FA Microbiology PDF

HIGH-YIELD PRINCIPLES IN Microbiology “That within one linear centimeter of your lower colon there lives and ` Basic Bacteriology 122 works more bacteria (about 100 billion) than all humans who have ever been born. Yet many people con...

HIGH-YIELD PRINCIPLES IN Microbiology “That within one linear centimeter of your lower colon there lives and ` Basic Bacteriology 122 works more bacteria (about 100 billion) than all humans who have ever been born. Yet many people continue to assert that it is we who are in ` Clinical Bacteriology 132 charge of the world.” —Neil deGrasse Tyson ` Mycology 149 “What lies behind us and what lies ahead of us are tiny matters ` Parasitology 152 compared to what lies within us.” —Henry S. Haskins ` Virology 159 “Wise and humane management of the patient is the best safeguard ` Systems 175 against infection.” —Florence Nightingale ` Antimicrobials 184 “I sing and play the guitar, and I’m a walking, talking bacterial infection.” —Kurt Cobain Microbiology questions on the Step 1 exam often require two (or more) steps: Given a certain clinical presentation, you will first need to identify the most likely causative organism, and you will then need to provide an answer regarding some features of that organism or relevant antimicrobial agents. For example, a description of a child with fever and a petechial rash will be followed by a question that reads, “From what site does the responsible organism usually enter the blood?” This section therefore presents organisms in two major ways: in individual microbial “profiles” and in the context of the systems they infect and the clinical presentations they produce. You should become familiar with both formats. When reviewing the systems approach, remind yourself of the features of each microbe by returning to the individual profiles. Also be sure to memorize the laboratory characteristics that allow you to identify microbes. 121 FAS1_2023_03-Microbiology.indd 121 11/22/22 4:10 PM  122 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY Bacterial structures STRUCTURE CHEMICAL COMPOSITION FUNCTION Appendages Flagellum Proteins Motility Pilus/fimbria Glycoprotein Mediate adherence of bacteria to cell surface; sex pilus forms during conjugation Specialized structures Spore Keratinlike coat; dipicolinic acid; peptidoglycan, Gram ⊕ only DNA Survival: resist dehydration, heat, chemicals Cell envelope Capsule Discrete layer usually made of polysaccharides Protects against phagocytosis (and rarely proteins) Slime (S) layer Loose network of polysaccharides Mediates adherence to surfaces, plays a role in biofilm formation (eg, indwelling catheters) Outer membrane Outer leaflet: contains endotoxin (LPS/LOS) Gram ⊝ only Embedded proteins: porins and other outer Endotoxin: lipid A induces TNF and IL-1; membrane proteins (OMPs) antigenic O polysaccharide component Inner leaflet: phospholipids Most OMPs are antigenic Porins: transport across outer membrane Periplasm Space between cytoplasmic membrane Accumulates components exiting gram and outer membrane in gram ⊝ bacteria ⊝ cells, including hydrolytic enzymes (peptidoglycan in middle) (eg, β-lactamases) Cell wall Peptidoglycan is a sugar backbone with peptide Netlike structure gives rigid support, protects side chains cross-linked by transpeptidase against osmotic pressure damage Cytoplasmic Phospholipid bilayer sac with embedded Site of oxidative and transport enzymes; PBPs membrane proteins (eg, penicillin-binding proteins involved in cell wall synthesis [PBPs]) and other enzymes Lipoteichoic acids induce TNF-α and IL-1 Lipoteichoic acids (gram positive) only extend from membrane to exterior Cell envelope Unique to Common to both Unique to gram ⊕ gram ⊝ Flagellum Lipoteichoic acid Pilus Capsule Endotoxin/LPS Outer Porin membrane Cell wall Peptidoglycan Wide periplasmic space containing β-lactamase Cytoplasmic membrane Gram ⊕ Gram ⊝ FAS1_2023_03-Microbiology.indd 122 11/22/22 4:10 PM  MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY SEC TION II 123 Stains Gram stain First-line lab test in bacterial identification. Bacteria with thick peptidoglycan layer retain crystal violet dye (gram ⊕); bacteria with thin peptidoglycan layer turn red or pink (gram ⊝) with counterstain. These bugs do not Gram stain well (These Little Microbes May Unfortunately Lack Real Color But Are Everywhere): Treponema, Leptospira Too thin to be visualized Mycobacteria Cell wall has high lipid content Mycoplasma, Ureaplasma No cell wall Legionella, Rickettsia, Chlamydia, Bartonella, Primarily intracellular; also, Chlamydia lack Anaplasma, Ehrlichia classic peptidoglycan because of muramic acid Giemsa stain Chlamydia, Rickettsia, Trypanosomes A , Clumsy Rick Tripped on a Borrowed Borrelia, Helicobacter pylori, Plasmodium Helicopter Plastered in Gems Periodic acid–Schiff Stains glycogen, mucopolysaccharides; used PaSs the sugar stain to diagnose Whipple disease (Tropheryma whipplei B ) Ziehl-Neelsen stain Acid-fast bacteria (eg, Mycobacteria C , Auramine-rhodamine stain is more often used (carbol fuchsin) Nocardia; stains mycolic acid in cell wall); for screening (inexpensive, more sensitive) protozoa (eg, Cryptosporidium oocysts) India ink stain Cryptococcus neoformans D ; mucicarmine can also be used to stain thick polysaccharide capsule red Silver stain Helicobacter pylori, Legionella, Bartonella HeLiCoPters Are silver henselae, and fungi (eg, Coccidioides E , Pneumocystis jirovecii, Aspergillus fumigatus) Fluorescent antibody Used to identify many bacteria, viruses, Example is FTA-ABS for syphilis stain Pneumocystis jirovecii, Giardia, and Cryptosporidium A B C D E FAS1_2023_03-Microbiology.indd 123 11/22/22 4:12 PM  124 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY Special culture requirements BUG MEDIA USED FOR ISOLATION MEDIA CONTENTS/OTHER H