P eface
A well-developed knowledge of clinical microbiology is 4) Create a conceptual, organized approach to the or- critical for the practicing physician in any medical field. ganisms studied so the student relies less on memory Bacteria, viruses, and protozoans have no respect for and more on logical pathophysiology. the distinction between ophthalmology, pediatrics, The text has been updated to include current infor- trauma surgery, or geriatric medicine. As a physician mation on rapidly developing topics, such as HIV and you will be faced daily with the concepts of microbial AIDS (vaccine efforts and all the new anti-HIV medica- disease and antimicrobial therapy. Microbiology is one tions), Ebola virus, Hantavirus, E. outbreaks, Mad of the few courses where much of the "minutia" is regu- larly used by the practicing physician. Cow Disease, and brand-new antimicrobial antibiotics. This book attempts to facilitate the learning of mi- The mnemonics and cartoons in this book do not in- tend disrespect for any particular patient population or crobiology by presenting the information in a clear and entertaining manner brimming with memory aids. racial or ethnic group but are solely presented as mem- Our approach has been to: ory devices to assist in the learning of a complex and im- portant medical subject. 1) Write in a conversational style for rapid assimi- We welcome suggestions for future editions. lation. 2) Include numerous figures serving as "visual mem- MARK GLADWIN, MD ory tools" and summary charts at the end of each chap- BILL TRATTLER, MD ter. These can be used for "cram sessions" after the concepts have been studied in the text. 3) Concentrate more on clinical and infectious dis- ease issues that are both interesting and vital to the ac- tual practice of medicine.
D CONTENTS
Preface v
PART 1 1 1 BACTERIAL TAXONOMY 1 2 CELL STRUCTURES, VIRULENCE FACTORS, and TOXINS 8 3 BACTERIAL SE( GENETICS 16
GRAM-POSITIVE BACTERIA 22 4 STREPTOCOCCUS 22 5 STAPHYLOCOCCUS 31 6 BACILLUS and CLOSTRIDIUM (SPORE-FORMING RODS) 38 7 CORYNEBACTERIUM and LISTERIA (NON-SPORE-FORMING RODS) 45
GRAM-NEGATNE BACTERIA 49 8 NEISSERIA 49 9 THE ENTERICS 54 10 HAEMOPHILUS, BORDETELLA, and LEGIONELLA 68 11 YERSINIA, FRANCISELLA, BRUCELLA, and PASTEURELLA 73 12 CHLAMYDIA, RICKETTSIA, and FRIENDS 78 13 SPIROCHETES 91
ACID-FAST BACTERIA 102 14 MYCOBACTERIUM 102
BACTERIA WITHOUT CELL WALLS 111 15 MYCOPLASMA 111
ANTI-BACTERIAL MEDICATIONS 114 16 PENICILLIN FAMILY ANTIBIOTICS 114 17 ANTI-RIBOSOMAL ANTIBIOTICS 125 18 ANTI-TB and ANTI-LEPROSY ANTIBIOTICS 133 19 MISCELLANEOUS ANTIBIOTICS 139
PART 2. FUNGI 144 20 THE FUNGI 144 21 ANTI-FUNGAL MEDICATIONS 155
PART 3 161 22 VIRAL REPLICATION and TAXONOMY 161 23 ORTHOMYXO and PARAMYXOVIRIDAE 172 24 HEPATITIS VIRIDAE 180 25 RETROVIRIDAE, HIV, and AIDS 190 26 HERPESVIRIDAE 204 27 REST OF THE DNA VIRUSES 209 28 REST OF THE RNA VIRUSES 214 29 ANTI-VIRAL MEDICATIONS 224
PART 4. PARASITES 231 30 PROTOZOANS 231 31 HELMINTHS 248
vi PART 5. VERY STRANGE CRITTERS 265 32 PRIONS (contributing author: Hans Henrik Larsen, M.D.) 265 PART 6. 33 ANTIMICROBIAL RESISTANCE: ONE STEP TOWARD THE POST-ANTIBIOTIC ERA? (contributing author: Earnest Alexander, Pharm.D.) 269 BIOTERRORISM DEFENSE UPDATES: http://www.medmaster.netBioterrorismDefense.html
P eface
