FOCUS MICROBIOLOGY TIER I HANDOUT.pdf

OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY In 1876, Robert Koch (1843-1910) established that microbes...

OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY In 1876, Robert Koch (1843-1910) established that microbes can cause disease. Chain of Infection Infectious agent – bacteria, virus, fungi, parasite Reservoir – humans, water, medical equipment Portal of exit – secretion, droplets, feces, excretion Mode of transmission – contact (direct/indirect), air, vector Portal of entry – mucosa lining, open wound, respiratory and urinary tract TIER I: Susceptible host – Immunocompromised, very young or very old age, people with chronic disease, post-operative MICROBIOLOGY AND patients, post-transplant PARASITOLOGY Part I: Bacteriology and Parasitology Prepared by: Dione Kirk D. Manatad, MD Contributors: Kristian Danielle R. Pascual-Hernandez, MD and Renz Michael Hart Bautista, RMT, MD References: The Chain of infection Jawetz Clinical Microbiology Antiseptic Process USMLE Step 1 2024 Edition Sanitation is the removal of visible dirt (e.g., organic and CDC Website for Parasitology life cycles inorganic material) from objects and surfaces and normally is accomplished manually or mechanically using water with I. INTRODUCTION TO MICROBIOLOGY AND REVIEW OF detergents or enzymatic products. BASIC EPIDEMIOLOGY Disinfection describes a process that eliminates many or Objectives all pathogenic microorganisms, except bacterial spores, To be able to incorporate in your hearts and minds the distinct on inanimate objects characteristic of each infectious disease through studying Sterilization describes a process that destroys or eliminates bacteria and parasite's life cycle and key terms all forms of microbial life and is carried out in health-care To be able to associate PrevMed, IM, pedia, and pharma in facilities by physical or chemical methods. the simplest way. Types of Disease Distribution Definition of Terms Bacteriology – the study of bacteria, the morphology, processes, and clinical manifestations Parasitology – Parasites biology, life cycle, and clinical manifestations Virology – Study of viruses and associated diseases, vaccination Mycology – Medically important fungi, pharmacologic agents A microbe or microorganism is a microscopic organism that comprises either a single cell (unicellular); cell clusters; or multicellular, relatively complex organisms. History The study of microorganisms is called microbiology, a subject that began with Anton van Leeuwenhoek's discovery of microorganisms in 1675, using a microscope of his own design. Lazzaro Spallanzani (1729-1799) found that boiling broth would sterilize it and kill any microorganisms in it. Louis Pasteur (1822-1895) dealt the death blow to the theory of spontaneous generation and supported germ theory instead. II. MEDICAL BACTERIOLOGY Microbial Growth and Control FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 1 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY Plasmids Extrachromosomal, double- stranded, circular DNA capable of replicating independently of the bacterial chromosome. Can sometimes be integrated into the bacterial chromosome called episomes Significance of Plasmids o Antibiotic resistance o Resistance to heavy metals o Resistance to UV light o Pili (fimbriae) o Exotoxins and several enterotoxins. o Bacteriocins - toxic proteins produced by certain bacteria that are lethal for other bacteria. Flagellar Arrangements Atrichous – no flagellum Monotrichous – flagellum at one pole Amphitrichous – single flagellum on both poles Lag phase - little or no multiplication (Adjustment period) Lophotrichous – tuft of flagella at one or both poles Log or Exponential phase – organisms are most Peritrichous – flagella all over the organism metabolically active, grow at maximum rate Periplasmic flagella – endoflagella/ axial filaments Stationary or plateau phase – No growth because nutrients are exhausted or toxic metabolic products have accumulated (no. of living= no. of dead) Death phase – Viable count decreases (no. of dead> no. of living) Parts of a Bacteria Cytoplasmic membrane o lipoprotein bilayer without sterols o Site of oxidative and transport enzymes Ribosome o RNA and protein in 50s and 30s subunits o Protein synthesis Nucleoid Forms of Bacterial Genetic Transfer o DNA o Genetic material Mesosome o invagination of plasma membrane o Participates in cell division and secretion Periplasm o Space between plasma membrane and outer membrane o Contains many hydrolytic enzymes, including S- lactamases Capsule o Polysaccharide; Protects against Phagocytosis Pillus or Fimbria o Glycoprotein; for Attachment; conjugation Glycocalyx o Polysaccharide: mediates adherences to surfaces Flagellum o Protein: for motility Spore o Keratin-like coat; dipicolinic acid o Resistance to heat and chemicals o Need to autoclave at 121C for 15 mins; H2O2 and iodine based agents are sporicidal Plasmid o Glycogen, lipids, polyphosphates o Genes for antibiotic resistance and toxins Granule o Glycogen, lipids, polyphosphates o Site of nutrients in cytoplasm FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 2 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY Mechanism of Resistance: Beta-Lactamase o Obligate intracellular – rely on Host’s ATP ▪ Genus Rickettsia, Chlamydia, Coxiella Write your notes here: Mnemonic: Stay inside (cells) when it is