ExpertMD Microbiology Quick Notes PDF

Microbiology Quick Notes MICROBIOLOGY PHYSICIAN LICENSURE EXAM APRIL 2024 EXPERTMD MEDICINE BOARD REVIEW...

Microbiology Quick Notes MICROBIOLOGY PHYSICIAN LICENSURE EXAM APRIL 2024 EXPERTMD MEDICINE BOARD REVIEW BACTERIOLOGY © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 1 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW ii. Nutrient Agar BACTERIAL STAIN iii. Tryptone Soya Broth c) Tissue Culture Mediu  For isolation of Obligate Intracellular Bacteria 1. Simple stain  Ex: 2. Differential Stain Hela 229 cells a) Gram stain McCoy cells Reagent Gram (+) Gram (-) W138 Primary Stain Crystal Violet Purple Purple 3. Based on Dispensing Mordant Gram Iodine Purple Purple a) Tube Media Decolorizer 95% Alcohol Purple Colorless b) Plated Secondary Saffranin Purple Red 4. Based on Use Stain a) Simple/General Purpose -Without added supplement; Routinely used in b) Acid fast stain laboratory Ziehl Nilsen (Hot) C- Kinyoun (Cold) C-A-M Example: A-M  Tryptone Soya Broth (TSB) Primary Stain Carbol-Fuchsin Carbol-Fuchsin  Nutrient Agar Broth b) Enrichment Media Mordant Heat Phenol - Contain Specific Nutrients Decolorizer 3% Acid Alcohol 3% Acid- Alcohol  Buffered charcoal yeast extract (Nocardia-1%  Alkaline peptone water H2SO4)  Thioglycollate Counterstain Methylene Blue Malachite Green  Selenite F Result AFO- RED AFO-RED c) Enriched Media NAFO- Blue NAFO-Green - With added supplement for Growth of Fastidious Organisms 3. Special stain  Blood Agar Plate (BAP) - Used to visualize a certain part of bacteria  Chocolate Agar Plate (CAP) a) Nigrosin stain - Capsule d) Differential Media b) Schaeffer futton- Endospore - Allows visualization of metabolic differences between c) Welch method- Capsule group of species of bacteria d) Fuelgen stain- Nucleic acid  Hektoen Enteric Agar e) Leifson - Flagella  Eosin Methylene Blue f) L.A.M.B- Granule stain  Mac Conkey Agar 4. Negative stain: Nigrosin  Blood Agar Plate e) Selective Media CULTURE MEDIA - Incorporated w/ antibiotics, dyes or chemicals to INHIBIT growth of other organisms while prompting GROWTH of desired organism Causative Agent Medium Used  Hektoen Enteric Agar Neisseria Thayer Martin/ NYC  Mac Conkey Agar (Inhibits Gram +) Clostridium/ Bacteroides Thiglycollate  Bismuth Sulfite Agar (BSA) Vibrio cholerae Thiosulfate, CItrate, Bile salt,  Mannitor Salt Agar (7.5% Salt) Sucrose (TCBS)  Xylose Lysine Decarboxylase Agar Corynebacterium Loeffler diphtheriae BACTERIAL RECOMBINATION Helicobacter pylori/ Skirrow Clostridium jejuni A. TRANSFORMATION Mycobacterium Lowenstein-Jensen  Donor cell lyse, a fragment of DNA is released and Bordotella Pertussis Bordet-Gengou/Gengou passed into a recipient cell. Enzyme dissolves one Bordotella Pertussis Fletcher strand of the fragment, and the other stand displaces a H Influenzae Chocolate agar (CAP) homologous segment of the recipient’s DNA. The recipeint then has a recombinant DNA  Involves direct uptake of donor DNA by recipient cells which depends on their competence for transformation Classification of Culture Medium 1. Based on Consistency B. CONJUGATION a) Solid  It involves two live bacteria, donor and recipient, with  2.3% Agar transfer of genetic material from a plasmid  Mac Conkey Agar, Triple Sugar Iron, Chocolate  The donot is F+ has a fertility factor and codes for sex Agar pilus. b) Semi-solid  Once there is contact with the F- or recipient, plasmid  0.5-1% Agar DNA begins to replicate by the rolling circle method  Sulfide Indole Motility c) Liquid  No agar  Brain Heart Infusion  Tryptone Soya Broth  Thioglycollate 2. Based on Composition a) Synthetic/ Define Medium  All substances are known to the user  For RESEARCH purposes b) Non Synthetic/ Complex medium  Composed of some unknown substances  For isolation of bacteria  Ex: i. Mac Conkey Agar © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 2 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW C. TRANSDUCTION d) Obligate Anaerobes -Cannot grow in presence of Oxygen Ex: Clostridium, Bacteroides C. Based on Carbon and Energy Source a) Phototrophs- Need Light as source of energy b) Chemolithotrops- Need Inorganic compounds c) Methylotrophs- Need Organic Compoun D. By Morphology a) Shape  Spherical (Cocci)  Rod (Bacilli)  Spiral (Spirilla)  Filamentous b) Aggregates  Diploccoci (Pairs)  Streptococci (Chains)  Tetrads (Fours)  Staphylococci (Clusters)  Sarcinae (Cubes) D. TRANSPOSITION  Process of transferring genes through “Jumping genes” Bacterial Enzymes Enzymes Activity Bacteria Result Oxidase Cytochrome Gram (-) rids Black Catalase H2O2 Staphylococcus Hydrolysis, Bubbles Urease Urea H pylori pH change S. saprophyticus Hydrolysis Coagulase Fibrin Clot Staphyloccus Clots serum Gram Positive BACTERIAL CLASSIFICATION A. Based on Temperature Requirement a) Psychrophilic- 0-10C b) Mesophilic- 20-40C (Most human pathogens belong to this type c) Thermophilic- 50-60C B. Based on Oxygen Requirement a) Obligate Aerobes - Needs Oxygen for survival -Have all enzymes -Tricarboxylic, Electron Transport chain Ex: Neisseria, Pseudomonas, Legionella b) Facultative Aerobes - Aerobic; but can also survive in the absence of Oxygen Ex: Listeria, Bacillus anthracis, Mycoplasma, Staphylococcus c) Microaerophilic - Requires small amounth of Oxygen -No ETC; Fermentation Ex: Streptococcus, Leptospira, Campylobacter © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 3 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW Gram Positive Organisms  S. Saprophyticus- Coagulase Negative; 1. Branching Filaments Novobiocin Resistant a) Nocardia- Weakly Acid Fast b) Catalase Negative b) ActiNOmyces- Not Acid Fast i. Streptococcus 2. Bacilli  Viridans- Alpha Hemolysis; Optochin Resistant a) Aerobic  Pneumoniae- Alpha Hemolyisis- Optochin i. Listeria Sensitive ii. Bacillus  Group A Streptococcus (S. pyogenes) -Beta iii. Corynebacterium Complete hemolysis; Bacitracin Sensitive b) Anaerobic  Group B Streptococcus (S. agalactiae) - Beta i. Clostridium Complete hemolysis; Bacitracin Resistant ii. Propriotropium  Enterococcus 3. Cocci E. faecium - Gamma-No hemolysis; a) Catalase positive Grow in 6.5% NaCl i. Staphylococcus E. fecalis- Gamma No hemolysis- Grow  S. aureus- Coagulase Positive in 6.5% NaCl  S. epidermidis- Coagulase Negative,  Non Enterococcus Novobiocin Sensitive S. bovis- Gama- No Hemolysis; No growth in 6.5% NaCl Gram Positive with Branching Filaments Nocardia asteroides Actinomyces israelli Weakly acid fast (Fite Faraco Not acid fast stain) Found in soil Normal oral, reporoductive and GI flora Pulmonary infections in Oral/ Facial Abscess that immunocompromised (Can drain through the sinus tracts mimic TB but with negative PPD) Often associated with dental caries/extraction Cutaneous infections after trauma in immunocompetent Forms yellow sulfur granules Can spread to CNS - Brain abcesses (Orange colonies) Can cause PID with IUDs Treatment: Sulfonamides Treatment: Penicillin (TMP-SMX) Treatment is a SNAP Sulfonamides- Nocardia, Actinomyces- Penicillin COCCI Staphylococci © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 4 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW * Review the virulence factor in the lecture Streptococci © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 5 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW Bacilli Bacterial spore  Postion:  Central  Terminal (Clostridium tetani)  Subterminal (Clostridium botulinum)  Bacterial spores are reproductive structures formed by certain types of bacteria as a means of surviving adverse environmental conditions  The process of spore formation is called sporulation, it involves the transformation of a vegetative bacterial cell into a spore. © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 6 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW Gram Negative Test for Identification of Gram Negative Bacteria For Gram negative Diplococci  Mannose utilization For Gram negative Bacilli  