A well-developed knowledge of clinical microbiology is 4) Create a conceptual, organized approach to the or- critical for the practicing physician in any medical field. ganisms studied so the student relies less on memory Bacteria, viruses, and protozoans have no respect for and more on logical pathophysiology. the distinction between ophthalmology, pediatrics, The text has been updated to include current infor- trauma surgery, or geriatric medicine. As a physician mation on rapidly developing topics, such as HIV and you will be faced daily with the concepts of microbial AIDS (vaccine efforts and all the new anti-HIV medica- disease and antimicrobial therapy. Microbiology is one tions), Ebola virus, Hantavirus, E. outbreaks, Mad of the few courses where much of the "minutia" is regu- larly used by the practicing physician. Cow Disease, and brand-new antimicrobial antibiotics. This book attempts to facilitate the learning of mi- The mnemonics and cartoons in this book do not in- tend disrespect for any particular patient population or crobiology by presenting the information in a clear and entertaining manner brimming with memory aids. racial or ethnic group but are solely presented as mem- Our approach has been to: ory devices to assist in the learning of a complex and im- portant medical subject. 1) Write in a conversational style for rapid assimi- We welcome suggestions for future editions. lation. 2) Include numerous figures serving as "visual mem- MARK GLADWIN, MD ory tools" and summary charts at the end of each chap- BILL TRATTLER, MD ter. These can be used for "cram sessions" after the concepts have been studied in the text. 3) Concentrate more on clinical and infectious dis- ease issues that are both interesting and vital to the ac- tual practice of medicine.
D CONTENTS
Preface v
PART 1 1 1 BACTERIAL TAXONOMY 1 2 CELL STRUCTURES, VIRULENCE FACTORS, and TOXINS 8 3 BACTERIAL SE( GENETICS 16
GRAM-POSITIVE BACTERIA 22 4 STREPTOCOCCUS 22 5 STAPHYLOCOCCUS 31 6 BACILLUS and CLOSTRIDIUM (SPORE-FORMING RODS) 38 7 CORYNEBACTERIUM and LISTERIA (NON-SPORE-FORMING RODS) 45
GRAM-NEGATNE BACTERIA 49 8 NEISSERIA 49 9 THE ENTERICS 54 10 HAEMOPHILUS, BORDETELLA, and LEGIONELLA 68 11 YERSINIA, FRANCISELLA, BRUCELLA, and PASTEURELLA 73 12 CHLAMYDIA, RICKETTSIA, and FRIENDS 78 13 SPIROCHETES 91
ACID-FAST BACTERIA 102 14 MYCOBACTERIUM 102
BACTERIA WITHOUT CELL WALLS 111 15 MYCOPLASMA 111
ANTI-BACTERIAL MEDICATIONS 114 16 PENICILLIN FAMILY ANTIBIOTICS 114 17 ANTI-RIBOSOMAL ANTIBIOTICS 125 18 ANTI-TB and ANTI-LEPROSY ANTIBIOTICS 133 19 MISCELLANEOUS ANTIBIOTICS 139
PART 2. FUNGI 144 20 THE FUNGI 144 21 ANTI-FUNGAL MEDICATIONS 155
PART 3 161 22 VIRAL REPLICATION and TAXONOMY 161 23 ORTHOMYXO and PARAMYXOVIRIDAE 172 24 HEPATITIS VIRIDAE 180 25 RETROVIRIDAE, HIV, and AIDS 190 26 HERPESVIRIDAE 204 27 REST OF THE DNA VIRUSES 209 28 REST OF THE RNA VIRUSES 214 29 ANTI-VIRAL MEDICATIONS 224
PART 4. PARASITES 231 30 PROTOZOANS 231 31 HELMINTHS 248
vi PART 5. VERY STRANGE CRITTERS 265 32 PRIONS (contributing author: Hans Henrik Larsen, M.D.) 265 PART 6. 33 ANTIMICROBIAL RESISTANCE: ONE STEP TOWARD THE POST-ANTIBIOTIC ERA? (contributing author: Earnest Alexander, Pharm.D.) 269 BIOTERRORISM DEFENSE UPDATES: http://www.medmaster.netBioterrorismDefense.html PART 1. BACTERIA
CHAPTER 1. BACTERIAL TAXONOMY
All organisms have a name consisting of two parts: the genus followed by the species (i.e., Homo sapiens). Bac- DISACCHARIDE teria have been grouped and named primarily on their morphological and biochemical/metabolic differences. However, bacteria are now also being classified accord- ing to their immunologic and genetic characteristics. This chapter focuses on the Gram stain, bacterial mor- phology, and metabolic characteristics, all of which en- able the clinician to rapidly determine the organism causing a patient's infection.