influenzae Chocolate agar Factors V (NAD+) and X (hematin) N gonorrhoeae, Thayer-Martin agar Selectively favors growth of Neisseria by N meningitidis inhibiting growth of gram ⊕ organisms with vancomycin, gram ⊝ organisms except Neisseria with trimethoprim and colistin, and fungi with nystatin Very typically cultures Neisseria B pertussis Bordet-Gengou agar (Bordet for Bordetella) Potato extract Regan-Lowe medium Charcoal, blood, and antibiotic C diphtheriae Tellurite agar, Löffler medium M tuberculosis Löwenstein-Jensen medium, Middlebrook medium, rapid automated broth cultures M pneumoniae Eaton agar Requires cholesterol Lactose-fermenting MacConkey agar Fermentation produces acid, causing colonies to enterics turn pink E coli Eosin–methylene blue (EMB) agar Colonies with green metallic sheen Brucella, Francisella, Charcoal yeast extract agar buffered with The Ella siblings, Bruce, Francis, a Legionella, cysteine and iron legionnaire, and a pasteur (pastor), built the Pasteurella Sistine (cysteine) chapel out of charcoal and iron Fungi Sabouraud agar “Sab’s a fun guy!” FAS1_2023_03-Microbiology.indd 124 11/22/22 4:12 PM  MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY SEC TION II 125 Anaerobes Examples include Clostridium, Bacteroides, Anaerobes Can’t Breathe Fresh Air. Fusobacterium, and Actinomyces israelii. They Anaerobes are normal microbiota in GI lack catalase and/or superoxide dismutase tract, typically pathogenic elsewhere. and are thus susceptible to oxidative damage. AminO2glycosides are ineffective against Generally foul smelling (short-chain fatty anaerobes because these antibiotics require O2 acids), are difficult to culture, and produce gas to enter into bacterial cell. in tissue (CO2 and H2). Facultative anaerobes May use O2 as a terminal electron acceptor to Streptococci, staphylococci, and enteric gram ⊝ generate ATP, but can also use fermentation bacteria. and other O2-independent pathways. Intracellular bacteria Obligate intracellular Rickettsia, Chlamydia, Coxiella Stay inside (cells) when it is Really Chilly and Rely on host ATP Cold Facultative Salmonella, Neisseria, Brucella, Mycobacterium, Some Nasty Bugs May Live FacultativeLY intracellular Listeria, Francisella, Legionella, Yersinia pestis Encapsulated bacteria Examples are Pseudomonas aeruginosa, Please SHiNE my SKiS. A Streptococcus pneumoniae A , Haemophilus Are opsonized, and then cleared by spleen. influenzae type b, Neisseria meningitidis, Asplenics (No Spleen Here) have opsonizing Escherichia coli, Salmonella, Klebsiella ability and thus risk for severe infections; pneumoniae, and group B Strep. Their need vaccines to protect against: capsules serve as an antiphagocytic virulence N meningitidis factor. S pneumoniae Capsular polysaccharide +/– protein conjugate H influenzae can serve as an antigen in vaccines. A polysaccharide antigen alone cannot be presented to T cells; immunogenicity can be enhanced by conjugating capule antigens to a carrier protein. Urease-positive Proteus, Cryptococcus, H pylori, Ureaplasma, Pee CHUNKSS. organisms Nocardia, Klebsiella, S epidermidis, S saprophyticus. Urease hydrolyzes urea to release ammonia and CO2 pH. Predisposes to struvite (magnesium ammonium phosphate) stones, particularly Proteus. FAS1_2023_03-Microbiology.indd 125 11/22/22 4:12 PM  126 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY Catalase-positive Catalase degrades H2O2 into H2O and bubbles of O2 A before it can be converted to microbicidal organisms products by the enzyme myeloperoxidase. People with chronic granulomatous disease (NADPH A oxidase deficiency) have recurrent infections with certain catalase ⊕ organisms. Big Catalase ⊕ organisms include Bordetella pertussis, Helicobacter pylori, Burkholderia cepacia, Nocardia, Pseudomonas, Listeria, Aspergillus, Candida, E coli, Serratia, Staphylococci. Cats Have BeeN to PLACESS. Pigment-producing Actinomyces israelii—yellow “sulfur” granules, Israel has yellow sand bacteria which are composed of filaments of bacteria S aureus—golden yellow pigment Aureus (Latin) = gold P aeruginosa—blue-green pigment (pyocyanin Aerugula is green and pyoverdin) Serratia marcescens—red pigment Think red Sriracha hot sauce In vivo biofilm S epidermidis Catheter and prosthetic device infections producing bacteria Viridans streptococci (S mutans, S sanguinis) Dental plaques, infective endocarditis P aeruginosa Respiratory tree colonization in patients with cystic fibrosis, ventilator-associated pneumonia Contact lens–associated keratitis Nontypeable (unencapsulated) H influenzae Otitis media FAS1_2023_03-Microbiology.indd 126 11/22/22 4:13 PM  MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY SEC TION II 127 Spore-forming Some gram ⊕ bacteria can form spores when Examples: B anthracis (anthrax), B cereus (food bacteria nutrients are limited. Spores lack metabolic poisoning), C botulinum (botulism), C difficile activity and are highly resistant to heat (pseudomembranous colitis), C perfringens and chemicals. Core contains dipicolinic (gas gangrene), C tetani (tetanus). acid (responsible for heat resistance). Must Autoclave to kill Bacillus and Clostridium autoclave to kill spores (as is done to surgical (ABC). equipment) by steaming at 121°C for 15 minutes. Hydrogen peroxide and iodine-based agents are also sporicidal. Bacterial virulence factors These promote evasion of host immune response. Capsular Highly charged, hydrophilic structure. Acts as barrier to phagocytosis and complement-mediated polysaccharide lysis. Major determinant of virulence. Protein A Binds Fc region of IgG. Prevents opsonization and phagocytosis. Expressed by S aureus. IgA protease Enzyme that cleaves IgA, allowing bacteria to adhere to and colonize mucous membranes. Secreted by S pneumoniae, H influenzae type b, and Neisseria (SHiN). M protein Helps prevent