3 - MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT OCT 2024 JAMIE GAIL ALIMONDO-unlocked.pdf

TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid...

TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. PROKARYOTES EUKARYOTES IMPORTANT LEGAL INFORMATION DNA within a nuclear NO YES membrane? The handouts, videos and other review materials, provided by Topnotch Medical Board Mitotic division? NO YES Preparation Incorporated are duly protected by RA 8293 otherwise known as the DNA associated with Intellectual Property Code of the Philippines, and shall only be for the sole use of the person: NO YES a) whose name appear on the handout or review material, b) person subscribed to Topnotch histones? Medical Board Preparation Incorporated Program or c) is the recipient of this electronic Chromosome number? 1 >1 communication. No part of the handout, video or other review material may be reproduced, shared, sold and distributed through any printed form, audio or video recording, electronic Membrane-bound NO YES medium or machine-readable form, in whole or in part without the written consent of organelles? Topnotch Medical Board Preparation Incorporated. Any violation and or infringement, whether intended or otherwise shall be subject to legal action and prosecution to the full Size of ribosome? 50S + 30S = 70S 60S + 40S = 80s extent guaranteed by law. Cell wall containing YES NO peptidoglycan? DISCLOSURE As a mnemonic in remembering the size of the ribosomes The handouts/review materials must be treated with utmost confidentiality. It shall be the Prokaryotes = ODD first digit (i.e., 30s, 50s, 70s) responsibility of the person, whose name appears therein, that the handouts/review materials are not photocopied or in any way reproduced, shared or lent to any person or disposed in any Eukaryotes = EVEN first digit (i.e., 40s, 60s, 80s) Dr. Rubio manner. Any handout/review material found in the possession of another person whose name does not appear therein shall be prima facie evidence of violation of RA 8293. Topnotch review materials are updated every six (6) months based on the current trends and feedback. Please S stands for Svedberg unit buy all recommended review books and other materials listed below. THIS HANDOUT IS NOT FOR SALE! This handout is only valid for the October 2024 PLE batch. This will be rendered obsolete for the next batch © Topnotch Medical Board Prep since we update our handouts regularly. MICROBIOLOGY By Jan Bendric C. Borbe, RMT, MD Frinz Moey C. Rubio, MD Contributors: Pacifico Eric E. Calderon, MD Tiffany Grace C. Uy-Poon, MD Juan Lorenzo D. Santos, MD Rizal Michael R. Abello, MD TOPIC PAGE 1. Generalities 1 2. Bacteriology 9 3. Virology 35 4. Parasitology 48 © Topnotch Medical Board Prep 5. Entomology 64 This figure is useful for correlation to antimicrobial pharmacology. Note 6. Mycology 66 the groups of drugs that target the 30S and 50S ribosomal subunits: 30s – Aminoglycosides, Tetracyclines 50s – Chloramphenicol, macrolides (e.g., Erythromycin), Lincosamides (e.g., GENERALITIES clindamycin), Linezolid, Streptogramins (e.g., dalfopristin / quinupristin) Dr. Calderon MICROBIAL GROUPS Microorganisms – classified as such because they are ‘true’ MNEMONIC organisms because they have ‘cells’ BUYS AT 30, CELLS for 50! o Bacteria AT – aminoglycosides, tetracyclines o Protozoa CELLS – chloramphenicol, erythromycin, linezolid, o Microscopic algae lincosamides (clindamycin), streptogramin § The medically important one cause red tide poisoning – ✔GUIDE QUESTIONS which produces saxitoxin – Na+ channel blocker) Which of the following organisms lack membrane sterols? o Fungi A. Yeasts Acellular infectious agents – not true organisms because they B. Mycoplasmas lack cells C. Protozoa o Viruses D. Staphylococci Answer: D o Viroid – can cause agricultural crises Generally, bacteria do not have sterols in their membranes; but o Prions – infectious protein capable of causing chronic mycoplasmas are an exception. In fact, they are the only bacteria neurologic diseases WITH sterols. The other groups have sterols, as follows: Protozoa and animals – cholesterol Fungi – ergosterol By now, remember that ergosterol is found in fungi. This molecule is a common target in antifungal therapy, e.g., ketoconazole