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Mini Table
Microbe T S Other Sx Imaging Source At Risk Media/Labs.Dx Toxins/Virulence
Streptococcus pneumoniae G+ O

+ R
S: thin Pleurisy Lobar cons. Resp. flora Children hemolysis: a Optochin sens. Capsule Neuraminidase
Actinomyces isrealii G+ 0 S: purulent Empyema mass lesion Oral flora Farmers Sulfur “molar teeth” Granules
Klebsiella pneumonia G - 0 S: thick Cavity or Lobar cons. Resp. & GI flora EtOH, DM COPD MacConkey: pink Urease + Capsule (large) b-lactamase
Mycobacterium tuberculosis A 0 Ghon focus/ complex Upper lobes Cavitary lesions Humans Imm. supp., Immiigrants Catalase + PPD Skin test Mycolic acids Facult. Intracell.
Blastomyces dermatitidis * oo Arthralgias Ulcerative warts Reticulonodular infiltrates Lobar cons. Soil E. of Missis. Foresters Farmers EIA
Aspergillus spp. Y Allergic asthma Cavitary lesions
Lung cavities from TB Black colonies Aflatoxin Phopholipase
Pseudomonas aeruginosa G - 0 + G
Abscess Ubiquitious COPD, CF Imm. supp. Fruity odor Oxidase + Mutli-drug resis. Pyocyanin
Staphylococcus aureus G+ O

Empyema Patchy infil. Nostrils Nosocomial Manitol, salt agar Catalase + P-V Leukocidin b-lactamases
Burkholderia spp. G - 0

Tropical COPD Oxidase +
E. coli G - 0

GI flora COPD MacConkey: pink col. Eosin Meth. Blue: Green colonies lactose ferment. Endotoxin (Lipid A) Capsule
Proteus spp. G - 0

COPD Elderly Swarming col. Urease + Flagella (motile)
Serratia marcescens G - 0

Nosocomial Imm. supp. Red Gelatinase
Yersinia pestis G - 0 High Mortality
Rodents, fleas SW U.S.
Iron & cold env. “safety pin” stain YOP Capsule
Strongyloides stercoralis C Skin rash patchy infil. Soil Bare foot Fatal if Immunocomp. Eosinophilia Only sputum Hooks
Ascaris lumbricoides C Anorexia patchy infil. Worldwide Water, Soil
Eosinophilia Stool, sputum
Bacillus anthracis G+ 0

Chest edema Mediastinal shift Soil, Sheep, Wool Woolsorters Catalase + Edema factor-EF Lethal factor-LF
Coxsiella burnetti G - 0 Hepatitis
Farm animals Abbatoir Workers Weil-Felix Negative
Francisella tularensis G - 0 Burning pain patchy infil. Ticks, rabbits Hunters Cysteine req. Forshay’s test b-lactamase
Legionella pneumophilia G - 0 Diarrhea Pleural eff Warm water Tobbaco, EtOH Imm. supp. Cysteine, Iron & charcoal yeast extract. Capsule Facult., ntracell.
Nocardia asteroides A 0
Cavitary Lesions
Imm. supp. Wrinkled chalk-like colonies Partially acid fast
Chlamydophilia Psittaci /
Prominent infil. Birds/poultry Abbatoir workers Biohazard! Paired serology
Chlamydophila pneumonia /


Prominent infil. Humans Elderly

Mycoplasma pneumonia / Not severe. Raynaud's Patchy infil.
Students Soldiers Fried egg/mulberry col. Cold agglutinin P1 antigen HS production
Pneumocyctis jerovicii (carinii) oo
Ground glass infil.
AIDS BAL: Cysts, Trophozoites
Histoplasma capsulatum */oo Liver failure Coin lesions Cavitation Bat droppings OH, MO, & West of MS COPD Serology/BAL
Coccidioides immitis */oo Arthalgias Calcifications Dry soil In NM & AZ

Cytomeagovirus (CMV) E dsDNA

Humans Imm. supp. Serology 'Owls eyes'
Hantavirus E -ssRNA
Interstitial edema Rodent Leavings Outdoors Woods Biohazard! Elisa


T = Type of micobe
S = Sputum EtOH = alcoholics
A 0 Acid-fast, bacillus + = productive cough DM = diabetics
G+ O Gram positive, cocci + R = blood tinged sputum COPD = underlying pulmonary disease
G+ 0 Gram positive, bacillus + G = greem sputum BAL = bronchoalveolar lavage
G - 0 Gram negative, bacillus - = nonproductive cough
oo Yeast