Lactose fermentation  Oxidase test  H2S (Hydrogen sulfide) *Please refer to detailed lecture © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 7 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW ENTEROBACTERIACEAE Differential Media Eosin Methylene Blue  Differentiates E Coli with pathogenic, non-lactose fermenting Salmonella and Shigella  Inhibits Gram positive MacConkey Agar  Differentiates lactose and non lactose fermenters Selective Media Hektoen enteric media  Permits direct plating of feces and selective growth of pathogen  High concentration of Sodium thiosulfate and Sodium citrate Salmonella- Shigella Agar  Inhibits other Gram (+) and Gram (-) bacteria © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 8 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW VIBRIO SPECIES Lactose and Non Lactose Fermenters © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 9 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW ZOONOTIC INFECTIONS SPIROCHETES © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 10 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW ATYPICAL © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 11 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW MYCOLOGY FUNGI LABORATORY DIAGNOSIS OF FUNGI Arthroconidia are conidia formed by  Eukaryotic organisms laying down joints in hyphae followed by fragmentation True nucleus of the hyphal strand 80s ribosomes Mitochondria Fungal cell walls 1. MICROSCOPIC EXAMINATION:  Protect cells from osmotic shock, determine cell RAPID METHOD shape, and have components that are antigenic a) KOH Mount  Composed primarily of complex carbohydrates b) Nigrosin or India Ink such as chitin with glucans and mannose- protein -Highlights the capsule of Cryptococcus neoformans  Fungi Morphology but very insensitive (misses 50% of cases) Fugi include organisms called molds, mushrooms c) Giemsa or Wright’s Stain and yeasts -Detect intracellular Histoplasma capsulatum Thermally dimorphic fungi are capable of converting from a yeast or yeast-like form to filamentous form 2. HISTOLOGIC STAINING a) Gomori methenamine silver stain and vice versa -Fungi are dark gray to black Monomorphic fungi b) Periodic acid-Schiff (PAS) reaction  Aspergillus- Mold only - Fungi are hot pink to red  Cryptococcus- Yeast only c) Gridley fungus stain “Yeast in Heat; Mold in Cold” - Fungi are purplish rose with a yellow background Hyphae d) Calcofluor white stain  Are filamentous (tubelike) cells of molds. e) Immunofluorescent stains  Grow at the tips (Atypical growth) -Available for some fungal pathogens 1. Septae or septation - cross walls of hyphae and occur in the hyphae of the great majority of the 3. OTHERS disease causing fungi a) DNA probes 2. Non septate or aseptate hyphae- lacks regularly -For early detection of some systemic pathogens ocuring cross walls b) Cultures - These cells are multinucleated -Uses special media (e.g Sabouraud’s dextrose - Also called coenocytic medium), and enriched media (e.g blood agar)  Hyphae may be dematiaceous (Dark colored) c) Fungal antigen detection or Hyaline (Colorless) - Uses known antibodies to identify circulating fungal antigens in a patient serum, CSF or urine.  Pseudohyphae are fromed by some yeasts -Used for Histoplasma and Cryptococcus when they elongate but remain attached to each other d) Serologic testing FUNGI LIFE CYCLE AND REPRODUCTION  Fungal spores are formed either asexually or by a sexual process involving nuclear fusion and then meiosis. Fungal morphology including spores may be used in identification Sexual spores: Conidia are asexual spores of filamentous fungi (molds) or mushrooms Blastoconidia are the new yeast “buds” Chlamydosposres are “resting spores’ © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 12 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW SUPERFICIAL MYCOSES © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 13 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW CUTANEOUS