phagocytosis. Expressed by group A streptococci. Sequence homology with human cardiac myosin (molecular mimicry); possibly underlies the autoimmune response seen in acute rheumatic fever. FAS1_2023_03-Microbiology.indd 127 11/22/22 4:13 PM  128 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY Bacterial genetics Transformation Competent bacteria can bind and import short Degraded uncombined Recipient DNA pieces of environmental naked bacterial DNA Donor DNA chromosomal DNA (from bacterial cell lysis). The transfer and expression of newly Naked DNA Recipient cell Transformed cell transferred genes is called transformation. A feature of many bacteria, especially S pneumoniae, H influenzae type b, and Neisseria (SHiN). Adding deoxyribonuclease degrades naked DNA, preventing transformation. Conjugation F+ × F– F+ plasmid contains genes required for sex pilus and conjugation. Bacteria without this plasmid F+ plasmid contains genes for sex pilus and Sex pilus forming congugal Single strand of plasmid DNA No transfer of are termed F–. Sex pilus on F+ bacterium conjugation bridge “mating bridge” transferred chromosomal DNA contacts F− bacterium. A single strand F+ plasmid contains genes for sex pilus and Sex pilus forming congugal Single strand of plasmid DNA No transfer of of plasmid DNA is transferred across the conjugation F+ cell F– cell bridge “mating bridge” F+ cell F– cell transferred F+ cell F– cell chromosomal DNA F+ cell F+ cell conjugal bridge (“mating bridge”). No transfer High-frequency recombination Leading portion of plasmid of chromosomal DNA. (Hfr) cell contains F+ plasmid incorporated F+ cell F+ cell DNA. F– cell into bacterial F– cell transfers along with flanking F+ cell chromosome bacterial F– cell F+ cell F+ cell – + Hfr × F F plasmid can become incorporated into High-frequency recombination Leading portion of plasmid Plasmid transfers along with flanking bacterial chromosomal DNA, termed high- (Hfr) cell contains F+ plasmid incorporated into bacterial DNA. bacterial chromosome frequency recombination (Hfr) cell. Transfer F+ cell F– cell Hfr cell F– cell Hfr cell F– cell Hfr cell Recombinant F– cell Plasmid of leading part of plasmid and a few flanking F– cell F+ cell cell +F– cell + Recombinant plasmid copy chromosomal genes. High-frequency F+ cell F– cell Hfr cell F– cell bacterial Hfr DNA bacterial DNA Hfr cell F– cell recombination may integrate some of those F– cell F+ cell bacterial DNA + bacterial DNA + plasmid copy bacterial genes. Recipient cell remains F– but now may have new bacterial genes. Transduction Generalized A “packaging” error. Lytic phage infects Lytic Cleavage of Bacterial DNA packaged Bacteria bacterial DNA in phage capsids bacterium, leading to cleavage of bacterial phage DNA. Parts of bacterial chromosomal DNA may become packaged in phage capsid. Phage infects another bacterium, transferring these genes. Release of new phage Infects other Genes transferred from lysed cell bacteria to new bacteria Specialized An “excision” event. Lysogenic phage infects Viral DNA Viral DNA Lysogenic incorporates in Phage particles bacterium; viral DNA incorporates into phage Bacteria bacterial DNA carry bacterial DNA bacterial chromosome. When phage DNA is excised, flanking bacterial genes may be excised with it. DNA is packaged into phage capsid and can infect another bacterium. Genes for the following 5 bacterial toxins are encoded in a lysogenic phage (ABCD’S): Group A strep erythrogenic toxin, Botulinum toxin, Release of new phage Infects other Genes different from Cholera toxin, Diphtheria toxin, Shiga toxin. from lysed cell bacteria donor and recipient FAS1_2023_03-Microbiology.indd 128 11/22/22 4:13 PM  MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY SEC TION II 129 Bacterial genetics (continued) Transposition A “jumping” process involving a transposon Plasmid (specialized segment of DNA), which can copy and excise itself and then insert into the same DNA molecule or an unrelated DNA (eg, Integration of genes Transposon plasmid or chromosome). Critical in creating Bacterial plasmids with multiple drug resistance and DNA transfer across species lines (eg, Tn1546 with Target site vanA from Enterococcus to S aureus). Main features of exotoxins and endotoxins Exotoxins Endotoxins SOURCE Certain species of gram ⊕ and gram ⊝ bacteria Outer cell membrane of most gram ⊝ bacteria SECRETED FROM CELL Yes No CHEMISTRY Polypeptide Lipid A component of LPS (structural part of bacteria; released when lysed) LOCATION OF GENES Plasmid or bacteriophage Bacterial chromosome TOXICITY High (fatal dose on the order of 1 µg) Low (fatal dose on the order of hundreds of micrograms) CLINICAL EFFECTS Various effects (see following pages) Fever, shock (hypotension), DIC MODE OF ACTION Various modes (see following pages) Induces TNF, IL-1, and IL-6 ANTIGENICITY Induces high-titer antibodies called antitoxins Poorly antigenic VACCINES Toxoids used as vaccines No toxoids formed and no vaccine available HEAT STABILITY Destroyed rapidly at 60°C (except Stable at 100°C for 1 hr staphylococcal enterotoxin and E coli heat- stable toxin) TYPICAL DISEASES Tetanus, botulism, diphtheria, cholera Meningococcemia; sepsis by gram ⊝ rods Exotoxin Endotoxin TNF, IL-1, Downstream IL-6 cellular reaction Host cell FAS1_2023_03-Microbiology.indd 129 11/22/22 4:14 PM  130 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY Bacteria with exotoxins BACTERIA TOXIN MECHANISM MANIFESTATION Inhibit protein synthesis Corynebacterium Diphtheria toxina Pharyngitis with pseudomembranes in throat diphtheriae Inactivate elongation and severe lymphadenopathy (bull neck), factor (EF-2) through myocarditis Pseudomonas Exotoxin A a ADP-ribosylation Host cell death aeruginosa Shigella spp Shiga toxina Inactivate 60S ribosome by Damages GI mucosa dysentery Enterohemorrhagic removing adenine from