*/oo Dimorphic: fungus & yeast AZ = Arizona
Y Fungus, branching MO = Missouri
C Nematodes MS = Mississippi
/ No cell wall NM = New Mexico
E dsDNA Enveloped Double stranded DNA OH = ohio
E -ssRNA Enveloped Negative sense RNA

Clinical Table
Microbe Clinical presentation Diseases Imaging Source/Trans. At Risk Treatment/Prev.
Streptococcus pneumoniae Productive cough Sputum: blood tinged, thin Pleurisy High fevers, shaking chills Lobar pneumonia (typical) Meningitis Otitis media Sinusitis Lobar consolidation possible Normal respiratory flora Children Penicillin G Polyvalent vaccine
Staphylococcus aureus Productive cough Empyema Pneumonia (typical) Endocarditis, Sepsis Pneumonia Food Poisoning Osteomyelytis Infective arthritis Furuncles, Carbuncles Patchy infiltrates Nostrils Acquired by aspiration, or hematogenously Hospitalized patients Post-viral infections Nafcillin Vancomycin Bacitracin
Actinomyces isrealii Productive cough Sputum: purulent Hemoptysis Empyema Pneumonia (typical) Dental abscess Farmer's lung (pneumonitis) mass lesion Oral flora Farmers Penicillin G
Pseudomonas aeruginosa Productive cough Sputum: green Fever, chills Cyanosis, confusion Pneumonia (typical) Burn tissue colonization Ecthyma gangrenosum Septicemia UTI Hot tub folliculitis Corneal Keratitis (ulcers) Endophathalmitis GI colonization (loose stools) Abscess formation Ubiquitious in Enviornement Colonized in CF Pt's Patients with: Cystic Fibrosis, COPD, Neutropenia Ventilated patients Immunocompromised Multi-drug combos Cephalosporins Aminoglycosides Aztreonam Penicillins
Burkholderia spp. Productive cough Sputum: no pigment Mild bronchitis to Severe pneumonia Pneumonia (typical) Skin infection Surgical wound infection
Tropical climates Moist surfaces Underlying chronic Pulmonary disease Penicillin Doxycycline Imipenem
E. coli Productive cough Pneumonia (typical) Other infections
Normal intestinal flora Aspiration Underlying COPD Caution: risk of Endotoxin release Ampicillin Cephaosporins
Klebsiella pneumonia Productive cough Sputum: red, thick 'currant jelly' Pneumonia (typical) UTI Sepsis Cavity formation Lobar consolidation possible Respiratory/GI flora Aspiration, Repiratory droplets Alcoholics Diabetics Underlying COPD Combos: Cefotaxime+ Gentamycin TMP-SMX = bactrim
Proteus spp. Productive cough UTIs Pneumonia (typical) Nephrolithiasis

Underlying COPD Elderly Ampicillin Bactrim
Serratia marcescens Productive cough Pneumonia (typical) UTIs, Bactermia Endocarditis