Really Chilly and Cold o Facultative Intracellular ▪ Salmonella, Neisseria, Brucella, Mycobacterium, Listeria, Francisella, Legionella, Yersinia pestis Mnemonic: Some Nasty Bugs May Live FacultativeLY Staining Techniques Review on Antimicrobial Drugs Gram staining – single most important initial test in bacteriology o Bacteria with thick peptidoglycan layer retain crystal violet dye (gram ⊕); bacteria with thin peptidoglycan layer turn red or pink (gram ⊝) with counterstain. Bacterial Metabolism Aerobic Metabolism o Obligate Aerobes ▪ completely dependent on oxygen for ATP- generation o Microaerophiles Microorganisms that do not take up the gram stain well ▪ use fermentation hut can tolerate low amounts of oxygen because they have SOD Mnemonic: These Little Microbes May Unfortunately Lack (Superoxide Dismutase) Real Color; But Are Everywhere) Anaerobic Metabolism o Obligate Anaerobes ▪ Genus Clostridium, Bacteroides, Fusobacterium, Actinomyces ▪ lack catalase and/or superoxide dismutase and are thus susceptible to oxidative damage. ▪ Generally foul smelling (short-chain fatty acids) Other stains ▪ difficult to culture o Giemsa stain ▪ produce gas in tissue (CO2 and H2). ▪ H. pylori, Chlamydia, Borrelia, Rickettsia, ▪ Aminoglycoside are ineffective against Trypanosomes, Plasmodium Anaerobes because these antibiotics require o Silver Stain O2 to enter the bacterial cell ▪ Helicobacter pylori, Legionella, Bartonella henselae, and fungi (eg, Coccidioides, Pneumocystis jirovecii, Aspergillus fumigatus) o Periodic Acid Schiff Stain Mnemonic: Anaerobes Cant Breath Fresh Air ▪ Stains glycogen, mucopolysaccharides; Clostridium, Bacteroides, Fusobacterium, Actinomyces ▪ Used to diagnose Whipple disease o Facultative Anaerobes (Tropheryma whipplei) ▪ utilize oxygen if it is present, but can use o Carbolfuchsin fermentation in its absence ▪ Mycobacteria, Nocardia, Cryptosporidium spp. o Aerotolerant Anaerobes o India ink ▪ exclusively anaerobic but insensitive to the ▪ Cryptococcus neoformans (mucicarmine can presence of oxygen also be used – Red) Intracellular Organisms FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 3 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY Gram positive vs. Gram Negative Bacteria Cell Walls Tests to differentiate Gram positive cocci o Catalase test Component Gram (+) Gram (-) Peptidoglycan Thicker, multilayer Thinner Teichoic acid Present Absent Lipopolysaccharide Absent Present Periplasmic Space Absent Present o Coagulase Test Exotoxins and Endotoxins Gram – Positive Cocci o In Clusters: Staphylococci ▪ Staphylococcus aureus Catalase + Coagulase + ▪ Staphylococcus epidermidis Catalase + Coagulase – Novobiocin Sensitive ▪ Staphylococcus saprophyticus Catalase + Coagulase – Novobiocin Resistant ▪ All staphylococci are catalase positive o In Chains: Streptococci Gram – Positive Bacteria ▪ Streptococcus pneumoniae Catalase – alpha hemolytic Bile optochin sensitive ▪ Viridans streptococci Catalase – alpha hemolytic Bile optochin resistant ▪ Streptococcus pyogenes (Group A Beta- Hemolytic Streptococci) Catalase – Beta hemolytic Bacitracin sensitive ▪ Streptococcus agalactiae (Group B Beta- hemolytic Streptococci) Catalase – Beta hemolytic FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 4 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY Bacitracin resistant o Tx: Antistaphylococcal penicillins (Nafcillin, Oxacillin); ▪ Group D streptococci Vancomycin (MRSA), Linezolid (VRSA) Catalase – Clinical syndromes gamma hemolytic o Skin, soft tissue infections bullous impetigo, folliculitis, ▪ All streptococci are catalase negative carbuncle, furuncle, cellulitis, hidradenitis suppurativa, Gram Positive Bacilli SSI o Spore – formers o Abscess – S. aureus makes coagulase and forms fibrin around itself forming the abscess o Acute endocarditis ▪ MCC of acute endocarditis (Tricuspid in IV drug Mnemonic: Remember your ABCS: Autoclave kills Bacillus users) and Clostridia Spores o Nosocomial pneumonia, empyema, necrotizing ▪ Bacillus anthracis- pneumonia Box car shaped o Osteomyelitis and septic Arthritis (Brodie Abscess) o Gastroenteritis: salad with mayonnaise medusa head ▪ due to ingestion of preformed nonmotile toxin ▪ Bacillus cereus ▪ short incubation period reheated fried rice ▪ (2–6 hr) followed by nonbloody motile diarrhea and emesis. ▪ Clostridium botulinum ▪ Enterotoxin is heat stable →not bulging cans ▪ destroyed by cooking. ▪ Clostridium tetani o SSS (Ritter disease) separation of epidermo- dermal tennis racket, drumstick, or lollipop junction ▪ Clostridium/Clostridioides perfringens o Toxic Shock Syndrome (TSS) tampon using Gas forming menstruation or patients with nasal pack o Non – spore formers ▪ Increse in AST, ALT, bilirubin. ▪ Corynebacterium diphtheria MRSA (methicillin-resistant S aureus) Chinese characters, curved o important cause of serious healthcare associated and non-motile community-acquired infections. ▪ Listeria monocytogenes o Resistance due to altered penicillin binding proteins Curved (conferred by mecA gene). Tumbling motility o Some strains release Panton-Valentine leukocidin (PVL), which kills leukocytes and causes tissue necrosis. Staphylococcus aureus Metabolism: Staphylococcus epidermidis o Catalase positive Metabolism: o Coagulase positive o Catalase + o Facultative anaerobe o Coagulase – Transmission: o Facultative anaerobe o Reservoir is anterior nares and skin transmitted through