GRAM STAIN Because bacteria are colorless and usually invisible to light microscopy, colorful stains have been developed to visualize them. The most useful is the Gram stain, which separates organisms into 2 groups: gram-positive bugs and gram-negative bugs. This stain also allows the clinician to determine whether the organism is round or rod-shaped. For any stain you must first smear the substance to be stained (sputum, pus, etc.) onto a slide and then heat AMINO ACIDS it to fix the bacteria on the slide. There are 4 steps to the Gram stain: 1) Pour on crystal violet stain (a blue dye) and wait 60 seconds. Fig e 1-1 2) Wash off with water and flood with iodine solu- tion. Wait 60 seconds. Both gram-positive and gram-negative organisms 3) Wash off with water and then "decolorize" with have more than 1 layer protecting their cytoplasm and 95% alcohol. nucleus from the extracellular environment, unlike an- 4) Finally, counter-stain with safranin (a red dye). imal cells, which have only a single cytoplasmic mem- Wait 30 seconds and wash off with water. brane composed of a phospholipid bilayer. The layer just outside the bacterial cytoplasmic membrane is the pep- When the slide is studied microscopically, cells that tidoglycan layer or cell wall. It is present in both absorb the crystal violet and hold onto it will appear gram-positive and gram-negative organisms. blue. These are called gram-positive organisms. How- ever, if the crystal violet is washed off by the alcohol, Fig. 1-1. The peptidoglycan layer or cell wall is these cells will absorb the safranin and appear red. composed of repeating disaccharides with 4 amino acids These are called gram-negative organisms. in a side chain extending from each disaccharide. Gram-positive = BLUE Fig. 1-2. The amino-acid chains of the peptidoglycan I'm positively BLUE over you!! covalently bind to other amino acids from neighboring chains. This results in a stable cross-linked structure. Gram-negative = RED The enzyme that catalyzes the formation of this linkage No (negative) RED commies!! is called transpeptidase and is located in the inner cy- toplasmic membrane. The antibiotic penicillin binds to The different stains are the result of differences in the and inhibits this enzyme. For this reason the enzyme is cell walls of gram-positive and gram-negative bacteria. also called penicillin binding protein (see page 114).
1 CHAPTER 1. BACTERIAL TAXONOMY
Figure 1-2 ( ) - . A - . I , - - . Figure 1-3 Fig. 1-5. T - S , . L - Fig. 1-3. T - , 1) - - 2) . 3) I , - . I , - . - . T ( - ) - Fig. 1-4. T - . G - - - - , , , . . T T - - . T . T . T - ,
Figure 1-4
2 CHAPTER 1. BACTERIAL TAXONOMY
GRAM-NEGATIVE CELL ENVELOPE
OUTER MEMBRANE
MUREIN LIPOPROTEIN PEPTIDOGLYCAN LAYER (CELL WALL) PERIPLASMIC SPACE
CYTOPLASMIC MEMBRANE
EMBEDDED PROTEINS
Figure 1-5
lipoprotein called murein lipoprotein. This lipopro- tein is important because it originates from the peptido- glycan layer and extends outward to bind the unique third outer membrane. This last membrane is similar to other cell membranes in that it is composed of two lay- ers of phospholipid (bilayer) with hydrophobic tails in the center. What makes it unique is that the outermost portion of the bilayer contains lipopolysaccharide (LPS). Fig. 1-6. Lipopolysaccharide (LPS) is composed of 3 covalently linked components:
1) Outer carbohydrate chains of 1-50 oligosaccha- ride units that extend into the surrounding media. These differ from one organism to another and are anti- Figure 1-6 genic determinants. This part is called the 0-specific
3 CHAPTER 1. BACTERIAL TAXONOMY