Nosocomial Immunocompromised Ampicillin Bactrim
Yersinia pestis Productive cough Fever, Malaise High Mortality! Pneumonia (typical) Enlarged, necrotic lymph nodes (Bubonic plague)
Rodents Transmitted by fleas Endemic in SW U.S.
Streptomycin Isolation IV fluids, pressors Vaccine available
Mycobacterium tuberculosis Productive cough Sputum: blood tinged Pneumonia (typical) Cavitary pulmonary granulomas Ghon focus & complex Potts disease Scrofuloderma Meningitis Cavitary Lesions in lower lobes Reactivation in upper lobes Humans Immunocompromised Homeless Immiigrants Prsoners, AIDS '4x2 + 2x4' regimen Isoniazid, Rifampin, Pyrazinamide, Ethambutol x2 months Then Isoniazide + Rifampin x 4 months
Aspergillus spp. Cough Hemoptysis Pneumonia (atypical) Sinusitis Allergic asthma Hepatic cancer (aflatoxin related) Cavitary lesions
Pre-existing lung Cavities (e.g. TB) Surgery: remove fungus balls Amphoterecin B
Blastomyces dermatitidis Productive cough Hemoptysis Arthralgias Myalgias Pneumonia (typical) Skin: wart-like, ulcerative lesions reticulonodular infiltrates, +/- Lobar Consolidation Moist soil Dust clouds Woods East of Mississippi Foresters Farmers Amphotericin B
Coccidioides immitis Nonproductive cough Self limiting Pneumonia (atypical) Erythema nodosum Erythema multiforme Arthalgias Calcifications & granulomas Soil (hot & dry) Unpaved roads Not contageous New Mexico, Arizona
Amphotericin B
Histoplasma capsulatum Nonproductive cough Asymptomatic in most Dissemination in immunocompromised Pneumonia (atypical) Skin lesions Pulmonary fibrosis Respiratory & Liver failure Coin lesions (calcifications, granulomas) Cavitation Soil Bat droppings Ohio, Missouri & West of Mississippi Underlying Pulmonary disease Amphotericin B Ketoconazole
Bacillus anthracis Nonproductive cough Chest edema Hemorrhagic mediastinal lymphadenitis Cyanosis Shock Eschars, with paiful Lymphadenopathy Pneumonia (atypical) Mediastinal hemorrhagic lymphadenitis Vomiting, Dysentery Mediastinal shift Soil Grazing herbivores e.g. sheep Wool Woolsorter’s disease Ciprofloxacin Vaccine to Pa (protective antigen)
Francisella tularensis Nonproductive cough Burning sensation Ronchis Ulceroglandular disease Pneumonia (atypical) Skin ulcers patchy infiltrates Tick bites Handling rabbit meat Hunters Streptomycin
Coxsiella burnetti Nonproductive cough Flu-like in adults (Q-fever) Crackles Pneumonia (atypical) Angina Photophobia Hepatitis
Farm animals Milk Abbatoir workers Tetracycline Vaccine available
Legionella pneumophilia Nonproductive cough Watery diarrhea Pneumonia (atypical) Diarrhea Pontiac Fever Renal failure Pleural effusion Warm water sources Humidifiers Not contageous Middle age Smokers Alcoholics Immunocomrpomised Azithromycin Levofloxacin
Mycoplasma pneumonia Nonproductive cough Bronchitis Patients not as ill Wheezing, rhales Pneumonia (atypical) Raynauds Phenomenon Patchy Infiltrates: unilateral lower lobe
College Barracks Macrolides Doxycycline
Chlamydophila pneumonia Nonproductive cough Minor symptoms Pneumonia (atypical) Prominent infiltrates Humans Elderly Doxycycline Azithromycin
Chlamydophilia Psittaci Nonproductive cough Minor symptoms Pneumonia (atypical) Sinusitis Hematogenous spread Prominent infiltrates Zoonotic Birds/poultry Abbatoir workers Doxycycline Fluoroquinalones
Nocardia asteroides Nonproductive cough Pneumonia (atypical) Cavitating pulmonary Abscesses Brain abscess Pustules Lymphadenitis Cavitary lesions Resembles tuberculosis
Immunocompromised Surgical resection Drainage Sulfonamides
Pneumocyctis jerovicii (carinii) Nonproductive cough Pnemonia (atypical) Ground glass infiltrates
AIDS patients TMP-SMX (Bactrim) Pentamidine Isothionate
Cytomeagovirus (CMV) Nonproductive cough Fever Dyspnea Pneumonia (atypical) Infectious 'mono' (choreo-)retinitis Hepatitis Encephalitis
Humans are reservior Immunocompromised AIDS Bone marrow Transplants Ganciclovir HAART for AIDS
Hantavirus Nonproductive cough Early - fever, Headaches, myalgia Late - dyspnea, Respiratory failure Pneumonia (atypical) Hemorrhagic fever Renal function Affected Interstitial Pulmonary edema Aerosolization of Rodent urine/feces Outdoors/Woods Rodent control
Ascaris lumbricoides Pneumonitis Anorexia Pneumonia (typical) Intestinal obstruction patchy infiltrates Worldwide (1 billion inf.) Fecal contamination: Water / Soil
Strongyloides stercoralis Pneumonitis Pneumonia (typical) Serpiginous Urticarial rash Perianal pruritis Abdominal pain patchy infiltrates Soil: latches to skin With hooks Walking bare foot Immunocompromised: Autoinfection. Fatal Thiabendazole

