatrics due to improved drugs Topic 1: Disease-causing micro-organisms Gram + bacteria: Mycobacterium tuberculosis * > 100 sp.; non-motile, non-sporing, obligate aerobes * leading cause of death from a single microbe – affects 1.7 billion people / yr; causes tubercles in lungs, bones * poor health, crowding play a role (communicable) * 90% of infected have asymptomatic TB; death rate for active + untreated TB is 50% Infant vaccine in Ireland Topic 1: Disease-causing micro-organisms Gram - bacteria: Escherichia coli * commensal, motile, G- rods * used as indicator of faecal contamination * most commonly used species in gen eng - but not GRAS * diverse range of infections depending on genes; incl. infantile diarrhea, traveller's diarrhea, enteroinvasive - ulceration of mucosa; enteropathogenic - wasting disease of newborns Topic 1: Disease-causing micro-organisms Gram - bacteria: Escherichia coli * commensal, motile, G- rods * used as indicator of faecal contamination * most commonly used species in gen eng - but not GRAS * diverse range of infections depending on genes; incl. infantile diarrhea, traveller's diarrhea, enteroinvasive - ulceration of mucosa; enteropathogenic - wasting disease of newborns WHO: Don’t eat raw vegetables (or other raw food). Make sure what you eat is thoroughly cooked. Remember – salad is raw food Peel fruit yourself before eating Drink bottled water (that you open yourself) and canned drinks Avoid ice cubes Topic 1: Disease-causing micro-organisms Gram - bacteria: Salmonella typhi * huge variability in antigens: > 2000 antigenic types * S. enterica causes food poisoning * S. typhi causes typhoid fever: pink spots on chest, abdomen; fever; apathetic-lethargic state; severe headache * typically transferred via water, food Topic 1: Disease-causing micro-organisms Gram - bacteria: Salmonella typhi * huge variability in antigens: > 2000 antigenic types * other species (e.g. S. enterica) cause food poisoning * S. typhi causes typhoid fever: pink spots on chest, abdomen; fever; apathetic-lethargic state; severe headache * typically transferred via water, food “Typhoid Mary”: cook in NY, early 1900s; Mary Mallon, naturally immune; famous for her peaches and ice cream; after 1st outbreak(s), locked up for 3 y; on release, went back cooking and caused a 2nd... locked up for her last 23 years. Topic 1: Disease-causing micro-organisms Gram - bacteria: Vibrio cholerae * commonly aquatic organism * short rod, motile by single polar flagellum * sudden onset of effortless vomiting, profuse diarrhoea * rapid dehydration can cause death in 12-24 h * ~ 100,000 deaths / y; often epidemics – war, natural disasters Worldwide cases of cholera, 2022 (ECDC) (WHO: 1.3M – 4.0M cases / y; 21K – 143K deaths / y) Topic 1: Disease-causing micro-organisms Gram - bacteria: Vibrio cholerae * commonly aquatic organism * short rod, motile by single polar flagellum * sudden onset of effortless vomiting, profuse diarrhoea * rapid dehydration can cause death in 12-24 h * ~ 100,000 deaths / y; often epidemics – war, natural disasters * classical disease tracing / epidemiological history Haiti: Jan 2010 earthquake, ~ 300,000 deaths London, 1854: 616 deaths in small area in 8 days Oct 2010 cholera outbreak; > 9,000 John Snow’s mapdeaths … Broad St pump Topic 1: Disease-causing micro-organisms Fungi: Candida albicans * of > 100,000 fungi, only ~ 500 known to cause animal diseases * C. albicans: common causative agent of superficial infections of skin, nails Skin of newborn hours after birth Topic 1: Disease-causing micro-organisms Fungi: Candida albicans * of > 100,000 fungi, only ~ 500 known to cause animal diseases * C. albicans: common causative agent of superficial infections of skin, nails, mouth and vagina * can cause infection in mouth, vagina when normal microbial flora is altered or due to other infections * as fungi are eukaryotes, many treatments also toxic to human * relatively easy to treat (topically), also complementary meds Patient after radiation therapy Topic 1: Disease-causing micro-organisms Viruses: Pox viruses * large viruses, large number of family members * smallpox: spread through respiratory tract; characteristic rash, then 10-50% fatal * eradicated due to vaccination – Edward Jenner’s work with cowpox critical; last natural case occurred in Somalia in 1977 * lab strains still in USA, Russia; vaccines in case of bioterrorism (1980) Jenner: vaccinated with cowpox material … → Mass vaccination immunity to smallpox in Africa, 1966 Topic 1: Disease-causing micro-organisms Viruses: Orthomyxoviruses * 4 genera, incl. influenza A, B and C * 8 segments of -ssRNA as genome in helical nucleocapsid * great antigenic variation due to mutation, “antigenic shift” * multifactorial pathogenesis – virus, host, environment factors * occurs in epidemics: 1918-9 (~30 million deaths), 1957, 1968 1918, England Topic 1: Disease-causing micro-organisms Viruses: Orthomyxoviruses * 4 genera, incl. influenza A, B and C * 8 segments of -ssRNA as genome in helical nucleocapsid * great antigenic variation due to mutation, “antigenic shift” * multifactorial pathogenesis – virus, host, environment factors * occurs in epidemics: 1918-9 (~30 million deaths), 1957, 1968 Course content: Topic 1: Disease-causing micro-organisms Topic 2: Diagnosis, control, therapy Topic 2: Detection, control, etc; uses of rec. DNA techniques Infectious disease Ideally we want to 1. Detect 2. Characterise 3. Treat 4. Prevent (5. Cure) Nanoparticle for drug delivery / targeting 5 h test to identify methicillin- resistant S. aureus EIAs: antibody-based identification Topic 2: Detection, control, etc; uses of rec. DNA techniques Detection of disease-causing organisms Q. What do you look for? A. Organism - “antigens” (protein, glycan chain, etc) - DNA (or RNA – retroviruses) - immune response against the organism Want detection / test to be: * sensitive * specific * non-invasive * easy to use, easy to interpret * cheap (population screening?) BSE: BSE:detection Enfer (IE)’sofEIA spongiforms – Ig binds in deer HIV-1 brain virion PrPsc, biopsy, postmortem colourimetric, 3h * … * (for genetic diseases: pre-natal; pre-symptomatic; carriers; etc – even DNA fingerprinting) Topic 2: Detection, control, etc; uses of rec. DNA techniques Detection of disease-causing organisms Immunosensors: detect an Ab-Ag interaction Need: * an immobilised antibody (or antibody fragment) * (add test sample) * a method of reporting the signal (colour appearance) Advantages: Potential to be sensitive, reasonably accurate (to threshold levels), cheap, reusable (env monitoring), usable in situ Disadvantages: Usually not quantitative; not as Trinity Uni-Gold Recombigen HIV-1 sensitive as HPLC, etc; specificity Blood Test Kit: Fingerprick test. dependent on Ab; have to raise Ab Sensitivity: 100% Specificity: 99.7% Results in 10 minutes Topic 2: Detection, control, etc; uses of rec. DNA techniques Detection of disease-causing organisms Alternative to detecting the surface of the pathogen: DNA Identify an unique DNA sequence Devise a test to detect it * amplification * should be definitive Almost all tests are based on PCR: * highly specific * detects 1-10 copies; * amplifies 1,000,000 x; * in 2 h Topic 2: Detection, control, etc; uses of rec. DNA techniques (Genetic diagnostics) Same principle as infectious disease: find an unique sequence (not usually an antigen), PCR it, sequence it For large numbers – genetic Diagnosing CF: 3 children fingerprinting – do multiple polymorphic have CF – so assume parents loci; stats then become important both heterozygotes; what about the other 2 children? Australia: Topic 2: Detection, control, etc; uses of rec. DNA techniques Enormous potential: * pre-clinical, pre-symptomatic diagnosis of disease (carriers) * pre-natal diagnosis * pre-implantation diagnosis * genetic fingerprinting: paternity testing forensics The first genetic fingerprint, 1984 Alec Jeffreys, Leicester Topic 2: Detection, control, etc; uses of rec. DNA techniques Characterisation of disease-causing organisms Often need to characterise an organism below the species level: It’s not sufficient just to identify, e.g., Staph. aureus – commonly found in the nose but also causes wound infections. The (clinically important) Q is … is it MRSA? Therefore PCR of mecA gene, possibly sequence it too, before prescribing medication. Highly varied ways in which bacteria avoid destruction: Amplification of mecA gene. 2:-ve; 5:+ve Topic 2: Detection, control, etc; uses of rec. DNA techniques Treatment of disease Traditionally, antibiotics – naturally occurring anti-microbials; then chemically modified – major pharma Now screening of various environments: The beta-lactam core structures Topic 2: Detection, control, etc; uses of rec. DNA techniques Prevention of disease Of course it would be better to prevent the infection. One of the main ways of doing this (other than avoidance of, e.g., STDs) is vaccination – generating immune protection Exposure to a “pathogen” leads to ongoing protective immunity Vaccination successes include: Now, we can use recombinant DNA techniques to inject a pathogen component to inject: * gives protective immunity * no possibility of causing disease Topic 2: Detection, control, etc; uses of rec. DNA techniques (Curing disease) Ideally, we would like to cure rather than treat the symptoms of a disease. But if we know the genetic basis of disease … * we can supplement with a missing gene * we could add an inhibitor of an overexpressed / mutated gene Once integrated into the cell’s genome, it will be stably expressed – and inherited by daughter cells Delivery can be using a “gene gun” … or using a cell-specific delivery approach Course content: Topic 1: Disease-causing micro-organisms Topic 2: Diagnosis, control, therapy  BO101 Medical Microbiology Prof. Gerard Wall [email protected]