inhibits ergosterol synthesis, amphotericin directly targets membrane sterols. Which of the following infectious agents lack nucleic acids? A. Viruses B. Bacteria C. Viroid D. Prions Answer: D Prions lack nucleic acids. They are made of PRroteIns Only (proteinaceous infectious particle). In reference to the preceding question, however, it will still require DNA and RNA to direct its synthesis, but its final product will be purely protein, that is, it is composed of amino Mastering Biology Pearson acids. The rest of the infectious agents contain nucleic acids, either DNA or RNA or both. TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO Page 1 of 73 For inquiries visit www.topnotchboardprep.com.ph or email us at [email protected] This handout is only valid for the October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly.  TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. PROTOZOA AND CHARACTERISTIC VIRUSES BACTERIA FUNGI HELMINTHS Cells No Yes Yes Yes Approximate diameter (µm) 0.02 – 0.2 1–5 3 – 10 (yeasts) 15 – 25 (trophozoites) Nucleic acid Either DNA or RNA Both DNA and RNA Both DNA and RNA Both DNA and RNA Eukaryotic Type of nucleus None Prokaryotic Eukaryotic (unicellular – protozoa) (multicellular – helminths) Ribosomes Absent (30S + 50S = 70S) (40S + 60S = 80S) 80S Mitochondria Absent Absent Present Present Protein capsid and Rigid wall containing Rigid wall Nature of outer surface Flexible membrane lipoprotein envelope peptidoglycan containing chitin Motility None Some None Most Not binary fission Method of replication Binary fission Mitosis via budding Mitosis (refer to viral genetics) TRANSPOSONS Classic or a.k.a. “transposable” elements or “Jumping genes” Sporadic Kuru Variant CJD DNA pieces that move readily from one site to another either CJD within or between the DNA of bacteria, plasmids, and Associated with bacteriophages consumption of Etiology Sporadic Cannibalism Code for drug-resistant enzymes, toxins, or metabolic enzymes meat from cows Two methods of transposition: with BSE o cut-and-paste (direct transposition) Diagnosis Histopathology o copy-and-paste (replicative transposition) Higher Cortical Dysfunction and Dementia ↓ Clinical Cerebellar manifestations PRIONS Presentation Dysdiadochokinesia, ataxia, myoclonic jerks, Noncellular infectious proteins etc. These are misfolded proteins with the ability to transmit their * - bovine spongiform encephalopathy (a.k.a. mad cow disease) misfolded shape onto normal variants of the same protein. Kuru = to shake Causes several fatal and transmissible neurodegenerative o Fatal neurodegenerative prion protein (PrP) disease in man diseases in humans and many other animals o Cerebellar syndrome Pathology: dysfunction due to protein misfolding o With characteristics and relentless progression of neurological symptoms through well-defined clinical stages o Initially, cognition is fairly well-preserved o Disease presentation is sufficiently distinctive to be easily recognized by patients, their relatives, and the local community ANIMAL PRION DISEASES Scrapie (sheep, goats, mice, hamsters) Transmissible mink encephalopathy (mink) Bovine spongiform encephalopathy (BSE) Mayo Foundation of Medical Education and Research o Also known as mad cow disease CORRELATION BIOCHEMISTRY Chronic wasting disease (mule, deer, elk) ‘Normal’ prion proteins (PrPc) have alpha helices (they are TRANSMISSION normally expressed in neurons to aid in proper neuronal Sporadic functioning). ‘Abnormal prion proteins (PrPsc) have more Infection beta-pleated sheets, which are more resistant to proteases and o use of bovine growth hormone (from dead cows) chemicals. o transplantation of contaminated tissues (cornea) ‘Pathological’ prions suffer from a misfolding, where the beta o use of contaminated medical devices (brain electrodes) sheets are produced. o ingestion of infected tissue (cannibalism: ‘kuru’) This misfolding makes pathological prions resistant to Inherited syndrome proteases, many chemicals, and normal autoclaving. Hence, they SUSCEPTIBLE POPULATION are resistant to fundamental microbial control, making them the women and children of the Fore tribe in the jungles of New Guinea ‘most stubborn’ among all infectious agents (most difficult to