Laboratory Table
Microbe Form Media/Stain Labs/Diagnosis Toxins Virulence Factors
Streptococcus pneumoniae Gram + Cocci in chains or coupled
hemolysis: a Optochin Sensitive
Capsule IgA protease Neuraminidase
Staphylococcus aureus Gram + Cocci in clusters manitol, salt Catalase + Coagulase + hemolysis: b Dnase + TSST-1 P-V Leukocidin Enterotoxins A & F Exfoliatin Biofilm b-lactamases Panton-Valentine Leukocidin Mutant penicillin binding proteins Protein A
Actinomyces isrealii Gram + Rods (branching) Sulfur “molar teeth” Granules

Pseudomonas aeruginosa Gram - Rods Fruity odor Oxidase + Exotoxin A (EF2 inhibitor) PLC (phospholipase C) Capsule Pyocyanin Leukocidins Mutli-drug resisitance Iron chelation
Burkholderia spp. Gram - Rods Non-lactose Fermenter Oxidase +

E. coli Gram - Rods MacConkey agar (pink colonies) Eosin Methylene Blue (green colonies) Indole + lactose ferment.
Endotoxin (Lipid A) Capsule
Klebsiella pneumonia Gram - Rods MacConkey (pink colonies) Urease + lactose ferment.
Capsule (large) b-lactamase
Proteus spp. Gram - Rods Swarming colonies Urease + TSI (H2S) + Indole –
Flagella (motile)
Serratia marcescens Gram - Rods Produces Red pigment

Drug resistance Dnase Lipase Gelatinase
Yersinia pestis Gram - Rods Iron & cold enrichment. Bipolar “safety pin” staining Catalase + Urease – YOP Disrupts actin Inhibits phagocytosis Envelope antigen (F-1) Type III secretion system Capsule Coagulase
Mycobacterium tuberculosis Acid-fast Rods Heat-sensitive Lowenstein-Jensen media Auramine-rhodamine stain Catalase + PPD skin (Mantoux) test Makes naicin
Mycolic acids In cell wall Facultative intracellular

Aspergillus spp. 45 degree branching septate Black colonies Check sputum Lung biopsy Aflatoxin Phopholipase
Blastomyces dermatitidis Dimorphic Mold in enviornment Broad based budding yeast in body Grocott’s Methenamine silver stain EIA

Coccidioides immitis Dimorphic Mold – enviornment Yeast – infection Spherules within cells 'Owl's eyes'
Spherules Serology: IgM

Histoplasma capsulatum Dimorphic Mold – enviornment Yeast – infection Sabourad agar Gomori's stain Immunocom.: Histoplasmin in serum/urine Immunity intact: Serology BAL

Bacillus anthracis Gram + Rods
Catalase + Edema factor (EF) ++cAMP Lethal factor (LF) Protetive antigen (PA) Spore former D-glutamate peptide capsule
Francisella tularensis Gram - Rods Cysteine required Catalase + Biohazard! Serology- IgM Forshay’s test
Coxsiella burnetti Gram - Rods
Weil-Felix Negative

Legionella pneumophilia Gram - Rods (pleomorphic) Cysteine, Iron & charcoal yeast extract. Dieterl Silver stain Dx: DFA Catalase +
Capsule Flagella (motile) Facultative intracellular
Mycoplasma pneumonia No cell wall “Fried egg/mulberry” shape colonies Cold agglutinin + Glucose ferment. Slow cluture Dx: serology
P1 antigen: ciliastasis Hydrogen sulfide production
Chlamydophila pneumonia No peptidoglycan Elementary (EB) & Reticulate Bodies (RB) 'Eb' = 'E'nfective 'Rb' = 'R'eplicative

Chlamydophilia Psittaci No peptidoglycan
Biohazard! Paired serology

Nocardia asteroides Acid-fast Coccobacillus (branching) Wrinkled chalk-like colonies Catalase + Urease +
Peptidoglycan Mesodiaminopimelic acid
Pneumocyctis jerovicii (carinii) Monomorphic yeast
BAL: Cysts, Trophozoites

Cytomeagovirus (CMV) Enveloped Icosahedral dsDNA Herpesviridae
Serology 'Owls eyes'

Hantavirus Enveloped, helical -ssRNA (circular) Bunyaviridae
Biohazard! Elisa (IgM , paired sera IgG)

Ascaris lumbricoides Roundworm (nematodes)
Stool: ova, parasite Sputum: larvae CBC: eosinophilia

Strongyloides stercoralis Roundworm (nematodes)
Stool: negative Sputum: larvae CBC: eosinophilia

By Kashyap Patel