o Novobiocin SENSITIVE direct contact and fomites, contaminated food Transmission: Virulence Factors: o Reservoir is skin o Coagulase allows insoluble fibrin formation around o Transmitted through direct contact organism, protecting from phagocytosis o autoinfection o Leukocidin for WBC Virulence Factors: o Catalase detoxifies H202 o Polysaccharide capsule adheres to variety of prosthetic o Penicillinase disrupts beta lactam portion of the penicillin devices, forms biofiim molecule o Highly resistant to antibiotics o Hyaluronidase (spreading factor), breaks down Clinical Syndromes proteoglycans in CT o MCC of Prosthetic valve endocarditis o Protein A - binds Fc-IgG, inhibiting complement o Septic arthritis in prostheses activation and phagocytosis. o Ventriculoperitoneal Shunt infections Toxins: Diagnosis and Treatment: o Exfoliatin – Scalded Skin Syndrome o Culture o Enterotoxin – Food Poisoning ▪ White, non-hemolytic colonies o TSST – Superantigen causing Toxic Shock Syndrome o Antibiotic: Vancomycin o Alpha Toxin – Necrosis of skin and hemolysis o Removal of prosthetic device Diagnosis and Treatment: o Gram Positive cocci in grape-like Staphylococcus saprophyticus clusters Metabolism: o Beta hemolytic, golden colonies o Catalase + on Blood Agar o Coagulase – o PCR – mecA gene o Facultative anaerobe o Novobiocin RESISTANT Transmission: FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 5 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY o Reservoir are humans ▪ deeper infection Virulence Factors: involves o None subcutaneous Clinical syndromes o Pharyngitis o UTI in women ▪ MCC bacterial ▪ 2nd MCC of UTI in sexually active women pharyngitis Diagnosis and Treatment: o Scarlet fever o Fluoroquinolone and cotrimoxazole ▪ 2nd disease, strawberry tongue, Streptococcus pyogenes (GABHS) desquamation, sandpaper like Metabolism: centrifugal rash o Catalase negative o Necrotizing fasciitis, Fournier gangrene o Bacitracin SENSITIVE ▪ involves male genital area o Acute Rheumatic Fever ▪ post- pharyngitis cross Mnemonic: Bacitracin’s BRAS reacting antibodies to M B (grp B Strep) is RESISTANT proteins and antigens of A (grp A strep) is SENSITIVE joint, heart and brain Transmission: tissue o Reservoir: Humans ▪ Diagnosed using the o Transmitted through respiratory droplets JONES CRITERIA Virulence Factors: ▪ Rheumatic fever patients require long term o Hyaluronic acid capsule and M protein inhibit antibiotic prophylaxis to prevent recurrence of phagocytosis. the disease o Antibodies to M protein enhance host defenses. o APSGN- Acute post streptococcal Glomerulephritis o Structurally similar to host proteins (ie, myosin); can lead ▪ Postpharyngitic or post-impetigo M proteins to autoimmunity (ie, carditis seen in acute rheumatic incite immune-complex deposition fever). ▪ S/s: Hypertension, periorbital edema, o Hyaluronidase hematuria ▪ Spreading factor, degrades hyaluronic acid o Streptokinase Streptococcus agalactiae (GBS) ▪ Fibrinolysin Metabolism: ▪ Lyses fibrin, management in acute MI o Catalase negative o DNAse o Bacitracin RESISTANT ▪ Degrades DNA in exudates or necrotic tissue Transmission: Toxins: o Reservoir: Vagina o Erythrogenic Toxin o Transvaginal and transplacental ▪ Scarlet fever Clinical syndromes o Streptolysin O ▪ Reason for beta hemolysis, pharyngitis o UTI in pregnant women o Neonatal pneumonia, sepsis and meningitis o Exotoxin A ▪ MCC is GBS ▪ Pyogeninc; superantigen similar to TSS toxin o Exotoxin B ▪ Rapidly destroys tissue, necrotizing fasciitis Diagnosis and Treatment: o Gram Stain: Gram positive in chains Causative Agents of Neonatal Meningitis (B – E – L) group B strep, E.coli, Listeria o Beta hemolytic o Positive PYR test Diagnosis o Tx: Penicillin G o Gram stain: Gram Positive Cocci in chains o Beta Hemolytic Clinical Syndrome Treatment: o Impetigo o Penicillin G + Aminoglycoside for serious infections contagiosa ▪ honey Group D Streptococci colored Metabolism: crust, o Catalase Negative perioral o Bile Optochin Resistant blisters Transmission: with accumulation of neutrophils o Reservoir: Human o Erysipelas o Urethra and Female Genitalia may be colonized ▪ superficial infection up to dermal layer Clinical syndromes o Cellulitis o UTI due to indwelling urinary catheter and instrumentation o Biliary tract infections FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 6 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY o Endocarditis in patients who underwent GIT surgery Diagnosis and Treatment: o Marantic endocarditis in patients with abdominal o Penicillin G +/- Gentamicin malignancy (Streptococcus bovis) o Vancomycin for penicillin resistance Diagnosis and Treatment: o Linezolid for vancomycin resistance o Dx: Gram positive in chains; Gamma hemolytic o Tx: Penicillin + gentamicinVancomycin for resistant, Streptococcus gallolyticus Linezolid Previously S. bovis Can cause bacteremia and infective endocarditis. Streptococcus pneumoniae Patients with S gallolyticus endocarditis have Increase Metabolism: incidence of colon cancer. o Catalase negative o Bile Optochin Sensitive Enterococci E faecalis and E faecium normal colonic microbiota Catalase ⊝, PYR ⊕, typically nonhemolytic. Optochin Test Mnemonic: OVeR PaSs penicillin G resistant Viridans (and grp D) – RESISTANT cause UTI, biliary tract infections, and infective endocarditis Pneumoniae - SENSITIVE (following GI/GU procedures). VRE (vancomycin-resistant