MYCOSES SUBCUTANEOUS MYCOSES © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 14 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW SYSTEMIC MYCOSES © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 15 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW VIROLOGY VIRAL STRUCTURE VIRAL REPLICATION Attachment of virus to host cell General Features of Viruses Adsorption or Attachment receptor  Obligate intracellular  Acellular (no organelles) Virus enters host cell by direct Penetration or Virus Entry penetration, endocytosis or fusion  With either RNA or DNA, never both with cell membrane  Haploid (contain only one copy of genes) except RETROVIRUSES (diploid) Loss of capsid Genome enters cytoplasm (for most Complete virus particle; Infectious Uncoating VIRION RNA viruses) or nucleus (for most unit DNA viruses) DNA or RNA (Genome) Production of nucleic acids and NUCLEID ACID Single-or-Double Stranded Macromolecular Synthesis protein polymers Linear or Circular Structural proteins, genomes, viral Protein coat that encloses genetic enzymes are into virus particles material Viral Assembly Envelopes acquired during viral May be helical (rod-like) or “budding” from membrane icosahedral (cuboid) or complex. CAPSID Occurs after cell lysis (lytic virus) or Composed of protein subunits called Release by virus particle budding from capsomeres cytoplasmic membranes Protects nucleic acid, enables virus to attach to and enter host cell NUCLEOCAPSID Nucleic acid + capsid VIRUS AT A GLANCE Outer membrane surrounding capsid DNA VIRUSES AT A GLANCE in some viruses  Double stranded DNA except PARVOVIRUS (Single stranded) ENVELOPE Aids in attachment to host cell  Naked except POX VIRUS, HERPESVIRUS, Enveloped Virus- Ether-sensitive HEPADNAVIRUS (Envelope) Naked Virus- Ether-resistant  Icosahedral capsids except POXVIRUS (Complex)  Replicate in the NUCLEUS except for POXVIRUS (Cytoplasm)  Largest DNA Virus- POXVIRUS  Smallest DNA Virus- PARVOVIRUS  Can cause latent infection- HERPESVIRIDAE  Only DNA Hepatic Virus- HEPATITIS B © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 16 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW RNA VIRUS AT A GLANCE  Single Stranded RNA except REOVIRUS (Double stranded)  Enveloped except CALICIVIRUS, PICORNAVIRUS, REOVIRUS (Naked)  Helical capsids except Picornavirus, Reovirus, Calicivirus, Togavirus, Retrovirus, Hepevirus (Icosahedral) Flavivirus (Spherical and icosahedral) Arenavirus (irregular shaped) Bunyavirus (Spherical or Phleomorphic) Filiovirus (Long, filamentous and irregular)  Replicate in the Cytoplasm - except for Orthomyxovirus, Retrovirus (Both have cytoplasmic and nuclear phase)  Largest RNA Virus- PARAMYXOVIRUS  Smallest RNA Virus- PICORNAVIRUS (Poliovirus)  “F” protein (Fusion protein)- RSV  With reverse transcriptase- RETROVIRUS  With surface antigens: Neuraminidase activity (NA) and Hemagglutinin activity (HA)- Orthomyxovirus (Influenza viruses) NA- assists in the release of virion from host cell HA- used for attachment  Undergoes antigenic shift and drift- Orthomyxovivrus Antigenic drift- results from minor mutations; responsible for local outbreaks  Influenza B primarily human virus Antigenic shift- results from major mutations; associated with pandemic  Influenza A replicates in various types of hosts (humans, animals) Acid stable- Enteroviruses Acid labile- Rhinoviruses DNA VIRUS Adenoviridae Human adenovirus Hepatitis B virus (the only DNA Hepadnaviridae hepatitis virus) HSV types I and II, VZV, CMV, EBC, Herpesviridae HHV 6,7 and 8 Papillomaviridae HPV Parvoviridae Parvovirus B-19 Polyomaviridae BK and JC polyomavirus Variola (Smallpox), Vaccina, Orf, Poxviridae Molluscum contagiosum, Monkeypox viruses © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 17 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW RNA VIRUS Family Viral Members Arenaviridae Gastroenteritis-causing astroviruses Arboviruses: California encephalitis and Lacrosse viruses Bunyaviridae