Enhances cytokine release hemolytic-uremic E coli rRNA syndrome (HUS; prototypically in EHEC serotype O157:H7) Unlike Shigella, EHEC does not invade host cells Increase fl id secretion Enterotoxigenic Heat-labile Overactivates adenylate Watery diarrhea: “labile in the Air (Adenylate E coli toxin (LT)a cyclase ( cAMP) Cl− cyclase), stable on the Ground (Guanylate secretion in gut and H2O cyclase)” efflux Bacteria that cAMP include Cholera, Heat-stable Overactivates guanylate Anthracis, Pertussis, E coli; “Increase cAMP toxin (ST) cyclase ( cGMP) with CAPE resorption of NaCl and H2O in gut Bacillus anthracis Anthrax toxina Mimics adenylate cyclase Likely responsible for characteristic edematous ( cAMP) borders of black eschar in cutaneous anthrax Vibrio cholerae Cholera toxina Overactivates adenylate Voluminous “rice-water” diarrhea cyclase ( cAMP) by permanently activating Gs Inhibit phagocytic ability Bordetella pertussis Pertussis toxina Activates adenylate cyclase Whooping cough—child coughs on expiration ( cAMP) by inactivating and “whoops” on inspiration; can cause inhibitory subunit (Gi). “100-day cough” in adults; associated with posttussive emesis Inhibit release of neurotransmitter Clostridium tetani Tetanospasmina Toxin prevents release of inhibitory (GABA Both are proteases that and glycine) neurotransmitters from Renshaw cleave SNARE (soluble cells in spinal cord spastic paralysis, risus NSF attachment sardonicus, trismus (lockjaw), opisthotonos Clostridium Botulinum toxina protein receptor), a set Infant botulism—caused by ingestion of spores botulinum of proteins required for (eg, from soil, raw honey). Toxin produced in neurotransmitter release vivo via vesicular fusion Foodborne botulism—caused by ingestion of preformed toxin (eg, from canned foods) a An AB toxin (also called two-component toxin [or three for anthrax]) with B enabling Binding and triggering uptake (endocytosis) of the Active A component. The A components are usually ADP ribosyltransferases; others have enzymatic activities as listed in chart. FAS1_2023_03-Microbiology.indd 130 11/22/22 4:14 PM  MICROBIOLOGY ` MICROBIOLOGY—BASIC BACTERIOLOGY SEC TION II 131 Bacteria with exotoxins (continued) BACTERIA TOXIN MECHANISM MANIFESTATION Lyse cell membranes Clostridium Alpha toxin Phospholipase (lecithinase) Degradation of phospholipids myonecrosis perfringens that degrades tissue and (“gas gangrene”) and hemolysis (“double zone” cell membranes of hemolysis on blood agar) Streptococcus Streptolysin O Protein that degrades cell Lyses RBCs; contributes to β-hemolysis; pyogenes membrane host antibodies against toxin (ASO) used to diagnose rheumatic fever (do not confuse with immune complexes of poststreptococcal glomerulonephritis) Superantigens causing shock Staphylococcus Toxic shock Cross-links β region of Toxic shock syndrome: fever, rash, shock; other aureus syndrome toxin TCR to MHC class II toxins cause scalded skin syndrome (exfoliative (TSST-1) on APCs outside of the toxin) and food poisoning (heat-stable antigen binding site enterotoxin) Streptococcus Erythrogenic overwhelming release Toxic shock–like syndrome: fever, rash, shock; pyogenes exotoxin A of IL-1, IL-2, IFN-γ, and scarlet fever TNF-α shock Endotoxin LPS found in outer membrane of gram ⊝ ENDOTOXINS: bacteria (both cocci and rods). Composed Edema of O-antigen + core polysaccharide + lipid Nitric oxide A (the toxic component). Neisseria have DIC/Death lipooligosaccharide. Outer membrane Released upon cell lysis or by living cells by TNF-α blebs detaching from outer surface membrane O-antigen + core polysaccharide + lipid A (vs exotoxin, which is actively secreted). eXtremely heat stable Three main effects: macrophage activation IL-1 and IL-6 (TLR4/CD14), complement activation, and Neutrophil chemotaxis tissue factor activation. Shock IL-1, IL-6 Fever Macrophage activation TNF-α Fever and hypotension (TLR4/CD14) Nitric oxide Hypotension Histamine release: C3a Endotoxin Hypotension and edema (lipid A component) Complement activation C5a Neutrophil chemotaxis Coagulation Tissue factor activation DIC cascade FAS1_2023_03-Microbiology.indd 131 11/22/22 4:14 PM  132 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY Gram-positive lab algorithm Gram (purple/blue) Branching Bacilli Cocci filaments Aerobic Anaerobic Aerobic Anaerobic Listeria Clostridium Nocardia Actinomyces Bacillus Cutibacterium (weakly acid fast) (not acid fast) Corynebacterium (formerly Propionibacterium) Catalase (Pairs or Streptococcus (Clusters) Staphylococcus chains) Hemolysis Coagulase α γ (Partial (Complete hemolysis, green) β hemolysis, clear) (No hemolysis, grows in bile) S aureus Novobiocin Optochin sensitivity Bacitracin sensitivity Growth in 6.5% NaCl sensitivity and bile solubility and PYR status and PYR Status Group B Group A S saprophyticus S epidermidis S agalactiae S pyogenes Viridans streptococci (no capsule) Enterococcus S pneumoniae Nonenterococcus E faecium S mutans (encapsulated) S gallolyticus S mitis E faecalis Important tests are in bold. Important pathogens are in bold italics. Note: Enterococcus is either ˜ - or ° -hemolytic. PYR, Pyrrolidonyl aminopeptidase. FAS1_2023_03-Microbiology.indd 132 11/22/22 4:14 PM  MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY SEC TION II 133 Hemolytic bacteria α-hemolytic bacteria Partial oxidation of hemoglobin greenish A or brownish color without clearing around growth on blood agar A. Include Streptococcus pneumoniae and viridans streptococci. β-hemolytic bacteria Complete lysis of RBCs pale/clear area surrounding colony on blood agar A. Include Staphylococcus aureus, Streptococcus pyogenes (group A strep), Streptococcus agalactiae (group B strep), Listeria monocytogenes. Staphylococcus aureus Gram ⊕, β-hemolytic, catalase ⊕, coagulase TSST-1 is a superantigen that binds to MHC ⊕ cocci in