neurosurgeons and brain surgery patients control!) transplant surgeons and transplant patients SPONGIFORM ENCEPHALOPATHIES SPECTRUM OF DISEASE Appearance of the vacuolated neurons, as well as their loss of progressive, neurodegenerative disease function and the lack of an immune response or inflammation o loss of muscle control o shivering, myoclonic jerks and tremors o loss of coordination o rapidly progressive dementia o death TREATMENT AND PREVENTION no treatment available cessation of ritual cannibalism https://neuropathology-web.org/chapter5/chapter5ePrions.html elimination of animal products from livestock feed HUMAN PRION DISEASES disinfection of neurosurgical tools and electrodes o 5% hypochlorite solution or 1.0 M sodium hydroxide or Creutzfeldt-Jakob disease (CJD) autoclaved at 15 psi for 1 hour Variant CJD (vCJD) Standard autoclave conditions. To be effective, the autoclave must Gerstmann-Sträussler-Scheinker (GSS syndrome) reach and maintain a temperature of 121° C for around 15-20 minutes Fatal familial insomnia (FFI) by using saturated steam under at least 15 psi of pressure. So, for prion Sporadic fatal insomnia control, the autoclaving time is extended to 1 hour! TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO Page 2 of 73 For inquiries visit www.topnotchboardprep.com.ph or email us at [email protected] This handout is only valid for the October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly.  TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. ✔GUIDE QUESTION Ampicillin is a beta-lactam drug that belongs to the penicillin group of antibacterial agents. It can be susceptible to hydrolysis by bacterial Prions are not normal and may cause disease because they exhibit beta-lactamases (a.k.a. penicillinases). The addition of beta- a problem with which of the following? lactamase inhibitors (e.g., sulbactam, clavulanic acid, tazobactam) A. Folding of segments of polypeptide into geometrically ordered can ‘protect’ the antibiotic from enzymatic hydrolysis and subsequent units inactivation. B. Amino acid sequence in a polypeptide chain C. Protein assembly into the mature polypeptide and its component Lysozymes are enzymes that kill bacteria by cleaving which part of domains the cell wall? D. Number and types of polypeptide units of oligomeric proteins A. Pentaglycine bridges and their spatial arrangement B. Multiple layers of peptidoglycan “net” Answer: A C. β 1→ 4 glycosidic bond between NAG and NAM Prion anomaly occurs because of the ‘straightening’ of alpha helices D. Tetrapeptide side chains Answer: C into beta sheets. This phenomenon falls within the concept of secondary protein structures. A 27 G1P1 consults because of a painful and erythematous right breast. Since the birth of her child three weeks ago, she has been breastfeeding exclusively. On PE, there are visible small fissures III. BACTERIAL STRUCTURE around the nipple. The breast feels warm. Purulent discharge from the nipple is noted. Culture of the discharge isolates Gram-positive BACTERIAL SHAPE AND SIZE bacteria. What is the most likely cellular morphology of the three shapes: organism? o cocci (spheres) A. Rod o bacilli (rods) B. Spherical, arranged in chains o spirochetes (spirals) C. Spherical, arranged in grapelike clusters § Leptospira D. Spiral Answer: C § Treponema § Borreliella (new name of Borrelia since 2019) cocci arranged in three patterns: GRAM-POSITIVE VS GRAM-NEGATIVE o pairs (diplococci) COMPONENT GRAM (+) CELLS GRAM (-) CELLS o chains (streptococci) Peptidoglycan Thick layer Thin layer o clusters (staphylococci) Teichoic acids Yes No o sarcina (eight-membered cocci formation) Lipopolysaccharide No Yes BACTERIAL CELL WALL Periplasmic space No Yes All bacteria have a cell wall composed of peptidoglycan except Porin proteins No Yes Mycoplasma – Mycoplasma do not have cells walls! Sensitivity to Yes No Peptidoglycan = sugar backbone (glycan) + peptide side chains lysozyme (peptido) cross-linked by transpeptidase PEPTIDOGLYCAN STRUCTURE Benjamin Cummings, an imprint of Addison Wesley Longman, Inc. Porin proteins – Facilitate passage of small, hydrophilic molecules into the cell. GRAM-NEGATIVE CELL WALLS In the outer membrane of gram-negative bacteria → channels allow the entry of essential substances