Microbiology Made Ridiculously Simple PDF

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Microbiology Made Ridiculously Simple

Part 1 Chapter 1: Bacterial Taxonomy Gram Positive Bacteria   

General characteristics: inner cytoplasmic membrane, thick PG layer, low lipid content, vulnerable to lysozymes and penicillins Gram positive cocci: Staphylococcus in clusters, Streptococcus in chains Gram positive bacilli: Bacillus (anthrax) and Clostridium (botulism) are spore forming o Corynebacterium and Listeria are non-spore forming

Gram Negative Bacteria 

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General characteristics: inner cytoplasmic membrane, thin PG layer, outer membrane with porins and LPS; high lipid content, endotoxins, periplasmic space, resistant to lysozymes and penicillins Only 1 gndc: Neisseria Only 1 spiral shaped: Spirochetes eg. Treponema pallidum – causes syphilis, seen with darkfield microscope Most are gnb: o Enterobacteria: E. coli, Shigella, Salmonella, Yersinia, Klebsiella, Proteus, Enterobacter, Serratia, vibrio, Campylobacter, Helicobacter, Pseudomonas o Brucella, Yersinia, Bordetella, Hemophilus

Other bacteria: Mycobacteria: stained using acid-fast staining, eg. TB Mycoplasma, Chlamydia, Rickettsiae: no cell wall, only cell memb

Some bacteria have oxidase and peroxidase enzymes that break down hydrogen peroxide.

Chapter 2: Cell structures, virulence factors, and toxins Virulence factors: Flagella are long and wavy: involved in movement, in E. coli and Vibrio Pilli are short and straight: has adherence factors Capsules: sugar coatings that evade phagocytosis by macrophages and neutrophils. Appear as halos in India ink staining. Humans have antibodies that can coat capsules and facilitate phagocytosis by opsonization.

Endospores: in Clostridium (anaerobic) and Bacillus (aerobic)  

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Metabolically dormant forms of bacteria that are resistant to heat (boiling), cold, drying and chemical agents Multiple protective layers: A) A cell membrane o B) A thick peptidoglycan mesh o C) Another cell membrane o D) A wall of keratin-like protein o E) An outer layer called the exosporium Destroyed by autoclave: 121 C, 15 psi, 15-30 mins

Exotoxins: eg. Listeria, Vibrio cholera, E. coli, anthrax, botulism, anthrax    

Can act on neural end plates and cause paralysis Enterotoxins: cause diarrhea Pyrogenic exotoxins: cause fever Tissue invasive exotoxins: cause tissue damage

Endotoxins: part of outer membrane in Gram negative bacteria, very toxic    

Can be released when bacteria lyses (dies), too much antibiotics is harmful Only present in Gram negative bacteria (except Listeria) Can result in endotoxic or septic shock: TNF causes release of IL-1 Symptoms of septic shock: vasodilation (decreased BP), myocardial depression (decreased CO), renal failure (decreased urine output), respiratory distress (hypoxia), liver failure, brain damage (change in mental status), change in coagulation (clotting or bleeding)

Bacteria Anthrax Diphtheria Pertussis C. difficile Pseudomonas aeruginosa

Symptoms Edema, death Myocarditis, nervous system effects Whooping cough Diarrhea, fever, abdominal pain Liver damage

Chapter 3: Bacterial genetics 4 ways in which bacteria exchange genetic fragments: 1) transformation: pick up fragment from dead bacteria, between same species 2) transduction: bacteriophage, adsorption, penetration, transcription/replication/translation, bacteriophage assembly, bacteria lysis  

Virulent phages do generalized transduction: bacterial DNA gets packed in capsid by accident Temperate phages do specialized transduction: phage DNA is incorporated into bacterial DNA -> prophage, splicing creates a combo of phage DNA and bacterial DNA

3) conjugation: sex pilus, F (+) donor cell will pass its F plasmid to an F (-) recipient cell

4) transposons: insert into the DNA of phages, plasmids, and bacterial chromosomes, transfer DNA between diff genera and species

Gram Positive Bacteria Chapter 4: Streptococcus Ways to differentiate between Strep and Staph:  

