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REFERENCES | * = Clinically Important |
| INTRODUCTION |
| IMMUNOLOGY |
| LABORATORY DIAGNOSIS |
| BACTERIOLOGY | > |
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STRUCTURES |
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CLASSIFICATION |
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GENETICS |
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METABOLISM & GROWTH |
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PATHOGENESIS |
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GRAM + |
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GRAM + COCCI |
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STAPHYLOCOCCUS & RELATED GRAM + COCCI |
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STREPTOCOCCUS & ENTEROCOCCUS |
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GRAM + RODS |
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BACILLUS |
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LISTERIA & RELATED GRAM + |
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CLOSTRIDIUM |
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MYCOBACTERIUM & RELATED ACID-FAST |
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DISEASES |
| VIROLOGY |
CLASSIFICATION | DISEASES | SLOW |
ONCOGENIC |
| PRIONS |
| MYCOLOGY |
| PARASITOLOGY |
| PROTOZOA |
| HELMINTHS |
| ARTHROPODS |
| SYSTEMS |
| ANTIMICROBIALS |
| GRAM + BRANCHING FILAMENTS RIGID FILAMENTOUS |
AEROBIC Nocardia (weakly acid fast) Nocardia asteroides Nocardia brasiliensis |
ANAEROBIC Actinomyces israelii (not acid fast) | SNAP Sulfonamides-Nocardia Actinomyces-Penicillin |
| GRAM - DIPLOCOCCI AEROBIC |
MALTOSE ACID DETECTION + Neisseria meningitidis * MeninGococci Maltose & Glucose Meningitis - Meningococcemia - Purulent Waterhouse-Friderichsen syndrome | MALTOSE ACID DETECTION - Neisseria gonorrhoeae * Glucose GoNOcocci NO polysaccharide capsule NO maltose acid detection NO vaccine due to antigenic variation of pilus proteins Gonorrhea - Salpingitis - PID Ophthalmia neonatorum Septic arthritis Moraxella catarrhalis Respiratory system, middle ear, eye, CNS, and joints. | Acinetobacter baumanii (Coccobacillus) Nosocomial (hospital-acquired) |
| GRAM - RODS Respiratory & Mucosal |
Bartonella quintana Bartonella henselae (Zoonotic) HaEMOPhilus influenzae * (Coccobacillus) Epiglottitis Meningitis Otitis media Pneumonia Upper respiratory tract infections Sinusitis Haemophilus ducreyi Bordetella pertussis * (Coccobacillus) Pertussis (whooping cough) Catarrhal phase Coryza Paroxysmal phase “whooP” Bordetella parapertussis |
Pasteurella multocida (Coccobacillus) Brucella * (Zoonotic) (Coccobacillus) Brucella abortus Brucella canis Brucella melitensis Brucella suis Brucellosis UNdulant fever UNpasteurized milk Francisella tularensis * (Zoonotic) (Coccobacillus) Tularemia |
Legionella pneumophila * Legionnaires disease Pontiac fever Yersinia pestis * (Zoonotic) Bubonic (septicemic) plague - Buboes Pneumonic plague Gardnerella vaginalis "I don’t have a clue why I smell fish in the vagina garden!" |
| GRAM - BACILLI LACTOSE FERMENTATION + "MacConKEY agar LACTOSE is KEY" Enteric |
FAST Escherichia coli * Urinary tract infection (UTI) Diarrhea EnteroInvasive EIEC - Dysentery EnteroToxigenic ETEC (EnteroToxins) - "Traveler’s diarrhea" EnteroPathogenic EPEC - Pediatrics EnteroHemorrhagic EHEC O157:H7 Hamburgers - Dysentery - Hemorrhagic colitis - Hemolytic uremic syndrome (Shiga like toxin) Meningitis in infants Klebsiella pneumoniae Klebsiella oxytoca A aBscess in lungs and liver “Currant jelly” sputum Diabetes EtOH abuse Enterobacter |
SLOW Citrobacter Serratia marcescens |