such as sugars, amino outer membrane of gram-negative bacteria contains endotoxin acids, vitamins, and metals as well as many antimicrobial drugs (lipopolysaccharide - LPS) such as Penicillins. COMPONENT FUNCTION Active component of LPS ✔GUIDE QUESTION Lipid A Induces TNF and IL-1 Combining drugs such as ampicillin and sulbactam circumvents Structure: beta-hydroxymyristic acid which mechanism of bacterial resistance? A. Enzymatic inactivation Core Contributes to stability of the outer B. Transpeptidase mutation oligosaccharide membrane C. Reprogramming of peptidoglycan precursors O polysaccharide Antigen structure D. Mutation of DNA topoisomerases All gram-positive bacteria have NO endotoxin EXCEPT Listeria Answer: A monocytogenes ✔GUIDE QUESTION Which component of the Gram-negative cell wall reduces its susceptibility to lysozymes? A. Teichoic acids B. Beta-lactamases in the periplasm C. M protein D. Outer membrane Answer: D The peptidoglycan layer in Gram-negative cells is ‘sandwiched’ between two membranes: an outer membrane and the plasma membrane (as an inner membrane). The outer membrane serves as a physical barrier that ‘protects’ the peptidoglycan immediately underneath from insult. Note that lysozymes result to cleavage of peptidoglycan glycosidic bonds: β 1→4 glycosidic bond between NAG and NAM. © Topnotch Medical Board Prep TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO Page 3 of 73 For inquiries visit www.topnotchboardprep.com.ph or email us at [email protected] This handout is only valid for the October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly.  TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. STAINING TECHNIQUES OTHER STAINING TECHNIQUES GRAM STAINING NAME REMARKS STEP PROCEDURES REAGENT Rickettsia, Chlamydia, Trypanosomes, Giemsa stain 1 Primary Stain CRYSTAL VIOLET Plasmodium, Borrelia, Helicobacter pylori 2 Mordant IODINE Stains glycogen, mucopolysaccharides Periodic acid- 3 Decolorizing Agent ALCOHOL/ACETONE Used to diagnose Whipple disease Schiff (PAS) 4 Counterstain SAFRANIN (Tropheryma whipplei) stain PAS the sugar (glycogen) MEMORY AID GRAM STAINING India Ink Uses negative staining technique V–I–A–S stain Cryptococcus neoformans Violet - Alcohol/Acetone - Iodine - Safranin Mucicarmine Directly stains the thick polysaccharide stain capsule of Cryptococcus neoformans red Coccidioides, Pneumocystis jirovecii, Silver stain Legionella, Helicobacter pylori Used to identify bacteria, viruses, P Fluorescent jirovecii, Giardia lamblia, Cryptosporidium antibody stain FTA-ABS for syphilis Tannic acid To visualize flagella of bacteria stain Feulgen stain To visualize the nucleoid of bacteria Malachite To visualize the spores of bacteria green stain CAPSULES All bacterial capsules are composed of polysaccharide EXCEPT Bacillus anthracis (polypeptide of D- glutamate) Spore: formed by gram-positive rods, especially Bacillus and Clostridium spp © Topnotch Medical Board Prep ✔GUIDE QUESTION Which of the following is the OLDEST acid-fast staining method, which requires heating the specimen during the procedure? A. Fluorochrome C. Kinyoun B. Ziehl-Neelsen D. Auramine-rhodamine BACTERIA NOT SEEN IN GRAM STAIN ALTERNATIVE NAME REASON APPROACH With mycolic acid ACID-FAST ✔GUIDE QUESTION Mycobacteriae (lipid) in cell wall so STAIN A herd of cattle dies of anthrax. Anthrax is caused by the bacterium dye cannot penetrate Bacillus anthracis, a spore-forming organism. To break the chain DARKFIELD of transmission, which of the following is probably the BEST way Spirochetes Too thin to see MICROSCOPY to handle the carcasses of the cattle? Mycoplasma A. Burying six feet below the ground No cell wall NONE B. Market sale and proper food preparation spp. Very small (SEROLOGIES) C. Incineration of the carcasses Ureaplasma sp. D. Treating the mass grave with antibiotic spray prior to burial Poor uptake of red Answer: C Legionella spp. counterstain SILVER STAIN A 24/M presents to his primary care physician with complaints of Intracellular burning with urination. Three days later, the patient also has fever, skin flushing, and altered level of consciousness. PE: BP Intracellular GIEMSA STAIN 60/40, HR 120/min. If blood cultures are positive for Klebsiella Lacks classic pneumoniae, which of the