clusters A. Protein A (virulence II and T-cell receptor, resulting in polyclonal A factor) binds Fc-IgG, inhibiting complement T-cell activation and cytokine release. activation and phagocytosis. Commonly Staphylococcal toxic shock syndrome (TSS)— colonizes the nares, ears, axilla, and groin. fever, vomiting, diarrhea, rash, desquamation, Causes: shock, end-organ failure. TSS results in AST, Inflammatory disease—skin infections, ALT, bilirubin. Associated with prolonged organ abscesses, pneumonia (often after use of vaginal tampons or nasal packing. influenza virus infection), infective Compare with Streptococcus pyogenes TSS (a endocarditis, septic arthritis, and toxic shock–like syndrome associated with osteomyelitis. painful skin infection). Toxin-mediated disease—toxic shock S aureus food poisoning due to ingestion of syndrome (TSST-1), scalded skin syndrome preformed toxin short incubation period (exfoliative toxin), rapid-onset food (2–6 hr) followed by nonbloody diarrhea poisoning (enterotoxins). and emesis. Enterotoxin is heat stable not MRSA (methicillin-resistant S aureus)— destroyed by cooking. important cause of serious healthcare- S aureus makes coagulase and toxins. Forms associated and community-acquired fibrin clot around itself abscess. infections. Resistance due to altered penicillin- binding proteins (conferred by mecA gene). Some strains release Panton-Valentine leukocidin (PVL), which kills leukocytes and causes tissue necrosis. Staphylococcus Gram ⊕, catalase ⊕, coagulase ⊝, urease ⊕ cocci in clusters. Novobiocin sensitive. Does not epidermidis ferment mannitol (vs S aureus). Normal microbiota of skin; contaminates blood cultures. Infects prosthetic devices (eg, hip implant, heart valve) and IV catheters by producing adherent biofilms. FAS1_2023_03-Microbiology.indd 133 11/22/22 4:14 PM  134 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY Staphylococcus Gram ⊕, catalase ⊕, coagulase ⊝, urease ⊕ cocci in clusters. Novobiocin resistant. saprophyticus Normal microbiota of female genital tract and perineum. Second most common cause of uncomplicated UTI in young females (most common is E coli). Streptococcus Gram ⊕, α-hemolytic, lancet-shaped Pneumococcal pneumonia is associated with pneumoniae diplococci A. “rusty” sputum. A Encapsulated. IgA protease. Optochin Patients with anatomic or functional sensitive and bile soluble. hyposplenia or asplenia are predisposed to Most commonly causes MOPS: infection. Meningitis No virulence without capsule. Otitis media (in children) Pneumococcal vaccines are available in both Pneumonia conjugate (PCV13, PCV15, PCV20) and Sinusitis polysaccharide (PPSV23) formulations. Viridans group Gram ⊕, α-hemolytic cocci. Optochin resistant Viridans group strep live in the mouth, because streptococci and bile insoluble. Normal microbiota of the they are not afraid of-the-chin (op-to-chin oropharynx. resistant). Streptococcus mutans and S mitis cause dental Sanguinis = blood. Think, “there is lots of caries. blood in the heart” (infective endocarditis). S sanguinis makes dextrans that bind to fibrin- platelet aggregates on damaged heart valves, causing infective endocarditis. Streptococcus Gram ⊕ cocci in chains A. Group A strep “Ph”yogenes pharyngitis can result in pyogenes (group A cause: rheumatic “phever” and glomerulonephritis. streptococci) Pyogenic—pharyngitis, cellulitis, impetigo Strains causing impetigo can induce A (“honey-crusted” lesions), erysipelas glomerulonephritis. Toxigenic—scarlet fever, toxic shock–like Key virulence factors include DNase, syndrome, necrotizing fasciitis erythrogenic exotoxin, streptokinase, Immunologic—rheumatic fever, streptolysin O. ASO titer or anti-DNase glomerulonephritis B antibodies indicate recent S pyogenes Bacitracin sensitive, β-hemolytic, pyrrolidonyl infection. arylamidase (PYR) ⊕. Hyaluronic acid Scarlet fever—blanching, sandpaperlike body capsule and M protein inhibit phagocytosis. rash, strawberry tongue, and circumoral Antibodies to M protein enhance host defenses. pallor in the setting of group A streptococcal Structurally similar to host proteins (ie, myosin); pharyngitis (erythrogenic toxin ⊕). can lead to autoimmunity (ie, carditis seen in acute rheumatic fever). Diagnose strep pharyngitis via throat swab, which can be tested with an antigen detection assay (rapid, in-office results) or cultured on blood agar (results in 48 hours). FAS1_2023_03-Microbiology.indd 134 11/22/22 4:15 PM  MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY SEC TION II 135 Streptococcus Gram ⊕ cocci, bacitracin resistant, β-hemolytic, Group B for Babies! agalactiae (group B colonizes vagina; causes pneumonia, streptococci) meningitis, and sepsis, mainly in babies. Polysaccharide capsule confers virulence. Produces CAMP factor, which enlarges the area of hemolysis formed by S aureus. (Note: CAMP stands for the authors of the test, not cyclic AMP.) Hippurate test ⊕. PYR ⊝. Screen pregnant patients at 35–37 weeks of gestation with rectal and vaginal swabs. Patients with ⊕ culture receive intrapartum penicillin/ampicillin prophylaxis. Streptococcus Formerly S bovis. Gram ⊕ cocci, colonizes Bovis in the blood = cancer in the colon. gallolyticus the gut. Can cause bacteremia and infective endocarditis. Patients with S gallolyticus endocarditis have incidence of colon cancer. Enterococci Gram ⊕ cocci. Enterococci (E faecalis and Enterococci are more resilient than E faecium) are normal colonic microbiota streptococci, can grow in 6.5% NaCl and bile that are penicillin G resistant and cause (lab test). UTI, biliary tract infections, and infective Entero = intestine, faecalis = feces, strepto = endocarditis (following GI/GU procedures). twisted (chains), coccus = berry. Catalase ⊝, PYR ⊕, typically nonhemolytic. VRE (vancomycin-resistant enterococci) are an important cause of healthcare-associated