enterococci) are an important Transmission: cause of healthcare-associated infection. o Upper Respiratory Tract Droplets Enterococci are more resilient than streptococci, can grow in Virulence Factors: 6.5% NaCl and bile o Polysaccharide capsule ▪ MAJO Virulence Factor ▪ Retards phagocytosis Bacillus anthracis o Positive Quellung Reaction Transmission: ▪ Swelling of capsule o Habitat: Soil o IgA protease for colonization o Via inhalation of spores from animal wool or hair Clinical syndromes o Human to human transmission has never been reported o Pneumonia Virulence Factors: ▪ MCC of CAP in adults o Protein capsule ▪ Rust-colored sputum ▪ Polymer of gamma-D-glutamic acid o Otitis Media ONLY Bacterium with Protein Capsule ▪ MCC in Children ▪ Antiphagocytic o Bacterial meningitis o Virulence depends on acquiring 2 plasmids o Sinusitis Toxins: o Septic Shock in splenectomy patients as it predisposes to o Exotoxin sepsis from encapsulated bacteria ▪ Contains 3 separate proteins by which by themselves are nontoxic but when together produce the systemic effects of anthrax Diagnosis S. pneumoniae most commonly causes MOPS o Aerobic gram positive Box-car shaped rod Meningitis o Spore forming Otitis media (in children) o Non motile Pneumonia o Medusa head morphology on culture Sinusitis o Serology o PCR of nasal swab Diagnosis and Treatment: Treatment o Penicillin G o Ciprofloxacin o Ceftriaxone plus Vancomycin for resistant o Doxycycline o Raxibacumab Viridans Streptococci ▪ Monoclonal Ab for use in inhalational anthrax Metabolism: o Vaccine for high risk individuals o Catalase negative Clinical Syndrome o Bile and Optochin resistant o Cutaneous anthrax Transmission: ▪ MC route of entry- o Enters through bloodstream during dental procedures Direct contact with Virulence Factors: the spores causes o Glycocalyx localized tissue ▪ enhances adhesion to damaged heart valves necrosis, evidence ▪ Protected from host defenses within by a painless round vegetations black lesion Clinical syndromes malignant pustule o Dental caries – S. mutans ▪ Mortality 20% o Subacute bacterial endocarditis – S. sanguis o inhalational anthrax o Brain abscess – S. intermedius FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 7 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY ▪ inhaled spores from animals (Woolsorter's Clostridium tetani disease) or from Transmission: bioterrorism, o Habitat: Soil weaponized o Endospores are introduced to break in skin preparations Virulence Factors: ▪ Causes o Flagella, H positive prolonged latent Toxins: period before o Tetanospasmin rapid ▪ Tetanus toxin is taken up at the NMJ deterioration transported to CNS acts as inhibitory, ▪ Massively preventing release of GABA, the inhibition of enlarged mediastinal LN pulmonary inhibitors results to tetany hemorrhage (MCC of death), meningeal symptoms ▪ Mortality 100% without immediate treatment o Gastrointestinal anthrax ▪ ingestion of spores leads to UGI ulceration, edema, and sepsis. ▪ Vomiting, abdominal pain, bloody diarrhea, ▪ rapidly progressive course. ▪ Mortality approaches 100% Bacillus cereus Clinical syndromes Transmission: o Tetanus o Endospores on grains survive steaming and rapid frying ▪ Hypertonia, Painful muscular contractions in ▪ Germinates when rice is kept warm for many jaw and neck, and generalized, muscle hours (reheated fried rice) spasms without any medical causes Toxins: ▪ Trismus, risus sardonicus, opisthotonos, o Enterotoxin respiratory muscle paralysis ▪ Heat – labile o Neonatal Tetanus Similar to enterotoxin of cholera ▪ A child with normal sucking and cry in the first Causes ADP ribosylation → inc. 2 days of life and losses these abilities between cAMP 3-28 days of life. ▪ Heat – stable ▪ Becomes rigid and has spasms Staphylococcal – like enterotoxin Diagnosis and Treatment: Functions as a superantigen o Anaerobic, with endophore at one end (drumstick, tennis o Virulence factor: no capsule racket, or lollipop) Clinical syndromes o Tx: Metronidazole (alt. is penicillin) o Emetic form ▪ Rice Clostridium botulinum ▪ Short incubation Transmission: ▪ Short duration o Habitat: Soil ▪ Heat stable similar to staphylococcal food o Endospores that are heat resistant stored in zip-locks, poisoning home-canned, smoked fish o Diarrheal form ▪ Meat o Bulging canned goods ▪ Long incubation Virulence Factors: ▪ Diarrhea o flagella ▪ Longer duration Toxins: ▪ Heat labile o Botulinum toxin o Ophthalmitis ▪ Neurotoxin inhibits the release of Ach from ▪ Penetrating injury of the eye with soil- peripheral nerves causes flaccid paralysis contaminated object ▪ Not secreted but released upon the death of ▪ Complete loss of light perception within 48 bacterium hours Diagnosis o Aerobic o Motile o Culture specimen from suspected food source Treatment: o Symptomatic Treatment o Resistant to beta lactam antibiotics o Vancomycin for the ophthalmitis Clinical syndromes o Botulism ▪ Food borne FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 8 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY Eye symptoms, anticholinergic signs, ▪ Is antibiotic- descending flaccid paralysis, associated respiratory paralysis diarrhea by ▪ Infant Botulism suppressing the Baby ingested honey or dust with normal flora spores allowing C. Floppy baby Syndrome difficile to ▪ Wound botulism overgrow Similar to food botulism but without GI Usually caused by Clindamycin, symptoms ampicillin, 2nd-3rd gen