following bacterial factors is most likely → Chlamydiae peptidoglycan responsible for this patient’s current condition? INCLUSION becomes of ↓ A. Capsule C. Peptidoglycan BODIES muramic acid B. Lipid A D. Flagellar antigen Answer: B GIEMSA/ Rickettsiae Intracellular The heat resistance of bacterial spores, such as B. anthracis, is TISSUE STAINS partly attributable to their dehydrated state and partly to the Bartonella, presence of substantial amounts of? Anaplasma, Intracellular TISSUE STAINS A. Diaminopimelic acid Ehrlichia B. D-glutamic acid C. Sulfhydryl containing proteins D. Calcium dipicolinate Answer: D TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO Page 4 of 73 For inquiries visit www.topnotchboardprep.com.ph or email us at [email protected] This handout is only valid for the October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly.  TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. GENETIC EXCHANGE Which of the following organisms will likely harbor plasmids that encode for beta lactamase production and high-level tetracycline Transformation – involves recipient cell uptake of naked (free) resistance? DNA released into the environment when another bacterial cell A. N. gonorrhoeae dies and undergoes lysis B. N. meningitidis Transduction – two bacteria may come together in one cell, C. Treponema pallidum thus allowing for recombination D. Chlamydia trachomatis Answer: A o mediated through Bacteriophages viruses capable of Which of the following microbial characteristics necessitate the infecting bacteria use of soap-based products over the alcohol rubs/gels commonly Conjugation – occurs between two living cells, involves cell-to-cell found in every patient room in the hospital? contact, and requires mobilization of the donor bacterium’s chromosome A. Aerobic growth D. Naked DNA virus proteins o Sex Pilus – originates from the donor and establishes a B. Cell wall teichoic acid E. Spore-forming conjugative bridge that serves as the conduit for DNA C. LPS Answer: E transfer The method employed in ensuring that hand hygiene is effective falls into one of two categories: Hand rubbing with an alcohol-based hand rub o Hand rubbing is the gold standard technique to perform hand hygiene on all occasions except for those described for handwashing with soap and water, i.e. hand rubbing is the action recommended for health- care workers for the routine, day-to-day decontamination of hands. Handwashing with soap and water: o Handwashing still plays a key role in hand hygiene and should be employed when hands are visibly dirty or visibly soiled with blood or other body fluids; after using the toilet; and when exposure to potential spore- forming pathogens is strongly suspected or proven, including during outbreaks of diarrhea. Alcohol-based hand sanitizers may be effective against the following organisms, except which one? A. Staphylococcus aureus C. HPV 16 PLASMIDS B. Clostridium difficile D. Candida albicans Answer: B Extrachromosomal, double-stranded, circular DNA capable of independent IV. BACTERIAL GROWTH replication Bacterial growth is a coordinated process of increase in May be transferred among unrelated individual cell mass and size and duplication of the chromosome, bacteria (broad host range) followed by cell division Can sometimes be integrated into the bacterial chromosome → Bacterial reproduction occurs via binary fission called episomes Generation time- time required for one cell to divide into 2 cells Significance of Plasmids (doubling time) o Antibiotic resistance o Resistance to heavy metals, 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. METHOD DEFINITION EXAMPLE BACTERIAL GROWTH CYCLE Autoclaving Exposure to Destroys or eliminating ALL ethylene oxide Sterilization forms of microbial life, gas (for surgical including bacterial spores instruments) Filtration (for most IV solutions) Eliminates many or all Application of pathogenic microorganisms, rubbing alcohol – Disinfection except bacterial spores, on to inanimate inanimate objects objects Review of Medical Microbiology and Immunology, 15th edition Refers to the application of PHASE REMARKS Preoperative skin Antisepsis chemicals on the surface of prep Phase during which vigorous the skin and mucous PHASE I: LAG