Strep is in chains, Staph is in clusters Staph is catalase positive (staff picture has a cat in it), Strep is catalase negative

Ways to differentiate between different Strep species:    

AH, BH or NH Lancefield grouping: based on a carbohydrate antigen on cell wall, ABCDE… S Other ways to differentiate biochemical reactions, growth characteristics, and genetic studies 5 are clinically significant: Lancefield A, B, D, Streptococcus pneumoniae, viridans group of Strep

Group A Strep: Streptococcus pyogenes    

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Causes "strep throat," scarlet fever, skin infection, rheumatic fever (myocarditis, arthritis), and post-streptococcal glomerulonephritis Lancefield group A: C carbohydrate M protein Pyrogenic exotoxin: causes scarlet fever (red rash, sore throat, fever), present in some species of Group A Strep, superantigens, can cause toxic shock syndrome (fever, rash, diarrhea, nausea, hypotension) Streptolysin O: destroys RBC, beta hemolytic Other enzymes: streptokinase, hyaluronidase, DNAases, anti-C5a peptidase Treated with clindamycin and penicillin G

Group B Strep: Streptococcus agalactiae   

Also beta hemolytic (BABY) 25% pregnant women carry Group B Strep in their vagina Causes neonatal (< 3 months of age) meningitis, pneumonia, and sepsis

Group D Strep  

Alpha hemolytic Similar to Enterococci: Enterococcus is part of normal gut flora o Causes UTI, biliary tract infection, chronic endocarditis – similar to Group D Strep o S. bovis causes colon cancer o Enterococci are now resistant to ampicillin and vancomycin o VRE: changes d-ala:d-ala to d-ala:d-lac, 2nd most common nosocomial infection

Viridans group of Strep    

Alpha hemolytic No Lancefield antigen Normal flora in resp and GI tract Cause 3 main types of infections: dental infections (cavities), chronic endocarditis (damaged heart valves)-also group D Strep, and abscesses (microaerophilic)

Streptococcus pneumoniae    

Alpha hemolytic Causes bacterial pneumonia and meningitis in adults and otitis media in children Lancet pairs of gpc microscopically Now resistant to penicillins

Chapter 5: Staphylococcus 

3 pathogenic species: Staphylococcus aureus (coagulase positive, golden), Staphylococcus epidermidis (coagulase negative), and Staphylococcus saprophyticus (coagulase negative)

Staphylococcus aureus      

Beta hemolytic Proteins against our immune system: Protein A, coagulase, hemolysins, leukocidins, penicillinase, altered PBP Proteins that tunnel thru tissue: hyaluronidase, staphylokinase, lipase, protease Exotoxins: exfoliatin, enterotoxins, toxic shock syndrome toxin (TSST) Diseases from direct organ invasion: pneumonia, meningitis, osteomyelitis, acute endocarditis, septic arthritis, skin infections MRSA is treated with vancomycin

Staphylococcus epidermidis   

A skin contaminant of blood cultures (false positive) Catalase positive, coagulase negative, white, non-hemolytic Foley urine catheters, IV lines, prosthetic devices

Staphylococcus saprophyticus 

Causes UTI in young women who are sexually active

Chapter 6: Bacillus and Clostridium (spore-forming bacilli)   

Both release exotoxins Bacillus is aerobic Bacillus anthracis causes anthrax. It forms a spore, lethal if inhaled, ingested or through skin contact with animal products. It is stable and small. Exotoxin has 3 proteins: Edema Factor, Protective Antigen and Lethal Factor.

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Bacillus cereus causes gastroenteritis (food poisoning). Motile, non-encapsulated and resistant to penicillin. Secretes enterotoxins. Clostridium is anaerobic Responsible for botulism, tetanus, gas gangrene, and diarrhea (C. difficile) Botulism: through ingestion of food in anaerobic enviro: cans, jars, ziplock bags. Neurotoxin: muscle paralysis, ventilation Tetanus: puncture wound by a rusty nail. Causes tetany: sustained muscle contraction. DPT (diphtheria-pertussis-tetanus) vaccination Diarrhea, abdominal cramping and fever caused by C. difficile: after use of broad-spectrum antibiotics, C. diff superinfects the colon. Treated with metronidazole and vancomycin by mouth.