infection. Bacillus anthracis Gram ⊕, spore-forming rod that produces anthrax toxin, exotoxins consisting of protective antigen, A lethal factor (inhibits MAP kinase macrophage apoptosis), and edema factor (acts as adenylyl cyclase intracellular cAMP, upsetting homeostasis edema, necrosis). Has a polypeptide capsule (poly d-glutamate). Colonies show a halo of projections, sometimes called “medusa head” appearance. Cutaneous anthrax—painless papule surrounded by vesicles ulcer with black eschar A (painless, necrotic) uncommonly progresses to bacteremia and death. Pulmonary anthrax—inhalation of spores, most commonly from contaminated animals or animal products, although also a potential bioweapon flulike symptoms that rapidly progress to fever, pulmonary hemorrhage, mediastinitis (CXR may show widened mediastinum), and shock. Also called woolsorter’s disease. Prophylaxis with ciprofloxacin or doxycycline when exposed. Both cutaneous and pulmonary anthrax may be complicated by hemorrhagic meningitis. FAS1_2023_03-Microbiology.indd 135 11/22/22 4:15 PM  136 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY Bacillus cereus Gram ⊕ rod. Causes food poisoning. Spores survive cooking rice (reheated rice syndrome). Keeping rice warm results in germination of spores and enterotoxin formation. Emetic type causes nausea and vomiting within 1–5 hours. Caused by cereulide, a preformed toxin. Diarrheal type causes watery, nonbloody diarrhea and GI pain within 8–18 hours. Management: supportive care (antibiotics are ineffective against toxins). Clostridioides difficile Produces toxins A and B, which damage Difficile causes diarrhea. A enterocytes. Both toxins lead to watery diarrhea Diagnosed by PCR or antigen detection of one pseudomembranous colitis A. Often 2° or both toxins in stool. to antibiotic use, especially clindamycin, Treatment: oral vancomycin or fidaxomicin. ampicillin, cephalosporins, fluoroquinolones; For recurrent cases, consider repeating prior associated with PPIs. regimen or fecal microbiota transplant. Fulminant infection: toxic megacolon, ileus, shock. Clostridia Gram ⊕, spore-forming, obligate anaerobic rods. Tetanus toxin and botulinum toxin are proteases that cleave SNARE proteins involved in neurotransmission. Clostridium tetani Pathogen is noninvasive and remains localized Tetanus is tetanic paralysis. to wound site. Produces tetanospasmin, an Prevent with tetanus vaccine. Treat with antitoxin exotoxin causing tetanus. Tetanospasmin +/− vaccine booster, antibiotics, diazepam (for spreads by retrograde axonal transport to CNS muscle spasms), and wound debridement. and blocks release of GABA and glycine from Renshaw cells in spinal cord. Causes spastic paralysis, trismus (lockjaw), risus sardonicus (raised eyebrows and open grin), opisthotonos (spasms of spinal extensors). Clostridium botulinum Produces a heat-labile toxin that inhibits ACh Botulinum is from bad bottles of food, juice, release at the neuromuscular junction, causing and honey. botulism. In babies, ingestion of spores Treatment: human botulinum immunoglobulin. (eg, in honey) leads to disease (floppy baby Local botulinum toxin A (Botox) injections used syndrome). In adults, disease is caused by to treat focal dystonia, hyperhidrosis, muscle ingestion of preformed toxin (eg, in canned spasms, and cosmetic reduction of facial food). wrinkles. Symptoms of botulism (the 5 D’s): diplopia, dysarthria, dysphagia, dyspnea, descending flaccid paralysis. Does not present with sensory deficits. Clostridium Produces α-toxin (lecithinase, a phospholipase) Perfringens perforates a gangrenous leg. perfringens that can cause myonecrosis (gas gangrene A ; Spontaneous gas gangrene (via hematogenous A presents as soft tissue crepitus) and hemolysis. seeding; associated with colonic malignancy) If heavily spore-contaminated food is cooked is most commonly caused by Clostridium but left standing too long at < 60°C, spores septicum. germinate vegetative bacteria heat-labile enterotoxin late-onset (10-12 hours) food poisoning symptoms, resolution in 24 hours. FAS1_2023_03-Microbiology.indd 136 11/22/22 4:16 PM  MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY SEC TION II 137 Corynebacterium Gram ⊕ rods occurring in angular Coryne = club shaped (metachromatic granules diphtheriae arrangements; transmitted via respiratory on Löffler media). droplets. Causes diphtheria via exotoxin Black colonies on cystine-tellurite agar. A encoded by β-prophage. Potent exotoxin ABCDEFG: inhibits protein synthesis via ADP-ribosylation ADP-ribosylation of EF-2, leading to possible necrosis in β-prophage pharynx, cardiac, and CNS tissue. Corynebacterium Symptoms include pseudomembranous Diphtheriae pharyngitis (grayish-white membrane A ) with Elongation Factor 2 lymphadenopathy (“bull’s neck” appearance). Granules Toxin dissemination may cause myocarditis, Treatment: diphtheria antitoxin +/– arrhythmias, neuropathies. erythromycin or penicillin. Lab diagnosis based on gram ⊕ rods with metachromatic (blue and red) granules and ⊕ Elek test for toxin. Toxoid vaccine prevents diphtheria. Listeria Gram ⊕, facultative intracellular rod; acquired by ingestion of unpasteurized dairy products and monocytogenes cold deli meats, transplacental transmission, by vaginal transmission during birth. Grows well at A refrigeration temperatures (“cold enrichment”). Forms “rocket tails” (red in A ) via actin polymerization that allow intracellular movement and cell- to-cell spread across cell membranes, thereby avoiding antibody. Listeriolysin generates pores in phagosomes, allowing its escape into cytoplasm. Characteristic tumbling motility in broth. Can cause amnionitis, septicemia, and spontaneous abortion in pregnant patients; granulomatosis infantiseptica; meningitis in immunocompromised patients, neonates, and older