| GRAM - BACILLI LACTOSE FERMENTATION - Enteric |
OXIDASE + PSEUDOMONACEAE (NON ENTERIC) Pseudomonas AER(obic)uginosa * Localized infections Systemic infections Pneumonia Sepsis Ecthyma gangrenosum UTIs Diabetes Osteomyelitis, Mucoid polysaccharide capsule Otitis externa Nosocomial infections Addicts Skin infections |
OXIDASE - H2S production on TSI agar + Salmonella enterica Serovars Enteritidis & Typhimurium * Enterocolitis (gastroenteritis, food poisoning) Salmonella enterica Serovar Typhi * Enteric (typhoid) fever & paratyphoid fever "Flagella Salmon Swim" Proteus mirabilis |
OXIDASE - H2S production on TSI agar - Shigella sonnei * Shigella dysenteriae * (Shiga toxin) Shigella flexneri * Shigella boydii * Shigella : Bacillary dysentery (shigellosis) Fingers, Flies, Food, Feces Yersinia enterocolitica (Pleomorphic rod/coccobacillus) Yersiniosis (gastroenteritis) Septicemia Yersinia pseudotuberculosis |
| OTHER ENTEROBACTERIACEAE Morganella Edwardsiella Providencia |
BACTEROIDIACEAE ANAEROBIC (ENTERIC) Bacteroides fragilis | Anaerobes : "Can’t - Clostridium G+ Breathe - Bacteroides G- Fresh - Fusobacterium G- Air - Actinomyces israelii G+ " |
| GRAM - CURVED RODS OXIDASE + VIBRIONACEAE |
GROWS IN 42°C HOT CAMPfire CAMPylobacter jejuni * Acute enteritis - Traveler's diarrhea - Pseudoappendicitis Campylobacter fetus |
GROWS IN ALKALINE MEDIA Vibrio cholerae * (Cholera toxin) Cholera - Rice-water stools Vibrio parahaemolyticus |
PRODUCES UREASE Triple + : Catalase Oxidase Urease Helicobacter pylori * Acute gastritis - Duodenal & gastric ulcers - Gastric carcinoma & Gastric B-cell lymphoma |
| RIGID FILAMENTOUS MYCOBACTERIA (Poorly G +) |
Mycobacterium tuberculosis * Tuberculosis |
Mycobacterium leprae * Hansen disease (leprosy) - Tuberculoid - Lepromatous - - Leonine - - Lethal |
Atypical Mycobacteria Mycobacterium abscessus Mycobacterium avium-intracellulare Mycobacterium bovis Mycobacterium chelonei Mycobacterium fortuitum Mycobacterium kansasii Mycobacterium marinum Mycobacterium scrofulaceum Mycobacterium ulcerans |
| LACKING CELL WALL MYCOPLASMA |
Mycoplasma pneumoniae * Primary atypical pneumonia |
Mycoplasma genitalium Mycoplasma hominis Ureaplasma urealyticum Genital |
Mycoplasma incognitus |
| RIGID CELL WALL SIMPLE UNICELLULAR OBLIGATE INTRACELLULAR CHLAMYDIA Elementary Body (small, dense) is “Enfectious” & Enters cell via Endocytosis; transforms into RB Reticulate Body Replicates in cell by fission; Reorganizes into EB |
Chlamydia pneumoniae * Community-acquired respiratory infection |
Chlamydia psittaci * (Zoonotic) Psittacosis (ornithosis) Parrots Atypical Pneumonia |
Chlamydia trachomatis * ABC = Africa, Blindness, Chronic infection Nongonococcal urethritis NGU D-K - PID Trachoma ABC - Chronic keratoconjunctivitis Inclusion conjunctivitis of the newborn ICN Lymphogranuloma venereum LGV L1 L2 L3 |
| RIGID CELL WALL SIMPLE UNICELLULAR OBLIGATE INTRACELLULAR RICKETTSIA Obligate intracellular : Rickettsia, Chlamydia, Coxiella "Stay inside when it is Really CHilly and COld" Facultative intracellular : Salmonella, Neisseria, Brucella, Mycobacterium, Listeria, Francisella, Legionella, Yersinia pestis "Some Nasty Bugs May Live FacultativeLY" |
Rickettsia rickettsii * Rocky Mountain spotted fever Rickettsii on the wRists |
Rickettsia akari Rickettsia canadensis Rickettsia conorii Rickettsia sibirica Rickettsia prowazekii Rickettsia typhi Typhus on the Trunk |
Ehrlichia chaffeensis Ehrlichia equi Monocytes Anaplasma phagocytophilum Neutrophils MEGA berry |
Coxiella burnetii Q fever |
| FLEXIBLE SPIROCHETES "BLT Borrelia is Big" |
