Physeo Microbiology PDF
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MICROBIOLOGY MEDICAL COURSE AND STEP 1 REVIEW FIRST EDITION Accompanies online videos taught by Michael Christensen & Rhett Thomson physeo.com Copyright © 2018 by Physeo All rights reserved. No part of this publication may be reproduced, distributed, or transmitted in any form or by any means, including photocopying, recording, or other electronic or mechanical methods, without the prior written permission of Physeo, except in the case of personal study purposes. TABLE OF CONTENTS MICROBIOLOGY FUNDAMENTALS ...............................................................................6 Section 1 - Bacterial Structures .....................................................................................................................................................6 Section 2 - Virulence ...................................................................................................................................................................10 Section 3 - Bacterial Genetics .....................................................................................................................................................20 Section 4 - Prion Diseases ...........................................................................................................................................................27 Section 5 - Introduction to Fungi ................................................................................................................................................29 Section 6 - Viral Structures .........................................................................................................................................................32 Section 7 - Viral Genetics ...........................................................................................................................................................35 Section 8 - Viral Genomes and Replication ................................................................................................................................38 BACTERIA ............................................................................................................................41 Section 1 - Clostridium tetani .....................................................................................................................................................42 Section 2 - Clostridium botulinum ..............................................................................................................................................44 Section 3 - Clostridium difficile .................................................................................................................................................46 Section 4 - Clostridium perfringens ............................................................................................................................................48 Section 5 - Bacillus anthracis .....................................................................................................................................................50 Section 6 - Bacillus cereus ..........................................................................................................................................................52 Section 7 - Listeria monocytogenes ............................................................................................................................................54 Section 8 - Corynebacterium diphtheriae ..................................................................................................................................56 Section 9 - Viridans streptococci ................................................................................................................................................58 Section 10 - Streptococcus pneumoniae .....................................................................................................................................60 Section 11 - Streptococcus pyogenes ..........................................................................................................................................62 Section 12 - Streptococcus agalactiae ........................................................................................................................................66 Section 13 - Streptococcus gallolyticus ......................................................................................................................................68 Section 14 - Enterococci .............................................................................................................................................................70 Section 15 - Staphylococcus aureus ............................................................................................................................................72 Section 16 - Staphylococcus epidermidis ...................................................................................................................................74 Section 17 - Staphylococcus saprophyticus ................................................................................................................................76 Section 18 - Nocardia ................................................................................................................................................................78 Section 19 - Actinomyces israelii ................................................................................................................................................80 Section 20 - Neisseria overview ................................................................................................................................................82 Section 21 - Neisseria meningitidis ............................................................................................................................................84 Section 22 - Neisseria gonorrhoeae ...........................................................................................................................................86 Section 23 - Moraxella catarrhalis ............................................................................................................................................88 Section 24 - Haemophilus influenzae ..........................................................................................................................................90 Section 25 - Bordetella pertussis ................................................................................................................................................94 Section 26 - Pasteurella multocida, Brucella spp., and Francisella tularensis ..........................................................................96 Section 27 - Salmonella spp. .......................................................................................................................................................98 Section 28 - Salmonella typhi ...................................................................................................................................................100 Section 29 - Shigella .................................................................................................................................................................102 Section 30 - E. coli ....................................................................................................................................................................104 Section 31 - Klebsiella ..............................................................................................................................................................108 Section 32 - Proteus mirabilis ..................................................................................................................................................110 Section 33 - Pseudomonas aeruginosa .....................................................................................................................................112 Section 34 - Yersinia pestis and enterocolitica .........................................................................................................................116 Section 35 - Enterobacter, Citrobacter, & Serratia marcescens ...............................................................................................118 Section 36 - Bartonella henselae .............................................................................................................................................120 Section 37 - Legionella pneumophila .......................................................................................................................................122 Section 38 - Campylobacter jejuni ...........................................................................................................................................124 Section 39 - Vibrio cholerae & Vibrio vulnificus ......................................................................................................................126 Section 40 - Helicobacter pylori ...............................................................................................................................................128 Section 41 - Mycobacterium tuberculosis .................................................................................................................................130 Section 42 - Mycobacterium leprae .........................................................................................................................................134 Section 43 - Mycobacterium avium-intracellulare, Scrofulaceum, and Marinum ...................................................................138 Section 44 - Borrelia burgdorferi .............................................................................................................................................140 Section 45 - Leptospira interrogans ..........................................................................................................................................142 Section 46 - Treponema pallidum .............................................................................................................................................144 Section 47 - Chlamydia trachomatis, Chlamydophila pneumoniae, and Chlamydophila psittaci ...........................................148 Section 48 - Coxiella burnetii ...................................................................................................................................................150 Section 49 - Gardnerella vaginalis ...........................................................................................................................................152 Section 50 - Mycoplasma pneumoniae .....................................................................................................................................154 Section 51 - Rickettsia prowazekii, Rickettsia rickettsii, and Rickettsia typhi .........................................................................156 Section 52 - Ehrlichia & Anaplasma ........................................................................................................................................158 Section 53 - Miscellaneous Organisms .....................................................................................................................................160 FUNGI ..................................................................................................................................165 Section 1 - Histoplasma capsulatum .........................................................................................................................................166 Section 2 - Blastomyces dermatitidis ........................................................................................................................................168 Section 3 - Coccidioides immitis ...............................................................................................................................................172 Section 4 - Paracoccidioides brasiliensis .................................................................................................................................174 Section 5 - Microsporum, Trichophyton, and Epidermophyton ................................................................................................176 Section 6 - Malassezia furfur ....................................................................................................................................................180 Section 7 - Sporothrix schenckii ...............................................................................................................................................182 Section 8 - Candida albicans ....................................................................................................................................................184 Section 9 - Aspergillus fumigatus .............................................................................................................................................188 Section 10 - Cryptococcus neoformans ....................................................................................................................................190 Section 11 - Mucor & Rhizopus spp. ........................................................................................................................................192 Section 12 - Pneumocystis jirovecii ..........................................................................................................................................194 PARASITES ........................................................................................................................197 Section 1 - Giardia lamblia ......................................................................................................................................................198 Section 2 - Entamoeba histolytica ............................................................................................................................................200 Section 3 - Cryptosporidium .....................................................................................................................................................202 Section 4 - Toxoplasma gondii ..................................................................................................................................................204 Section 5 - Naegleria fowleri ....................................................................................................................................................206 Section 6 - Trypanosoma brucei, gambiense, and rhodesiense ................................................................................................208 Section 7 - Malaria ...................................................................................................................................................................210 Section 8 - Babesia ...................................................................................................................................................................214 