cephalosporins Diagnosis ▪ Nonbloody diarrhea associated with o Requires anaerobic condition pseudomembranes o Thioglycolate agar ▪ Toxic megacolon o Patient’s serum injection to mice causing death Diagnosis Treatment and Prevention o Exotoxin detected by cytopathic effect on cultured cells o Antitoxin o ELISA o Human botulism Ig o Colonoscopy o Metronidazole or penicillin Treatment: o Supportive Tx o Withdraw causative antibiotic o Botox – used in wrinkle removal o Metronidazole, oral vancomycin o Replace fluids Clostridium perfringens o surgery Transmission: o Endospores Corynebacterium diphtheriae o Myonecrosis from Metabolism: contamination of wound o Facultative anaerobe with soil or feces o Catalase positive o Food poisoning by Transmission: ingestion of contaminated o Reservoir: throat food o Transmitted by respiratory Toxins: droplets o Alpha toxin Virulence Factors: ▪ Lecithinase o pseudomembrane splits lecithin Toxins: cleaves cell membranes o Exotoxin – from a temperate Clinical syndromes bacteriophage o Gas Gangrene ▪ Subunit A has ADP ribosylation activity which ▪ d/t alpha toxin, gas by anaerobic metabolism, blocks protein synthesis (like human antibiotic) pain ▪ Subunit B provides entry into cardiac and Diagnosis: neural tissue o Culture under anaerobic conditions Clinical syndromes o Double hemolysis on blood agar o Diphtheria o Growth on egg yolk agar, rapidly spreading ▪ Mild sore throat with fever initially Treatment: ▪ Pseudomembranes forms on the pharynx o Wound care, penicillin, radical surgery, supportive (results from death of mucosal epithelial cells o Myocarditis Clostridium/Clostridiodes difficile ▪ AV block o Neural involvement Transmission: ▪ GBS, palatal paralysis, neuropathies, o Carried in the colon, fecal oral ingestion of endospores peripheral nerve palsies o Hospital personnel hands are important intermediaries Diagnosis Toxins: o Club/comma – shaped rods arranged in V or L o Exotoxins A and B ▪ Looks like Chinese characters ▪ Inhibit GTPases then death of enterocytes o Culture: Potassium tellurite produces pseudomembranes o Modified Elek Test: for detection of antigenicity ▪ Toxin A – diarrhea o Shick test: determines susceptibility of infection ▪ Toxin B – Cytotoxic to colonic epithelial cells Treatment and Prevention Clinical syndromes o Antitoxin o Pseudomembranous enterocolitis o Penicillin or Erythromycin o Vaccine DPT is a formalin inactivated exotoxin Listeria monocytogenes Transmission: FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 9 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY o Ubiquitous and colonizes GIT and GUT transmitted by Gram – Negative Bacteria ingestion of contaminated raw milk or cheese from infected cows Toxins: o Listeriolysin O ▪ Allows escape from phagolysosomes o Actin rockets ▪ Propels through bacteria through one membrane to another o The only gram positive that produces LPS Clinical syndromes o Early onset neonatal listeriosis ▪ Granulomatosis infanseptica ▪ Leads to late miscarriage, birth complicated by sepsis, multiorgan abscesses, and disseminated granulomas o Late onset neonatal listeriosis ▪ Meningitis, meningoencephalitis o Adult listeriosis ▪ 2nd MCC of meningitis >50 yo Neisseria meningitidis ▪ MCC of meningitis in immunoompromised Metabolism: patients o Ferments both maltose and glucose o Septicemia o Oxidase Positive on chocolate agar ▪ In pregnant women o Grows best in high CO2 o Remember B-E-L Transmission: Diagnosis o URT droplets o Rods arranged in V or L shapes o high carriage in close quarters, dormitories, camps o Tumbling motility o Neonates are very susceptible from 6 – 24 months o Culture can grow at cold enrichment to isolate from Virulence Factors: normal flora o Capsule 13 serotypes o Facultative intracellular o Endotoxin LPS causes blood vessel destruction and Treatment and prevention sepsis o Ampicillin + Gentamicin o Pili allow attachement to human Nasopharynx and o TMP + SMX undergo antigenic variation to avoid attack by immune o NOT Cephalosporins system. Toxins: Gram Positive with Branching Elements o Endotoxin o Lipopolysaccharide Clinical syndromes: o Meningitis ▪ MCC among 2-18 yrs old ▪ SSx: fever, headache, stiff neck, and inc. level of PMNs in CSF !!!Review on the CSF fluid picture of the different forms of meningitis! -Dr. Manatad o Meningococcemia ▪ dissemination of meningococci into the bloodstream Multiorgan disease, petechial or purpuric rash (purpura fulminant) o Waterhouse-Friedrichsen Syndrome ▪ Most severe form of meningococcemia ▪ Ssx: high fever, shock, widespread purpura, DIC, thrombocytopenia, and adrenal insufficiency (bilateral hemorrhagic destruction of adrenal glands) Diagnosis: o Gram negative kidney bean diplococcus o Selective media prevents growth of bacteria using Thayer Martin Agar Treatment and Prevention: o Penicillin o Ceftriaxone for treatment of meningococcal meningitis FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 10 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY o Rifampin or ciprofloxacin prophylaxis for close contacts Vancomycin: Inhibits gram-positive o Vaccine flora Nyslatin: Inhibits yeast flora Neisseria gonorrhoeae Trimethoprim: Iinhibits swarming Metabolism: Proteus o Facultative anaerobe Treatment and Prevention: o Ferments Glucose ONLY o Ceftriaxone + Doxycycline to cover for Chlamydia o Oxidase positive in cholocolate agar o Erythromycin ointment or silver nitrate to