adults; mild, self- limited gastroenteritis in healthy individuals. Treatment: ampicillin. Nocardia vs Both are gram ⊕ and form long, branching filaments resembling fungi. Actinomyces Nocardia Actinomyces A Aerobe Anaerobe Acid fast (weak) A Not acid fast B Found in soil Normal oral, reproductive, and GI microbiota Causes pulmonary infections in Causes oral/facial abscesses that drain through immunocompromised (can mimic TB but sinus tracts; often associated with dental caries/ with ⊝ PPD); cutaneous infections after extraction and other maxillofacial trauma; trauma in immunocompetent; can spread to forms yellow “sulfur granules”; can also cause B CNS cerebral abscess PID with IUDs Treat with sulfonamides (TMP-SMX) Treat with penicillin Treatment is a SNAP: Sulfonamides—Nocardia; Actinomyces—Penicillin FAS1_2023_03-Microbiology.indd 137 11/22/22 4:16 PM  138 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY Mycobacteria Acid-fast rods (pink rods, arrows in A ). TB symptoms include fever, night sweats, A Mycobacterium tuberculosis (TB, often resistant weight loss, cough (nonproductive or to multiple drugs). productive), hemoptysis. M avium–intracellulare (causes disseminated, Cord factor creates a “serpentine cord” non-TB disease in AIDS; often resistant to appearance in virulent M tuberculosis multiple drugs). strains; activates macrophages (promoting M scrofulaceum (cervical lymphadenitis in granuloma formation) and induces release of children). TNF-α. Sulfatides (surface glycolipids) inhibit M marinum (hand infection in aquarium phagolysosomal fusion. handlers). Tuberculosis Mycobacterium PPD ⊕ if current infection or past exposure. tuberculosis Hilar nodes PPD ⊝ if no infection and in + immunocompromised patients (especially with Ghon complex Ghon focus low CD4+ cell count). (usually mid/ Interferon-γ release assay (IGRA) has fewer false lower lobes) Primary tuberculosis positives from BCG vaccination. > 90% < 10% Caseating granulomas with central necrosis and Healing by fibrosis Progressive primary tuberculosis Langhans giant cell (single example in A ) Calcification (AIDS, malnutrition) (PPD ) are characteristic of 2° tuberculosis. Do not Reactivation confuse Langhans giant cell (fused Progressive lung disease macrophages) with Langerhans cell (dermal 2° tuberculosis Fibrocaseous Bacteremia APC). cavitary lesion TB reactivation risk highest in (usually upper Miliary Meninges immunocompromised individuals (eg, HIV, lobes) tuberculosis organ transplant recipients, TNF-α inhibitor Vertebrae (Pott disease) use). Reactivation has a predilection for the Localized destructive disease apices of the lung (due to the bacteria being Lymph nodes Cavity highly aerobic). Caseation Lungs Caseation Spleen A Scar Liver Adrenal gland Joints and long bones FAS1_2023_03-Microbiology.indd 138 11/22/22 4:16 PM  MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY SEC TION II 139 Leprosy Also called Hansen disease. Caused by Mycobacterium leprae, an acid-fast bacillus that likes cool A temperatures (infects skin and superficial nerves—“glove and stocking” loss of sensation) and cannot be grown in vitro. Diagnosed via skin biopsy or tissue PCR. Reservoir in United States: armadillos. Leprosy has 2 forms (many cases fall temporarily between two extremes): Lepromatous—presents diffusely over the skin, with leonine (lionlike) facies A , and is communicable (high bacterial load); characterized by low cell-mediated immunity with a largely Th2 response. Lepromatous form can be lethal. Tuberculoid—limited to a few hypoesthetic, hairless skin plaques B ; characterized by high cell- B mediated immunity with a largely Th1-type response and low bacterial load. Treatment: dapsone and rifampin for tuberculoid form; clofazimine is added for lepromatous form. Gram-negative lab algorithm Gram (pink) Diplococci Coccobacilli Curved rods Aerobic Haemophilus influenzae Oxidase Bordetella pertussis Maltose fermentation Pasteurella Brucella Francisella tularensis Grows in 42°C Grows in alkaline media Produces urease Acinetobacter baumannii N gonorrhoeae Campylobacter jejuni Vibrio cholerae Helicobacter pylori N meningitidis Moraxella Bacilli Lactose fermentation Oxidase Fast Slow E coli Citrobacter Klebsiella Pseudomonas Serratia H2S production Burkholderia Enterobacter on TSI agar Shigella Salmonella Yersiniaa Proteus Important tests are in bold. Important pathogens are in bold italics. a Pleomorphic rod/coccobacillus FAS1_2023_03-Microbiology.indd 139 11/22/22 4:17 PM  140 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY Neisseria Gram ⊝ diplococci. Metabolize glucose N gonorrhoeae is often intracellular (within A and produce IgA proteases. Contain neutrophils) A. lipooligosaccharides (LOS) with strong Acid production: meningococci—maltose and endotoxin activity. glucose; gonococci—glucose. Gonococci Meningococci No polysaccharide capsule Polysaccharide capsule No maltose acid detection Maltose acid detection No vaccine due to antigenic variation of pilus Vaccine (type B vaccine available for at-risk B proteins individuals) Sexually or perinatally transmitted Transmitted via respiratory and oral secretions. More common among individuals in close quarters (eg, army barracks, college dorms) Causes gonorrhea, septic arthritis, neonatal Causes meningococcemia with petechial conjunctivitis (2–5 days after birth), pelvic hemorrhages and gangrene of toes B , inflammatory disease (PID), and Fitz-Hugh– meningitis, Waterhouse-Friderichsen Curtis syndrome syndrome (acute hemorrhagic adrenal insufficiency) Diagnosed with NAAT Diagnosed via culture-based tests or PCR Condoms sexual transmission, erythromycin Rifampin, ciprofloxacin, or ceftriaxone eye ointment prevents neonatal blindness prophylaxis in close contacts Treatment: single dose IM ceftriaxone; if Treatment: ceftriaxone or penicillin G chlamydial