Chapter 7: Corynebacterium and Listeria (non-spore forming bacilli)       

Corynebacterium diphtheriae and Listeria monocytogenes both infect children Diphtheria is facultative anaerobe, catalase positive Corynebacterium diphtheriae colonizes pharynx, bloodstream, damages heart and nerve cells Diphtheria is treated with antitoxin, penicillin/erythromycin, and Diphtheria Pertussis Tetanus vaccine Listeria is the only Gram-positive bacteria that produces endotoxin Listeria causes meningitis in neonates and immunosuppressed patients. Facultative intracellular organism. Induces cell-mediated immunity. Listeria is treated with ampicillin or SxT

Gram Negative Bacteria Chapter 8: Neisseria  

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The only gndc Neisseria meningitidis: causes meningitis and sepsis, o Symptoms: nervous, irritable o Virulence factors: capsule, endotoxin (LPS)-causes a petechiae rash, IgA1 protease Neisseria gonorrhoeae: causes gonorrhea, 2nd most common STD after chlamydia o Symptoms: painful urination/intercourse, purulent discharge from urethra o Virulence factors: pili, protein II o Can be transmitted from mom to baby during delivery: can cause blindness

Chapter 9: Enterobacteria     

Part of normal gut flora Enterobacteriaceae, Vibrionaceae, Pseudomonadaceae and Bacteroidaceae Biochemical classification: based on ability to ferment lactose, production of H2S, MacConkey agar E. coli can ferment lactose Antigenic classification: O antigen=LPS on outer membrane, K antigen=capsule, H antigen=flagella

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Can cause diarrhea, UTI, pneumonia, bacteremia, sepsis Eg. Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Enterobacter, Shigella, Salmonella, Yersinia, Vibrio, and Pseudomonas, Bacteriodes Escherichia coli 0157:H7 causes hemolytic uremic syndrome E. coli and cholera cause rice water stools Shigella causes diarrhea with RBC and WBC. It is nonmotile, does not ferment lactose and does not produce H2S. It releases shiga toxin, which causes destruction of intestinal epithelial cells. Always pathogenic, never part of normal flora. Klebsiella pneumoniae causes pneumonia Proteus mirabilis causes UTI and nosocomial infections Salmonella is a non-lactose fermenter, is motile (like a salmon), and produces H2S. Acquired from eating chicken and uncooked egg. Always pathogenic, never part of normal flora. Pseudomonas aeruginosa: obligate aerobic, gnb, pan-resistant, creates a bluish-green color, infects people with weak immune system o Pneumonia, osteomyelitis, burn-wound infections, sepsis, UTI, endocarditis Bacteriodes: 99% of the flora of our intestinal tract is made up of obligate anaerobic

Chapter 10: Haemophilus   

Haemophilus influenza: cultured from the upper respiratory tracts of "flu" patients Causes meningitis, epiglottitis, and septic arthritis in children Has 6 types of capsules, designated a, b, c, d, e, and f. B=bad.

Chapter 11: Yersinia, Francisella, Brucella and Pasteurella  

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All gnb, zoonotic diseases, very virulent, facultative intracellular organisms, induces cell mediated immunity Yersinia pestis: causes bubonic plague=black death. Human victim either touches a dead infected rodent or is bitten by an infected flea. Symptoms: red hot swollen lymph nodes, fever, headache, blackish discoloration under skin due to hemorrhages. Contracted during camping, hiking or hunting. Humans acquire Brucella from direct contact with infected animal meat or aborted placentas, or ingestion of infected milk products.

Chapter 12: Chlamydia, Rickettsia   

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Obligate intracellular parasites: use host's ATP as an energy source for their own cellular activity Impossible to culture on artificial media Chlamydia is an STD, has complex reproduction cycle: Elementary body is extracellular, inert, small and infectious; reticulate body is intracellular, active, big and non-infectious. Treated with tetracycline or erythromycin Rickettsia is spread by arthropod vector (tick). Rocky Mountain Spotted Fever: fever, conjunctiva redness, headache, rash

Chapter 13: Spirochetes   

Spiral shaped, 6 endoflagella, difficult to culture, too small to be seen by microscope Seen with darkfield microscopy, immunofluorescence, and silver stains. Also, diagnosed with serologic tests Treponema pallidum: syphilis