prevent o Grows best in high CO2 ophthalmia neonatorum Transmission: o Silver nitrate no longer used o Sexually transmitted, passage thorugh birth canal o No immunity to repeated infections Moraxella Catarrhalis Virulence Factors: Transmission: o Pili o Part of normal flora ▪ Adheres to epithelial cells Clinical syndromes: ▪ For antigenic variation o Otitis Media in children ▪ Antiphagocytic, binds bacteria tightly to host o COPD Exacerbation cells protecting from phagocytosis o Sinusitis, bronchitis, pneumonia ▪ Outer membrane promotes Invasion into Treatment and Prevention: epithelial cells o Azithromycin or Clarithromycin ▪ Opa protein for adherence and invasion o Co-Amoxiclav Toxins: o Cotrimoxazole o Endotoxin o Resistant to Penicillin o Lipopolysaccharide o No Exotoxin Haemophilus influenzae Clinical syndromes: Metabolism: o Gonococcal Urethritis o Required for growth ▪ MCC of urethritis. ▪ X factor (Hematin ▪ Plus Epididymitis in men. ▪ V factor (NAD+) o Cervical gonorrhea o Satellite growth around S. aureus colonies ▪ In women, can progress to Pelvic Transmission: inflammatory disease o Via respiratory route Complications: Sterility, Ectopic o Nontypable strains colonize the nasopharynx in up to pregnancy, dyspareunia, chronic pelvic 80% of individuals pain, Virulence Factors: perihepatitis o Capsule – type B is most virulent (Fitz-Hugh- o Composed of Polyribitol ribose phosphate Curtis o Pili - attachment syndrome) Clinical syndromes: violin string o Gonococcal arthritis o Meningitis ▪ MCC of septic arthritis in sexually active ▪ Most serious manifestation of HiB infection ▪ one of the primary causes of meningitis in individuals o Ophthalmia neonatorum infants from 3-36 mos of age. ▪ Antecendent URTI are common. ▪ purulent conjunctivitis in newborns o Acute epiglottitis o Bacterial conjunctivitis ▪ fever sore throat, dysphagia, DOB ▪ MCC of hyperacute bacterial ▪ thumb sign in Xray conjunctivitis also the most severe o Pneumonia o Asymptomatic gonococcal infection in women o Cellulitis ▪ site in endocervix o Septic arthritis o Sepsis in asplenic patients. o Complement deficiency (C6-C9) ▪ predispose to illness because it cannot form Diagnosis: membrane attack complexes. (Both Neisseria) o Coccobacillary rods Diagnosis: o Culture on blood agar heated to 80C o Gram negative kidney bean shaped diplococcus forming o Grows best when place in a high CO2 environment doughnut appearance o Positive Quellung test o Selective media prevents growth of bacteria using Treatment and Prevention: Thayer Martin Agar o Co-Amoxiclav for Otitis Media ▪ Components of Modified Thayer Martin Agar o Ceftriaxone for meningitis Colistin: Inhibits gram-negative flora o Rifampin for close contacts (N. gonorrhoeae and N. meningitidis o Hib Vaccine resistant to colistin, most saprophyic species of Neisseria susceptible) FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 11 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY Bordetella pertussis o visualized with silver stain Transmission: o Serology o Via respiratory droplets o Urine antigen test Virulence Factors: Treatment and Prevention: o Capsule o Azithromycin o Beta lactamase o Levofloxacin o Filamentous hemagglutinin mediates attachment o Doxycycline Toxins: o Reducing cigarette and alcohol consumption o Pertussis Toxin – ADP ribosylation activates G prtoeins o High temperatures and hyperchlorination in hospital → increase cAMP water supply o Extracytoplasmic adenylate cyclase – inhibits phagocytosis Escherichia coli o Tracheal cytotoxin kills epithelial cells and paralyze cilia Metabolism: causing the whooping cough o Indole Positive Clinical syndromes: o Lactose fermenter on EMB and MacConkey agar o Whooping cough o Green metallic sheen on EMB ▪ paroxysmal pattern of hacking coughs o Triple Sugar Iron Agar shows acid with gas and no H2S associated with production of copious amounts production of mucus. Transmission: ▪ Incubation period: 7-10 days o Habitat: Colon ▪ Catarrhal phase 1-2 weeks, highly contagious o Colonizes vagina and urethra antibiotics most effective o Ascending infection, fecal-oral, aspiration, or during birth ▪ Paroxysmal stage: Whooping, Antibiotics not Virulence Factors: effective o Fimbriae ▪ Convalescent stage: development of o Pili for attachment causes cystitis and pyelonephritis secondary complications o Capsule (K Antigen) Diagnosis: o Flagella (H Antigen) o Small rods o Siderophore obtains iron from human transferrin or o Culture in Bordet-gengou agar lactoferrin o ELISA Toxins: o PCR detection of bacterial DNA o Endotoxin – Lipid A portion of LPS Treatment and Prevention: o Entero toxins o Erythromycin Clinical syndromes: ▪ Most effective when given in catarrhal stage o BEL - Neonatal meningitis o DPT vaccine o UTI o Treat also household contacts o Nosocomial sepsis, o nosocomial pneumonia Legionella pneumophila o Diarrhea Metabolism: ▪ ETEC - releases LT and ST toxins, Traveller's o Growth depends on L-cysteine and Iron in chocolate diarrhea yeast extract agar ▪ EIEC- bloody diarrhea with pus in the stool Transmission: ▪ EPEC - watery diarrhea of long o Ubiquitous in man and natural water envlronments duration, Pediatric o Airconditioning systems ▪ EHEC - E.coli strain O157:H7 o No person-to-person transmission Transmitted via undercooked meat Virulence Factors: Secretes shiga-like toxin (verotoxin) o Facultative intracellular organism: cell- mediated causes hemorrhagic