metabolic activity occurs, but cells Hand rubbing membranes PHASE do not divide Reducing microbial See A in figure above Can last for minutes up to hours contamination to an Heating cutlery Sanitization acceptable “safe” level (e.g., at KFC!) Zero growth rate (terminology used in food safety) PHASE II: LOG OR When rapid cell division occurs Degerming Physical removal of EXPONENTIAL Handwashing b-lactam antibiotics are most or Cleaning microorganisms by using PHASE (a simpler with soap and See B in figure above efficacious during this phase such things as soaps or terminology used running water by the CDC) detergents Occurs when nutrition depletion or toxic products cause growth to slow PHASE III: until the number of new cells ✔GUIDE QUESTION STATIONARY Which of the following correctly describes the properties of produced balances the number of PHASE cells that die plasmids? See C in figure above A. Capable of independent replication When bacterial spores are formed B. Extrachromosomal genetic elements Zero growth rate C. Amenable to genetic manipulation PHASE IV: Marked by a decline in the number of D. Must be in circular form to replicate in the host DEATH PHASE viable bacteria E. All of the above Answer: E See D in figure above Negative growth rate TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO Page 5 of 73 For inquiries visit www.topnotchboardprep.com.ph or email us at [email protected] This handout is only valid for the October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly.  TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. MEMORY AID BACTERIAL OXYGEN METABOLISM EFFECT OF BACTERICIDAL OBLIGATE AEROBES & BACTERIOSTATIC ANTIMICROBIALS Nosy and Nagging Pests Must Breathe Lots of oxygen. Nocardia Neisseria Pseudomonas Mycobacteria Bordetella/Brucella/B. cereus Legionella OBLIGATE ANAEROBES Anaerobes Can’t Breathe Fresh Air Clostridium Bacteroides Fusobacterium Actinomyces V. BACTERIAL TOXIN PRODUCTION ©Topnotch Medical Board Prep V. BACTERIAL OXYGEN METABOLISM AEROBIC AND ANAEROBIC GROWTH oxygen metabolic generates toxic products such as superoxide and hydrogen peroxide superoxide dismutase, peroxidase and catalase are needed to survive in aerobic environment ENZYMATIC DETOXIFICATION Diagram showing exotoxin being produced by the organism vs endotoxin being part of the organism itself and how it induces immune response. (USMLE) Exotoxins Endotoxins Certain species of Outer cell membrane Source gram (+) and of most gram (-) gram (-) bacteria bacteria Secreted OXYGEN REQUIREMENT Yes No from cell Obligate Aerobes Lipid A component of o completely dependent on oxygen for ATP-generation Chemistry Polypeptide LPS Microaerophiles (released when lysed) o use fermentation but can tolerate low amounts of oxygen Location of Plasmid or Bacterial because they have SOD genes bacteriophage chromosome Facultative Anaerobes High Low o utilize oxygen if it is present, but can use fermentation in its (fatal dose on the order Toxicity (fatal dose on the order absence of hundreds of of 1 microgram) Aerotolerant Anaerobes micrograms) o exclusively anaerobic but insensitive to the presence of Clinical Various Fever, shock, DIC oxygen effects Obligate Anaerobes High; Induces high Low; Poorly o cannot grow in the presence of oxygen because they lack SOD, Antigenicity titer antibodies called antigenic peroxidase and catalase antitoxins No toxoids formed Toxoids used as Vaccines and no vaccine vaccines available Destroyed rapidly at Heat 60°C. Stable at 100°C for 1 (except staphylococcal stability hour enterotoxin and E coli heat stable toxin) Meningococcemia; Typical Tetanus, botulism, sepsis by gram (-) diseases diphtheria, cholera rods REPRESENTATIVE ORGANISMS Nocardia, Bacillus cereus, Neisseria, EXOTOXINS Obligate Pseudomonas, Bordetella, Legionella, polypeptides secreted by certain bacteria that alter specific cell Aerobes Brucella, Mycobacterium, Leptospira, functions resulting in the symptoms of disease Mycoplasma pneumoniae have an A–B subunit structure: Staphylococcus, Bacillus anthracis, o A subunit is the active (toxic) subunit Facultative o B subunit is the binding subunit Corynebacterium, Listeria, Mycoplasmas Anaerobes (in general) ✔GUIDE QUESTION Obligate When an exotoxin binds to a receptor, it