Section 9 - Trypanosoma cruzi .................................................................................................................................................216 Section 10 - Leishmania donovani ............................................................................................................................................218 Section 11 - Trichomonas vaginalis ..........................................................................................................................................220 Section 12 - Enterobius vermicularis (pinworm) .....................................................................................................................222 Section 13 - Ascaris lumbricoides (giant roundworm) .............................................................................................................224 Section 14 - Strongyloides stercoralis (threadworm) ...............................................................................................................226 Section 15 - Ancylostoma duodenale and Necator americanus (hookworms) .........................................................................228 Section 16 - Trichinella spiralis ................................................................................................................................................230 Section 17 - Trichuris trichiura (whipworm) ...........................................................................................................................232 Section 18 - Toxocara canis ......................................................................................................................................................234 Section 19 - Onchocerca volvulus ............................................................................................................................................236 Section 20 - Loa loa and Wuchereria bancrofti ........................................................................................................................238 Section 21 - Taenia solium ........................................................................................................................................................240 Section 22 - Diphyllobothrium latum .......................................................................................................................................243 Section 23 - Echinococcus granulosus .....................................................................................................................................244 Section 24 - Schistosoma haematobium, mansoni, and japanicom ..........................................................................................246 Section 25 - Clonorchis sinensis ...............................................................................................................................................248 Section 26 - Sarcoptes scabiei ..................................................................................................................................................250 Section 27 - Pediculus corporis, pubis and capitis ...................................................................................................................252 VIRUSES .............................................................................................................................254 Section 1 - Herpes simplex virus-1 (HSV-1) and herpes simplex virus-2 (HSV-2) .................................................................255 Section 2 - Varicella-zoster virus (VZV) ..................................................................................................................................260 Section 3 - Epstein-Barr Virus (EBV).......................................................................................................................................262 Section 4 - Cytomegalovirus (CMV) ........................................................................................................................................264 Section 5 - Roseola (HHV-6 and HHV-7) .................................................................................................................................266 Section 6 - Kaposi sarcoma (HHV-8) .......................................................................................................................................268 Section 7 - Hepatitis B Virus (HBV) ........................................................................................................................................270 Section 8 - Smallpox, Cowpox, and Molluscum contagiosum .................................................................................................274 Section 9 - Human papillomavirus ...........................................................................................................................................276 Section 10 - Adenovirus ............................................................................................................................................................280 Section 11 - JC Virus and BK Virus ..........................................................................................................................................282 Section 12 - Parvovirus B19 .....................................................................................................................................................284 Section 13 - Coronavirus and SARS .........................................................................................................................................286 Section 14 - Human immunodeficiency virus (HIV) ................................................................................................................288 Section 15 - Human T-lymphotropic virus (HTLV) ..................................................................................................................292 Section 16 - Hepatitis C Virus (HCV) ......................................................................................................................................294 Section 17 - Yellow fever .........................................................................................................................................................296 Section 18 - Dengue Fever ........................................................................................................................................................298 Section 19 - West Nile Virus and St. Louis Encephalitis ..........................................................................................................300 Section 20 - Zika Virus .............................................................................................................................................................302 Section 21 - Rubella ..................................................................................................................................................................304 Section 22 - Eastern, Western, and Venezuelan equine encephalitis viruses; Chikungunya virus ...........................................306 Section 23 - California Encephalitis .........................................................................................................................................308 Section 24 - Rift Valley Fever and Crimean-Congo Hemorrhagic Fever Virus .......................................................................310 Section 25 - Hantavirus .............................................................................................................................................................312 Section 26 - Influenza virus ......................................................................................................................................................314 Section 27 - Lassa fever encephalitis and Lymphocytic choriomeningitis virus ......................................................................316 Section 28 - Hepatitis D Virus ..................................................................................................................................................317 Section 29 - Parainfluenza Virus ...............................................................................................................................................320 Section 30 - RSV and hMPV ....................................................................................................................................................322 Section 31 - Measles .................................................................................................................................................................324 Section 32 - Mumps ..................................................................................................................................................................326 Section 33 - Rabies Virus ..........................................................................................................................................................328 Section 34 - Ebola Virus and Marburg Virus ............................................................................................................................332 Section 35 - Norovirus ..............................................................................................................................................................334 Section 36 - Hepatitis E virus ...................................................................................................................................................336 Section 37 - Rotavirus and Colorado Tick Fever ......................................................................................................................338 Section 38 - Poliovirus ..............................................................................................................................................................340 Section 39 - Echovirus ..............................................................................................................................................................342 Section 40 - Rhinovirus ............................................................................................................................................................344 Section 41 - Coxsackieviruses (A & B) ....................................................................................................................................346 Section 42 - Hepatitis A Virus ...................................................................................................................................................348 We would like to extend a special thanks to the following individuasl who have spent many hours tutoring, guiding and consulting this work, making Physeo Anatomy possible. Paloma F Cariello, MD, MPH Assistant Professor Division of Infectious Diseases University of Utah School of Medicine Salt Lake City, UT Karen Eilbeck, Ph.D. Professor Biomedical Informatics University of Utah Vicente Planelles, Ph.D. Professor Division of Microbiology and Immunology Department of Pathology University of Utah School of Medicine Salt Lake City, UT 6 MICROBIOLOGY FUNDAMENTALS Section 1 - Bacterial Structures I. There are several bacterial structures to be familiar with for board exams. These structures can help bacteria infect host cells and survive. Some structures are unique to certain groups and can be useful in distinguishing bacterial organisms. Structure Description • Phospholipid bilayer • Contains lipoteichoic acids in gram-positive bacteria → stimulates host immune response Cytoplasmic membrane via TNF-ɑ and IL-1 release • Contains penicillin-binding proteins (PBPs) • Peptidoglycan that provides rigidity and structural support to cell • Thick in gram-positive bacteria (gram staining with crystal violet causes blue appearance) • Thin in gram-negative bacteria Cell wall • Absent in Mycoplasma species which have added sterols to maintain stability (must grow on Eaton’s agar) • Contains mycolic acid in Mycobacteria species (must use acid-fast stain) Flagella • Provides bacterial motility • Allows bacteria to bind to host cells Pilus (fimbria) • Allows bacteria-bacteria binding during conjugation • Network of polysaccharides • Slime layer: disorganized and loosely attached to cell wall → creates biofilm on prosthetics Glycocalyx (capsule or (eg, S. epidermidis) slime layer) • Capsule: organized and firmly attached to cell wall → protects from phagocytosis (targeted by many vaccines) • Note: the capsule of Bacillus anthracis is made of a protein network of poly-ᴅ-glutamate • Only present in gram-negative organisms (gram counter-staining with safranin causes red appearance) Outer membrane • Contains porins → transfer of nutrients • Contains lipopolysaccharides (LPS: lipid A, core polysaccharide, and O antigen) • Lipid A stimulates host immune response via TNF and IL-1 release → fever, shock, diarrhea • Located between outer membrane and cytoplasmic membrane in gram-negative bacteria Periplasm • Contains hydrolytic enzymes (eg, β-lactamases) • Layer formed during dormant state → resists heat, chemicals, dehydration and starvation → survival of bacteria • Only present in gram-positive organisms (Clostridium and Bacillus) Endospore • Center containing DNA and dipicolinic acid (DPA) → cytoplasmic membrane (spore core) → peptidoglycan wall (spore cortex) → cytoplasmic membrane → keratin-like protein wall (spore coat) → exosporium (present only in B. anthracis and B. cereus) Table 5.1.1 - Bacterial structures 7 Figure 5.1.1 - Gram positive bacterial envelope Figure 5.1.2 - Gram negative bacterial envelope 8 Figure 5.1.3 - Envelope of Mycoplasma spp. Figure 5.1.4 - Envelope of Mycobacteria spp. Figure 5.1.5 - Acid-fast stain of Mycobacterium Tuberculosis 9 Figure 5.1.6 - Bacterial endospore A. Polymerases in bacteria 1. DNA polymerase (replication → more DNA) a) Mistakes can harm progeny 2. RNA polymerase (transcription → mRNA) a) Mistakes do not harm progeny REVIEW QUESTIONS ? 1. A researcher is attempting to create a novel • Correct answer: C staining agent that will only bind to certain • The question stem describes a gram bacterial species. This species cannot form an positive organism endospore, does not contain mycolic acids, and • Contains only one phospholipid contains only one phospholipid bilayer. Which of bilayer, so its not gram negative the following does the organism described most • Does not contain mycolic acids, so likely possess? its not mycobacteria • Gram positive organisms may contain A. A cytokine inducing structure in outer flagella membrane • Choice A is incorrect because this describes B. A layer that tightly binds to the safranin the endotoxin of gram negative bacteria counterstain C. A protein structure allowing for motility • Choice B is incorrect because Safranin binds D. A relatively thin layer of peptidoglycan to the outer membrane found only in gram negative bacteria • Choice D is incorrect because thin peptidoglycan layers are found in Mycobacteria and gram negative organisms, not in gram positive bacteria
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