colitis and immunity is important hemolytic uremic syndrome Toxins: Does not ferment sorbitol o Endotoxin No fever, no pus in stool o Cytotoxins: Kill hamster ovary cells Diagnosis: Clinical syndromes: o Facultattive gram negative rods o Pontiac fever o Beta hemolytic ▪ mild flu-like illness, self-limiting in a week o Typing by O and H antigen o Atypical pneumonia Treatment and Prevention: ▪ accompanied by nonbloody diarrhea, o Ampicillin or sulfonamides hyponatremia, confusion, hematuria o Rehydration is effective in Traveler’s diarrhea o Legionnaires disease ▪ was first discovered in 1976 after an outbreak Shigella spp. of pneumonia at an American Legion Metabolism: convention in Philadelphia. o No H2S productlon Diagnosis: o Non lactose fermenter o Nutritionally fastidious o Produce no gas from fermentation of glucose o pleomorphic o poorly gram-negative rods FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 12 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY Shigella is usually the “biochemically inert” enterobacteriaceae, as it Gastrectomy or use of antacids lowers yields negative biochemical tests infectious dose significantly. non-chalant si Shigella SSx: N/V, abdominal pain and - Dr. Manatad nonbloody diarrhea Transmission: o S. typhi o Fecal oral Route ▪ Typhoid fever ▪ 4 Fs Due to capsular antigen Food Organism enters Peyer's patches and Fingers then spread through reticuloendothelial system Feces Predilection for invasion to gall bladder Flies (chronic carrier state) Virulence Factors: o S. cholerasuis o Invades submucosa of intestinal tract but not lamina ▪ Septicemia propria Bacteremia results in seeding to many o Local inflammation with ulceration organs osteomyelitis, pneumonia, o It has a low infective rate therefore highly infectious meningitis o 200 bacilli vs Salmonelle infective dose is 10^5 to 10^8 o Invasion of m cells is key to pathogenicity Commonly seen in patients with sickle cell anemia Toxins: o Shiga Toxin Fever but without enterocolitis ▪ Inactivates the 60s Ribosomes, inhibiting protein synthesis and killing epithelial cells Diagnosis: ▪ Protein synthesis inhibitor of eukaryotes o Widal Test detects antibodies in serum Clinical syndromes: o XLD – culture o Bacillary dysentery o Bone marrow culture – Gold Standard Diagnosis ▪ Incubation is 1 – 4 days. Treatment and Prevention: ▪ Fever, abdominal cramps, diarrhea o In the PH ▪ Initially watery then bloody ▪ Amoxicillin, chloramphenicol, TMP- SMX ▪ Frequently resolves in 2 or 3 days ▪ lgA is best for immunity Vibrio spp. ▪ More toxic than Salmonella Metabolism: Diagnosis: o Oxidase positive o Gram negative nonmotile rods o Non lactose fermenters o Have O antigens Transmission: o Cultured in XLD agar (Xylose Lysine Deoxycholate) o V. cholerae – fecal oral route o Stool culture o V. parahemolyticus – contaminated raw seafood Treatment and Prevention: o V. vulnificus – trauma to skin esp. shellfish handlers o Ciprofloxacin in severe cases Virulence Factors: o Fluid and electrolyte replacement o Motile shooting star motility o Fimbriae helps with attachment Salmonella spp o Non-invasive Metabolism: Toxins: o Never part of normal flora o Choleragen o Facultative intracellular organism ▪ Acts by ADP ribosylation o Produces H2S ▪ Increase cAMP then secretion of electrolytes o Non lactose fermenter Clinical syndromes: Salmonella and shigella are usually compared with one another as o V. cholerae sometimes they can present with the same symptoms and present ▪ Cholera the same in initial gram staining and routine cultures. Severe diarrhea with rice water stools; -Dr. Manatad no pus Transmission: Washer woman's hands sign o Fecal oral route o wrinkled skin due to dehydration Virulence Factors: Diagnosis: o H antigen o Comma shaped with single polar flagellum o Capsule o Grows as flat yellow colonies on TCBS agar o Siderophores Treatment and Prevention: o Lives within macrophages in Lymph nodes and can live o Tetracycline or azithromycin shortens duration of cholera in Gall bladder for years o Minocycline plus fluoroquinolone o Asplenic patients are high risk o Cholera vaccine Clinical syndromes: o S. enteritidis Campylobacter jejuni ▪ Enterocolitis Metabolism: Invasion of the epithelial and o Microaerophilic subepithelial tissue of small and large o Oxidase positive intestine o Catalase positive FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 13 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY Transmission: ▪ MCC of duodenal ulcers o Fecal oral by ingesting undercooked chicken or o Associated with gastric CA and MALT Lymphoma unpasteurized milk Diagnosis: Virulence Factors: o Curved with tuft or polar flagella o Motile H antigen o Lophotrichous o Invasive but does not penetrate therefore sepsis rarely o EGD with biopsy occurs o Urease breath test and stool antigen for documenting cure Treatment and Prevention: o Triple therapy Catalase Positive Organisms ▪ Omeprazole Mnemonic: Catalase Positive: Notoriously Big Bubbling ▪ Clarithromycin HASSLE. ▪ Amoxicillin/Metronidazole o Quadruple therapy Candida, Pseudomonas, Nocardia, Bordetella pertussis, ▪ Tetracycline Burkholderia cepacia, Helicobacter pylori, Aspergillus, ▪ Omeprazole Staphylococci, Serratia, Listeria, E coli. ▪ Metronidazole Toxins: ▪ Bismuth salicylate o Enterotoxin similar to cholera o cytotoxin Klebsiella pneumoniae Clinical Syndromes: Metabolism: o Gastroenteritis o Urease positive ▪ MCC