activates T-cells by Actinomyces, Bacteroides, Clostridium binding SIMULTANEOUSLY to a T-cell receptor and MHC II anaerobes Aerotolerant Propionibacterium (Cutibacterium), molecule on an antigen-presenting cell WITHOUT requiring an antigen. It activates large number of T cells to cause a cytokine Anaerobes Lactobacillus storm. What is the nature of this exotoxin? Streptococcus, spirochetes (Borreliella, A. Superantigen Microaerophiles Treponema), Campylobacter, Helicobacter B. Protein synthesis inhibitor C. ADP-ribosylator D. Protease Answer: A TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO Page 6 of 73 For inquiries visit www.topnotchboardprep.com.ph or email us at [email protected] This handout is only valid for the October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly.  TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. BIOLOGICAL TOXIN NAME ORGANISM GENE LOCATION MECHANISM EFFECT Streptolysin 0 Streptococcus pyogenes Bacterial chromosome Forms membrane pore a toxin Clostridium perfringens Bacterial chromosome Degrades phospholipids → Alter cellular and plasmid myonecrosis components Type III cytotoxin Pseudomonas aeruginosa Phage Alters actin cytoskeleton Type III cytotoxin Salmonella sp. Bacterial chromosome Exfoliative toxins A, B Staphylococcus aureus Phage Release of cytokines TSST-1 Staphylococcus aureus Bacterial chromosome Release of cytokines Superantigens Enterotoxin Staphylococcus aureus Phage Release of cytokines Erythrogenic toxins A,C Streptococcus pyogenes Phage Release of cytokines Diphtheria toxin Corynebacterium diphtheriae Phage ADP ribosylates EF 2 Pseudomonas aeruginosa Inhibition of Exotoxin A Shigella dysenteriae Bacterial chromosome ADP ribosylates EF 2 protein Shiga toxin Enterohemorrhagic E. coli Plasmid Inactivates 60S ribosome synthesis Vero toxin (Shiga-like) Bacterial chromosome Inactivates 60S ribosome or phage Cholera toxin Vibrio cholerae Bacterial chromosome Turns on adenylate cyclase Heat labile toxin Enterotoxigenic E. coli Plasmid activity Anthrax toxin Bacillus anthracis Plasmid Turns on adenylate cyclase Increased Pertussis toxin Bordetella pertussis Bacterial chromosome activity synthesis of Mimics adenylate cyclase cAMP activity Turns off adenylate cyclase inhibition Increased Turns on guanylate cyclase synthesis of Heat stable toxin Enterotoxigenic E. coli Plasmid activity cGMP Tetanus toxin Clostridium tetani Plasmid Inhibits inhibitory neurotransmitter release from Altered nerve Renshaw cells transmission (GABA/glycinergic cells) Botulinum toxin Clostridium botulinum Phage Inhibits acetylcholine release from stimulatory neurons (Ach) ENDOTOXINS Antimicrobial Susceptibility: Microorganisms, particularly bacteria, are tested in vitro to determine whether they are Lipopolysaccharides (LPS) located in the outer membrane of susceptible to antimicrobial agents gram-negative bacteria Lipid A is the toxic component of LPS o induces the overproduction of cytokines, such as TNF & IL-1 MICROBIAL CULTURE o activates the complement cascade Culture – propagation of microorganisms in media conducive to o activates the coagulation cascade, resulting in disseminated their growth intravascular coagulation Culture medium – a nutritive substance in which cultures of MEMORY AID ENDOTOXIN microorganisms are grown eNdotoxin is an integral part of gram-Negative cell walls. May be a gel or liquid medium GENERALITIES ON BACTERIAL STRUCTURE SPECIALIZED MEDIA FOR BACTERIAL GROWTH All bacteria have cell walls composed Mycoplasma Bacteria Agar of peptidoglycan EXCEPT pneumoniae Clostridium perfringens Egg Yolk Agar All gram-positive bacteria have NO Listeria Cystine-Tellurite Agar, endotoxin EXCEPT monocytogenes Corynebacterium diphtheriae Loeffler Agar All bacterial capsules are composed Bacillus anthracis group D streptococci Bile Esculin Agar of polysaccharide EXCEPT (poly-D-glutamate) N. meningitidis, Staphylococcal N. gonorrhoeae from sterile Chocolate Agar All exotoxins are heat-labile EXCEPT enterotoxin sites N. gonorrhoeae from Thayer-Martin Agar IX. DIAGNOSTIC MICROBIOLOGY nonsterile sites ✔GUIDE QUESTION Chocolate + Factors X Haemophilus influenzae A 45/F consulted her physician for painless enlarging anterior (Heme) And V (NAD) neck masses accompanied by