Chapter 14: Mycobacteria: acid-fast bacteria     

Mycobacterium tuberculosis: stain red with acid-fast stain Mycolic acid in cell wall do not dissolve when acid-alcohol is applied Obligate aerobes: infect lungs People vulnerable to TB: elderly, AIDS patients and poor Facultative intracellular, induces cell-mediated immunity

Diagnosis of TB:          

Purified Protein Derivative (PPD) skin test: type 4 hypersensitivity Positive result: an area of induration (hardness) that is bigger in diameter than 10 mm after 48 hours, 5 mm for immunocompromised patients False positives: BCG vaccine False negatives: immunocompromised, malnutrition Chest X-ray: granuloma/tubercules, fibrosis, scarring of lungs Sputum acid-fast stain and culture Tuberculosis is usually a chronic disease; it presents slowly with weight loss, low-grade fever, and symptoms related to the organ system infected. Mode of transmission: aerosol, through coughing and talking Primary TB is usually asymptomatic Secondary TB: TB reactivates after being dormant for some time

Chapter 15: Mycoplasma: bacterial without cell wall     

Only cell membrane with sterols, no cell wall Pleomorphic, neither coccus nor bacillus Mycoplasma pneumoniae causes a mild, self-limited bronchitis and pneumonia Diagnostic tests: cold agglutinins, complement fixation test, sputum culture, mycoplasma DNA probe Treatment: erythromycin and tetracycline (penicillins don’t work due to lack of cell wall)

Anti-bacterial Medications Chapter 16: Beta lactam drugs Penicillins:         

Beta lactam ring with another 5-membered ring, 1 radical group Bactericidal Resistance to beta lactam drugs: altered porin channels, beta lactamase, altered PBP (MRSA) Can cause allergic reactions and anaphylaxis Penicillin G is parenteral. Penicillin V is oral. Ampicillin and amoxicillin are extended spectrum Methicillin and oxacillin are penicillinase-resistant penicillins Combo drugs: Amoxicillin and clavulanic acid = Augmentin (trade name) Piperacillin is effective against Pseudomonas aeruginosa

Cephalosporins:

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Beta lactam ring with a 6-membered ring, 2 radical groups MRSA and the Enterococci are resistant to the cephalosporins 1st generation: cefazolin, mostly Gram positives 2nd generation: cefoxitin, Gram positives and Gram negatives equally, covers anaerobes like Bacteroides 3rd generation: ceftazidime, mostly Gram negatives, effective against Pseudomonas aeruginosa 5th generation: ceftaroline, anti-MRSA Ten percent of patients who have allergic reactions to penicillin will also have a reaction to cephalosporins

Vancomycin: effective against all Gram positives even MRSA and Enterococci (Group D Streptococci). Targets D-ala:D-ala to inhibit cell wall synthesis. Not absorbed orally, can be used to treat C. difficile. Side effects: nephrotoxicity, red man syndrome, hearing loss

Chapter 17: Anti-ribosomal and anti-DNA antibiotics CLEan: 50 S TAG: 30 S CL for Chloramphenicol and Clindamycin E for Erythromycin T for Tetracycline AG for Aminoglycosides. Parenteral. Chloramphenicol is effective against Gram positives and negatives. Used to treat bacterial meningitis. Has severe side effects: bone marrow depression, aplastic anemia and gray baby syndrome Clindamycin covers anaerobe. Side effect: Pseudomembranous Colitis: overgrowth of C. difficile and colon inflammation and severe diarrhea. Pseudomembranous colitis is treated using vancomycin and metronidazole. Erythromycin covers Gram positives, used for penicillin resistance. Belongs to Macrolides. Tetracycline has many side effects: chelate Ca and Mg, photosensitivity, teeth discoloration and teratogen. Teratogen, not for children under 8. Aminoglycosides cover aerobic gnb only. Includes gentamicin, tobramycin and amikacin. Side effects: renal toxicity, vertigo Quinolone antibiotics include ciprofloxacin. Teratogen, Articular cartilage damage, tendinopathy, neuropathy, Not...