G am-Po i i e Cell G am-Nega i e Cell 2 La e : 3 La e : 1. Inne c opla mic memb ane 1. Inne c opla mic memb ane 2. O e hick pep idogl can la e 2. Thin pep idogl can la e (60-100% pep idogl can) (5- 10% pep idogl can) 3. O e memb ane i h lipopol accha ide (LPS) Lo lipid con en High lipid con en NO endotoxin (except Listeria Endo o in (LPS) - lipid A monocytogenes) NO pe ipla mic pace Pe ipla mic pace NO po in channel Po in channel V lne able o l o me and Re i an o l o me and penicillin a ack penicillin a ack Figure 1-7 DIFFERENCES BETWEEN GRAM- -POSITIVE AND GRAM-NEGATIVE ORGANISMS side chain or the 0-antigen. Think of O for Outer to dally dissolved by alcohol, thus washing out the crystal help remember this. violet and allowing the safranin counterstain to take. The center part is a water soluble core polysac- 2) Summary of differences between gram- charide. Fig. 1-7. positive and gram-negative bacteria. 3) Interior to the core polysaccharide is the third component, lipid A, which is a disaccharide with mul- BACTERIAL MORPHOLOGY tiple fatty acid tails reaching into the membrane. Lipid A is toxic to humans and is known as the gram-negative Bacteria have 4 major shapes: endotoxin. When bacterial cells are lysed by our effi- ciently working immune system, fragments of mem- 1) Cocci: spherical. brane containing lipid A are released into the 2) Bacilli: rods. Short bacilli are called coc- circulation, causing fever, diarrhea, and possibly fatal cobacilli. endotoxic shock (also called septic shock). 3) Spiral forms: comma-shaped, S-shaped, or spi- ral-shaped. Embedded in the gram-negative outer membrane are 4) Pleomorphic: lacking a distinct shape (like jello). porin proteins, which allow passage of nutrients. These The different shaped creatures organize together into are also unique to gram-negative organisms. more complex patterns, such as pairs (diplococci), clus- What does this mean clinically? ters, strips, and single bacteria with flagella. The differences between gram-positive and gram- Fig. 1-8. Bacterial morphology. negative organisms result in varied interactions with SO, WHAT ARE THE NAMES?!!!! the environment. The gram-positive thickly meshed peptidoglycan layer does not block diffusion of low mol- Gram-Positive ecular weight compounds, so substances that damage the cytoplasmic membrane (such as antibiotics, dyes, Start by remembering that there are 6 classic gram- and detergents) can pass through. However, the gram- positive bugs that cause disease in humans, and basi- negative outer lipopolysaccharide-containing cell mem- cally every other organism is gram-negative. brane blocks the passage of these substances to the Of the gram-positives, 2 are cocci, and the other 4 are peptidoglycan layer and sensitive inner cytoplasmic rod-shaped (bacilli). membrane. Therefore, antibiotics and chemicals that The 2 gram-positive cocci both have the word coccus attempt to attack the peptidoglycan cell wall (such as in their names: penicillins and lysozyme) are unable to pass through. 1) Streptococcus forms strips of cocci. Interestingly, the crystal violet stain used for Gram 2) Staphylococcus forms clusters of cocci. staining is a large dye complex that is trapped in the thick, cross-linked gram-positive cell wall, resulting in Two of the 4 gram-positive rods produce spores the gram-positive blue stain. The outer lipid-containing (spheres that protect a dormant bacterium from the cell membrane of the gram-negative organisms is par- harsh environment). They are:
4 CHAPTER 1. BACTERIAL TAXONOMY
G am-Nega i e COCCI Of the gram-negative organisms, there is only one group of gram-negative cocci. It is actually a diplococcus (looks like 2 coffee beans kissing): Neisseria. There is also just 1 group of spiral-shaped organisms: BACILLI o RODS the Spirochetes. This group includes the bacterium Tre- ponema pallidum, which causes syphilis. The rest are gram-negative rods or pleomorphic.
SPIRAL Exceptions: 1) Mycobacteria are weakly gram-positive but stain better with a special stain called the acid-fast COMMA stain (See Chapter 14). This special group includes or- ganisms that cause tuberculosis and leprosy. 2) Spirochetes have a gram-negative cell wall S-SHAPED but are too small to be seen with the light microscope and so must be visualized with a special darkfield microscope. 3) Mycoplasma do not have a cell wall. They only have a simple cell membrane, so they are neither gram- positive nor gram-negative. PLEOMORPHIC Fig. 1-9. Summary of morphological differences among the bacteria.