Non-arboviruses: Sin nombre and related hantaviruses Caliciviridae Noroviruses and Hepatities E virus Ebola and Marburg hemorrhagic Filoviridae fever viruses Arboviruses: Yellow fever, Dengue, West nile, Japanese encephalitis, Flaviviridae and St. Louis Encephalitis Non-arboviruses: Hepatitis C virus Orthomyxoviridae Influenza A, B and C viruses Parainfluenza viruses, mumps, Paramyxoviridae measles virus, RSV, Metapneumovirus, Nipah virus Polio viruses, Coxsackie A viruses, Coxsackie B viruses, Echoviruses, Picornaviridae Enterviruses 68-71 (Hepatitis A virus), Rhinoviruses Rotavirus spp, COlorado tick fever Reoviridae virus Rhabdoviridae Rabies virus Arboviruses: Eastern, Western, and Venezuela equine encephalitis Togaviridae viruses Non-arbovirus: Rubella virus © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 18 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 19 of 23  Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW PARASITOLOGY PARASITE-HOST RELATIONSHIP TERMS TYPES OF HOST TYPE DEFINITION OR DESCRIPTION TYPE DEFINITION OR DESCRIPTION Accidental/Incidental Host other than the normal one that Symbiosis Living together; the association of is harboring a parasite two living organisms, each of a Definitive Host in which the ADULT sexual different species phase of parasite develops Commensalism Association of two different species Intermediate Host in which the larval sexual of organisms that is beneficial to phase of parasite develops one and neutral to other Reservoir  Host harboring parasites that are Mutualism Association of two different species parasitic for humans and from of organisms that is beneficial to which humans may become both infected Parasitism Association of two different species  Allows a parasite life cycle to of organisms that is beneficial to continue one at the other’s expense  An animal host Commensal Relating to commensalism; the  Become an additional source of association between two different infection organisms in which one benefits Transport Host responsible for transferring a and has a neutral effect on the parasite from one location to other another Pathogenic Parasite that has demonstrated the Carrier Parasite-harboring host that is not ability to cause disease exhibiting any clinical symptoms but can infect other TYPES OF PARASITES Paratenic  Harbors a parasite that does not develop but remains alive  An animal host  Serve to bring parasite to its true host TYPE DEFINITION OR DESCRIPTION  Food for larger host Obligatory Parasite that CANNOT survive outside of a host Facultative Parasite that is capable of existing independently of a host Endoparasite Parasite that is established inside of a host Ectoparasite Parasite that is established in or on the exterior surface of a host Commensal Relating to commensalism; the association between two different organisms in which one benefits and has a neutral effect on the other Pathogenic Parasite that has demonstrated the ability to cause disease * Refer to Lecture for full review © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 20 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW AMOEBA CILIATE SPOROZOA FLAGELLATES Diagnosis Specimen: Blood Best time to collect: Before fever spikes Gold standard for detection: THICK and THIN Blood Smear THICK SMEAR – for rapid diagnosis, needs to be dehemoglobinized prior to staining THIN SMEAR- for species identification, to be fixed prior to staining MNEMONIC: Ferdinand Marcos experience Vibe of Singapore while Making Zesty Orange Juice FM- VS- MZ- OJ Falcifarum – Maurer’s Vivax- Schuffner Malariae- Ziemann Ovale- James © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 21 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW CESTODES NEMATODES © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 22 of 23 Microbiology Quick Notes EXPERTMD MEDICINE BOARD REVIEW © EXPERTMD MICROBIOLOGY QUICK NOTES Unauthorized copying, sharing or distribution is strictly prohibited. 23 of 23