of bacterial gastroenteritis and may o Indole negative mimic ulcerative colitis. Transmission: ▪ Watery and foul smelling followed by bloody o Aspiration or inhalation stools o Ascending spread of fecal flora o Gullain barre syndrome Virulence Factors: ▪ Antigenic cross reaction in bacterial o capsule oligosaccharides. Clinical syndromes: ▪ Often occurs after 2-4 weeks of C. jejuni o Necrotizing Pneumonia infection ▪ MCC in alcoholic o Reactive arthritis (Reiter syndrome) ▪ Usually nosocomial with thick bloody sputum ▪ Triad of Uveitis, Urethritis, Arthritis o UTI Can't see, can't pee, can't climb a tree o Sepsis Diagnosis: Diagnosis: o Comma shaped or S- shaped with single polar flagellum o Facultative with Large polysaccharide capsule o Skirrow’s agar o Currant jelly sputum Treatment and Prevention: Treatment and Prevention: o Symptomatic treatment o Culture guided treatment o Erythromycin for severe cases o Cephalosporins +/- Aminoglycosides Proteus mirabilis Helicobacter pylori Metabolism: Metabolism: o Urease positive o Microaerophilic o Indole negative o Oxidase positive o Non lactose fermenter o Catalase positive Virulence Factors: o Urease positive o Motile o Triple positive o Fimbriae for adherence Transmission: o LPS o Ingestion o Urease production o Habitat: human stomach Clinical syndromes: Virulence Factors: o Complicated UTI associated with nephrolithiasis o Urease produces ammonia makes the environment o Sepsis alkaline helps H. pylori survive acidic stomach Diagnosis: o Damages goblet cells o Facultative gram negative with peritrichous flagella o Swarming pattern Treatment and Prevention: o Ampicillin Urease Positive Organisms o TMP- SMX Mnemonic: Pee CHUNKSS. Pseudomonas aeruginosa Proteus, Cryptococcus, H. pylori, Ureaplasma, Nocardia, Klebsiella, S epidermidis, S. saprophyticus. Metabolism: o Non lactose fermenter Clinical syndromes: o Oxidase positive o Peptic ulcer disease Transmission: FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 14 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY o Habitat: environmental water sources Chlamydia trachomatis o Via water aerosols, aspiration and fecal contamination Metabolism: o Medical devices and hands of hospital personnel o Obligate intracellular parasite Virulence Factors: Transmission: o Motile o Sexual o Elastase – vascular necrosis o Passage through birth canal o Protease – destroy antibody and complement o Hand to eye contact o Pyocyanin – damages cilia and mucosal cells Virulence Factors: o Verdoglobin – from hemoglobin breakdown o Resistant to lysozyme o Phospholipase C Clinical syndromes: o DNAse o Trachoma o Antiphagocytic mucopolysaccharide capsule (biofilm) ▪ Leading infectious disease of blindness Toxins: o Chronic keratoconjunctivitis o Endotoxin ▪ Types A-C o Exotoxin A o Genital tract infection ▪ Similar to diphteria toxin; inhibits protein ▪ MCC of STDs synthesis by blocking EF2 ▪ Types D-K ▪ Causes tissue necrosis o Neonatal pneumonia Clinical Syndromes: ▪ Staccatio cough o Burn and wound infections o Lymphogranuloma venereum o Hot tub folliculitis ▪ Papules or vesicles that ulcerates into buboes ▪ spa pools, whirlpools, or inadequately ▪ Types L1-L3 chlorinated swimming pools and tubs Diagnosis: o Skin graft loss o Cytoplasmic inclusions o Green nail syndrome o PCR o Bone and cartilage infections o NAAT o Ear infections Treatment and Prevention: ▪ MCC of otitis EXTERNA o Doxycycline o Pneumonia - ventilator assisted o Erythromycin o Necrotizing pneumonia o Azithromycin ▪ fleur-de-lis pattern o Ceftriaxone o Gastrointestinal infections o Ecthyma gangrenosum Mycobacteria ▪ hemorrhagic lesions Mycobacterium tuberculosis Diagnosis: o Obligate aerobe Metabolism: o Culture on cetrimide agar o Slow grower o Greenish metallic colonies o Obligate aerobe o Sweet grape-like odor o Acid fast organism Treatment and Prevention: Transmission: o Antipseudomonal penicillins o Inhalation of respiratory droplet nuclei o 3rd and 4th gen cephalosporins o It survives and multiplies in macrophages o Carbapenem Virulence Factors: o Ciprofloxacin o Mycolic acid – large FA o Cord factor Bacteroides fragilis ▪ only found in virulent strain ▪ most important VF Transmission: ▪ it inhibits neutrophil migration and damages o Predominant anaerobe of the human colon mitochondria o Spreads to blood during bowel trauma o sulfatides Virulence Factors: o wax D o Capsular polysaccharide o tuberculin surface protein o Pili ▪ responsible for delayed hypersensitivity Toxins: Clinical syndromes: o Lipid A o Exudative and granulomatous lesions Clinical syndromes: ▪ Langhan’s type giant cells o Abdominal abscess o Primary Complex o Peritonitis ▪ Usually in middle or lower lobes o Pericarditis o Ghon Complex o Endocarditis o Ranke Complex o Cerebral abscess o Reactivation Tuberculosis Diagnosis: o Anaerobic gram negative Treatment and Prevention: o Metronidazole – DOC o Chloramphenicol FOCUS REVIEW CENTER | Focus Review Center | [email protected] Page 15 of 40 OCTOBER 2024 COMPREHENSIVE REVIEW PROGRAM | TIER I HANDOUT | MICROBIOLOGY AND PARASITOLOGY Mycobacterium leprae Transmission: o Prolonged exposure to nasal secretions with lepromatous form Clinical syndromes: o Leprosy/Hansen Disease ▪ MCC of crippling of the hand ▪ Glove ▪ 2 forms (many cases fall temporarily between two extremes): Lepromatous o presents diffusely over the skin, with leonine (lionlike) facies o communicable (high bacterial