CLUSTERS CYTOPLASMIC STRUCTURES Bacterial DNA usually consists of a single circle of double-stranded DNA. Smaller adjacent circles of STRIPS double-stranded DNA are called plasmids; they often contain antibiotic resistance genes. Ribosomes are composed of protein and RNA and are involved in the DIPLOCOCCI translation process, during the synthesis of proteins. Bacteria, which are procaryotes, have smaller ribo- somes (70S) than animals (80S), which are eucaryotes. WITH FLAGELLA Bacterial ribosomes consist of 2 subunits, a large sub- unit (50S) and a small subunit (30S). These numbers re- late to the rate of sedimentation. Antibiotics, such as erythromycin and tetracycline, have been developed that attack like magic bullets. They inhibit protein syn- thesis preferentially at the bacterial ribosomal subunits while leaving the animal ribosomes alone. Erythromy- cin works at the 50S subunit, while tetracycline blocks Fig e 1-8 protein synthesis at the 30S subunit. 3) Bacillus 4) Clostridium METABOLIC CHARACTERISTICS The last 2 gram-positive rods do not form spores: Bacteria can be divided into groups based on their metabolic properties. Two important properties include: 5) Cor nebacterium 1) how the organism deals with oxygen, and 2) what the 6) Listeria, which surprisingly has endotoxin-sur- organism uses as a carbon and energy source. Other prising because ALL other organisms with endotoxin properties include the different metabolic end-products are gram-negative. that bacteria produce such as acid and gas.
5 CHAPTER 1. BACTERIAL TAXONOMY
MORPHOLOGY GRAM-POSITIVE GRAM-NEGATIVE Ci c la (Cocc ) Streptococcus Neisseria Staphylococcus Rod (Bacillus) Corynebacterium ENTERICS (live in the GI tract): Listeria Escherichia coli Bacillus Shigella Clostridium Salmonella • Yersinia Klebsiella Proteus Enterobacter Mycobacterium (acid-fast) Se a ia Vibrio Campylobacter Helicobacter Pseudomonas BacteroIdes (anaerobic) Haemophilus Bordetella Legionella Yersinia Francisella Brucella Pasteurella Gardnerella Spiral Spirochetes: Treponema Borrelia Leptospira Branching filamentous growth Actinomyces (anaerobic) (like fungi) Nocardia (partially acid-fast) Pleomorphic Chlamydia Rickettsiae No cell all Mycoplasma Figure 1-9 MORPHOLOGICAL DIFFERENCES AMONG THE BACTERIA
Oxygen 3) S pe o ide di m a e breaks down the super- oxide radical in the following reaction: How bacteria deal with oxygen is a major factor in their classification. Molecular oxygen is very reactive, and when it snatches up electrons, it can form hydrogen peroxide (H2O2), superoxide radicals (02i, and a hy- Bacteria are classified on a continuum. At one end are droxyl radical (OH - ). All of these are toxic unless bro- those that love oxygen, have all the preceding protective ken down. In fact, our very own macrophages produce enzymes, and cannot live without oxygen. On the oppo- these oxygen radicals to pour over bacteria. There are 3 site end are bacteria which have no enzymes and pretty enzymes that some bacteria possess to break down much kick the bucket in the presence of oxygen: these oxygen products: 1) Obliga e ae obe : These critters are just like us in that they use glycolysis, the Krebs TCA cycle, and the 1) Ca ala e breaks down hydrogen peroxide in the electron transport chain with oxygen as the final elec- following reaction: tron acceptor. These guys have all the above enzymes. 2) Fac l a i e anae obe : Don t let this name fool you! These bacteria are aerobic. They use oxygen as an 2) Pe o ida e also breaks down hydrogen peroxide. electron acceptor in their electron transfer chain and
6 CHAPTER 1. BACTERIAL TAXONOMY
OBLIGATE FACULTATIVE MICROAEROPHILIC OBLIGATE AEROBES ANAEROBES ANAEROBES Gram-positive Nocardia Staphylococcus Streptococcus Clostridium ( eakl acid-fast) Bacillus anthracis Bacillus cereus Corynebacterium Listeria Actinomyces Gram-negative Neisseria Most other gram- Spirochetes Bacteroides Pseudomonas negative rods Treponema Bordetella Borrelia Legionella Leptospira Brucella Campylobacter Acid-fast Mycobacterium Nocardia No cell all Mycoplasma