fever, chills, weight loss and malaise. Staphylococcus aureus Mannitol Salt Agar Fine needle aspiration was done to rule out a malignancy. If the Eosin Methylene Blue Agar Escherichia coli physician suspects TB lymphadenitis, which of the following (+) green metallic sheen should he request to RAPIDLY identify the mycobacterial species? A. PCR OTHER MEDIA FOR BACTERIAL GROWTH (JAWETZ) B. Culture on blood agar plate Agar Bacteria Isolated C. Ziehl-Neelsen staining Löwenstein-Jensen, Mycobacterium D. Culture on Lowenstein-Jensen medium Middlebrook tuberculosis Answer: A Vibrio cholerae MICROBIOLOGIC EXAMINATION Thiosulfate Citrate Bile Salts (yellow colonies) Culture Sucrose (TCBS) Vibrio parahaemolyticus Microbial Identification: Colony and cellular morphology; (green colonies) growth characteristics under various conditions, utilization of Bordet-Gengou / Bordetella pertussis carbohydrates and other substrates; enzymatic activity, Regan-Lowe agar immunoassays, and genetic probes Buffered charcoal-yeast extract Legionella pneumophila Serodiagnosis: A high or rising titer of specific IgG antibodies or Skirrow’s medium Campylobacter the presence of specific IgM antibodies may suggest or confirm a Stuart’s medium Helicobacter pylori diagnosis Barbour-Stoenner-Kelly (BSK) Borrelia burgdorferi Eaton Mycoplasma pneumoniae Cetrimide Pseudomonas aeruginosa TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO Page 7 of 73 For inquiries visit www.topnotchboardprep.com.ph or email us at [email protected] This handout is only valid for the October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly.  TOPNOTCH MEDICAL BOARD PREP MICROBIOLOGY AND PARASITOLOGY MAIN HANDOUT BY DRS. BORBE AND RUBIO For inquiries visit www.topnotchboardprep.com.ph or https://www.facebook.com/topnotchmedicalboardprep/ This handout is only valid for October 2024 PLE batch. This will be rendered obsolete for the next batch since we update our handouts regularly. Agar Bacteria Isolated Enterobacteriaceae have complex antigenic structure Xylose-Lysine-Deoxycholate (XLD) Salmonella, Shigella O antigen- most external part of the cell wall polysaccharide Ellinghausen-McCullough-Johnson- o Resistant to heat and alcohol Leptospira interrogans K antigen- external to O antigen on some but not all Harris (EMJH) / Fletcher’s Cary-Blair Vibrio o May be polysaccharide or proteins Cefsulodin-Irgasan-Novobiocin H antigen- located on the flagella Yersinia o Denatured by heat or alcohol (CIN) ✔GUIDE QUESTION Identification of bacteria by serologic tests rely on presence of ✔GUIDE QUESTION specific antigens. Which bacterial component is least likely to An 18-year-old male presents with urinary tract infection. You have a useful antigen for serologic identification? suspect he has an E coli infection. What is the gold standard for A. Ribosomes diagnosis? B. Flagella A. Urethral swab and Gram stain C. Cell wall B. Urine dipstick test D. Capsule Answer: A C. Culture on eosin-methylene blue (EMB) agar D. Urinalysis Answer: C MOLECULAR TESTS The gold standard test for the detection of E coli is culture, which has nucleic acid amplification tests, nucleic acid probes, and nucleic high sensitivity and specificity. This also applies to MOST bacterial acid sequence analysis agents. Remember in culture media, you are able to isolate the organism. Moreover, the isolated colony can be checked under the highly specific, quite sensitive and much faster than culture microscope for direct identification of the bacterial agent. More or especially useful for those bacteria that are difficult to culture less, if you can see the organism DIRECTLY, it is the GOLD such as Chlamydia and Mycobacterium species STANDARD. Dr. Rubio ✔GUIDE QUESTION A 39/M consults because of chronic cough of one month. Sputum Which of the following molecular techniques represents a culture reveals colonies first observed after two weeks of variation of the polymerase chain reaction, involving the use of an incubation. The colonies appear rough, dry, and buff colored. enzyme to convert viral RNA or messenger RNA to DNA prior to What is the most likely organism? amplification? A. Mycobacterium tuberculosis A. Reverse transcriptase PCR B. Mycoplasma pneumoniae B. Real-time PCR C. Streptococcus pneumoniae