coinfection not excluded by molecular testing, add doxycycline Haemophilus Small gram ⊝ (coccobacillary) rod. Transmitted Vaccine contains type b capsular polysaccharide influenza through respiratory droplets. Nontypeable (polyribosylribitol phosphate) conjugated A (unencapsulated) strains are the most common to diphtheria toxoid or other protein. Given cause of mucosal infections (otitis media, between 2 and 18 months of age. conjunctivitis, bronchitis) as well as invasive Does not cause the flu (influenza virus does). infections since the vaccine for capsular type b Treatment: amoxicillin +/− clavulanate for was introduced. Produces IgA protease. mucosal infections; ceftriaxone for meningitis; Culture on chocolate agar, which contains rifampin prophylaxis for close contacts. factors V (NAD+) and X (hematin) for growth; can also be grown with S aureus, which provides factor V via RBC hemolysis. Haemophilus causes epiglottitis (endoscopic appearance can be “cherry red” in children; “thumb sign” on lateral neck x-ray A ), meningitis, otitis media, and pneumonia. Burkholderia cepacia Aerobic, catalase ⊕, gram ⊝ rod. Causes pneumonia in and can be transmitted between patients complex with cystic fibrosis. Often multidrug resistant. Infection is a relative contraindication to undergoing lung transplant due to its association with poor outcomes. FAS1_2023_03-Microbiology.indd 140 11/22/22 4:18 PM  MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY SEC TION II 141 Bordetella pertussis Gram ⊝, aerobic coccobacillus. Virulence factors include pertussis toxin (disables Gi), adenylate cyclase toxin ( cAMP), and tracheal cytotoxin. Three clinical stages: Catarrhal—low-grade fevers, coryza. Paroxysmal—paroxysms of intense cough followed by inspiratory “whoop” (“whooping cough”), posttussive vomiting. Convalescent—gradual recovery of chronic cough. Prevented by Tdap, DTaP vaccines. Produces lymphocytosis (unlike most acute bacterial infections). Treatment: macrolides; if allergic use TMP-SMX. Brucella Gram ⊝, aerobic coccobacillus. Transmitted via ingestion of contaminated animal products (eg, unpasteurized milk). Survives in macrophages in the reticuloendothelial system. Can form non- caseating granulomas. Typically presents with undulant fever, night sweats, and arthralgia. Treatment: doxycycline + rifampin or streptomycin. Legionella Gram ⊝ rod. Gram stains poorly—use silver Think of a French legionnaire (soldier) with pneumophila stain. Grow on charcoal yeast extract medium his silver helmet, sitting around a campfire A with iron and cysteine. Detected by presence of (charcoal) with his iron dagger—he is missing antigen in urine. Labs may show hyponatremia. his sister (cysteine). Aerosol transmission from environmental water Legionnaires’ disease—severe pneumonia source habitat (eg, air conditioning systems, (often unilateral and lobar A ), fever, GI and hot water tanks). Outbreaks associated with CNS symptoms. Risk factors include older age, cruise ships, nursing homes. No person-to- tobacco smoking, chronic lung disease. person transmission. Pontiac fever—mild flulike symptoms. Treatment: macrolide or quinolone. Pseudomonas Aeruginosa—aerobic; motile, catalase ⊕, gram ⊝ Corneal ulcers/keratitis in contact lens wearers/ aeruginosa rod. Non-lactose fermenting. Oxidase ⊕. minor eye trauma. A Frequently found in water. Increased virulence Ecthyma gangrenosum—rapidly progressive, in acidic environments. Has a grapelike odor. necrotic cutaneous lesion B caused by PSEUDOMONAS is associated with: Pseudomonas bacteremia. Typically seen in Pneumonia, Sepsis, Ecthyma gangrenosum, immunocompromised patients. UTIs, Diabetes, Osteomyelitis, Mucoid Treatments: polysaccharide capsule, Otitis externa Antipseudomonal penicillins in combination (swimmer’s ear), Nosocomial (healthcare- with β-lactamase inhibitor (eg, piperacillin- B associated) infections (eg, catheters, tazobactam) equipment), Addiction (injection drug use), 3rd- and 4th-generation cephalosporins (eg, Skin infections (eg, hot tub folliculitis, wound ceftazidime, cefepime) infection in burn victims). Monobactams Mucoid polysaccharide capsule may contribute Fluoroquinolones to chronic pneumonia in patients with cystic Carbapenems fibrosis due to biofilm formation. Despite antipseudomonal activity, Produces PEEP: Phospholipase C (degrades aminoglycoside monotherapy is avoided due to cell membranes); Endotoxin (fever, shock); poor performance in acidic environments. Exotoxin A (inactivates EF-2); Pigments: pyoverdine and pyocyanin (blue-green pigment A ; also generates ROS). FAS1_2023_03-Microbiology.indd 141 11/22/22 4:19 PM  142 SEC TION II MICROBIOLOGY ` MICROBIOLOGY—CLINICAL BACTERIOLOGY Salmonella vs Shigella Both Salmonella and Shigella are gram ⊝ rods, non-lactose fermenters, oxidase ⊝, and can invade the GI tract via M cells of Peyer patches. Salmonella typhi (ty-Vi) Salmonella spp. Shigella except S typhi RESERVOIRS Humans only Humans and animals Humans only SPREAD Hematogenous spread Hematogenous spread Cell to cell; no hematogenous spread H2S PRODUCTION Yes Yes No FLAGELLA Yes (salmon swim) Yes (salmon swim) No VIRULENCE FACTORS Endotoxin; Vi capsule Endotoxin Endotoxin; Shiga toxin (enterotoxin) (pronounce “tyVi”) INFECTIOUS DOSE (ID50) High—large inoculum High Low—very small inoculum required; required; acid-labile acid stable (resistant to gastric acids) (inactivated by gastric acids) EFFECT OF ANTIBIOTICS ON FECAL Prolongs duration Prolongs duration Shortens duration (shortens Shigella) EXCRETION IMMUNE RESPONSE Primarily monocytes PMNs in disseminated Primarily PMN infiltration disease GI MANIFESTATIONS Constipation, followed by Diarrhea (possibly bloody) Crampy abdominal pain tenesmus, diarrhea bloody mucoid stools (bacillary dysentery) VACCINE Oral vaccine contains live No vaccine No vaccine attenuated S typhi