Treponema pallidum * Syphilis - Chancre - Maculopapular rash - Condylomas - Syphilitic hepatitis, meningitis, nephritis & chorioretinitis - Gummas Congenital VDRL false positives Jarisch-Herxheimer reaction Nonvenereal Treponemal Infections |
Borrelia burgdorferi * Lyme disease Facial nerve palsy (typically bilateral) Arthritis Cardiac block Erythema migrans |
Borrelia reccurrentis and other Borrelia species Relapsing fever |
Leptospira interrogans * Leptospirosis = Infectious jaundice, Marsh fever, Weil disease, Swineherd's disease |
| BACTERIAL INFECTIONS |
| FUNGI |
| GENERAL CHARACTERISTICS |
MORPHOLOGY Yeast Filamentous |
| TRUE PATHOGENS |
CUTANEOUS SUPERFICIAL DERMATOPHYTES Epidermophyton species Microsporum species Trichophyton species Malassezia furfur |
SUBCUTANEOUS Phialophora & Cladosporium Chromomycosis Madurella grisea Mycetoma (“Madura foot”) Actinomadura madurae Sporothrix schenckii Sporotrichosis |
SYSTEMIC ENDEMIC Blastomyces dermatitidis Coccidioides immitis Histoplasma capsulatum Paracoccidioides brasiliensis |
| OPPORTUNISTIC |
Candida albicans Cryptococcus neoformans Aspergillus fumigatus Rhizopus oryzae (R. arrhizus) Pneumocystis jiroveci (formerly known as Pneumocystis carinii) |
Absidia corymbifera Rhizomucor pusillus Microsporidia Mucor and Rhizopus |
| FUNGAL INFECTIONS MYCOSES |
| Superficial Skin | Cutaneous | Mucocutaneous Candidiasis | Subcutaneous | Pneumonias/Systemic | Opportunistic |
| Immunocompetent Non Systemic Symptoms | Immunocompetent Systemic Symptoms | Immunocompromised Symptoms |
| PROTOZOA |
| INTESTINAL Entamoeba histolytica (Ameba) Amebic dysentery Giardia lamblia (Flagellate) Giardiasis Cryptosporidium parvum, Cyclospora & Cystoisospora (Sporozoan) Cryptosporidiosis Balantidium coli (Ciliate) Balantidiasis |
CNS Toxoplasma gondii (Sporozoan) Toxoplasmosis Naegleria fowleri (Ameba) Acanthamoeba castellanii (Ameba) Balamuthia mandrillaris (Ameba) Amebic encephalitis |
HEMATOLOGIC Plasmodium species (Sporozoan) Malaria Babesia microti (Sporozoan) Babesiosis |
VISCERAL Trypanosoma species (Flagellate) Trypanosomiasis Leishmania species (Flagellate) Leishmaniasis |
SEXUALLY TRANSMITTED UROGENITAL Trichomonas vaginalis (Flagellate) Trichomoniasis |
| PROTOZOA INFECTIONS |
| HELMINTHS |
| Gut Tissues Nematode routes of infection Immune response to helminths Parasite hints |
| CESTODES (TAPEWORMS) FLAT SEGMENTED Diphyllobothrium latum (Broad fish tapeworm) Echinococcus granulosus (Dog tapeworm) Taenia saginata (Beef tapeworm) Taenia solium (Pork tapeworm) |
TREMATODES (FLUKES) FLAT NONSEGMENTED Clonorchis sinensis (Chinese or Oriental liver fluke) Paragonimus westermani (Lung fluke) Schistosoma mansoni (Blood fluke) Schistosoma haematobium (Blood fluke) Schistosoma japonicum (Blood fluke) |
NEMATODES (ROUNDWORMS) NON SEGMENTED INTESTINAL Ancylostoma duodenale Necator americanus (Old World and New World hookworms) Ascaris lumbricoides (Giant roundworm) Enterobius vermicularis (Pinworm) Strongyloides stercoralis (threadworm) Trichinella spiralis Trichuris trichiura (Whipworm) |
NEMATODES (ROUNDWORMS) NON SEGMENTED TISSUE Brugia malayi Dracunculus medinensis (Guinea worm ) Loa loa (Filarial worm, or African eye worm) Onchocerca volvulus (Filarial worm) Toxocara canis (Dog worm) Wuchereria bancrofti (Filarial worm) |
| ARTHROPODES & ECTOPARASITES Sarcoptes scabiei Pediculus humanus / Phthirus pubis |
| VIRUSES |
| DNA NONENVELOPED SS LINEAR PARVOVIRIDAE Parvovirus B19 “PART-OF-A-VIRUS” | DNA NONENVELOPED DS CIRCULAR PAPOVAVIRIDAE PAPILLOMAVIRINAE Human Papillomavirus HPV * Hyperplastic epithelial lesions Cervical carcinoma Anogenital warts (condyloma acuminatum) Laryngeal papillomas Epidermodysplasia verruciformis Squamous cell carcinomas Common, flat, and plantar warts PAPOVAVIRIDAE POLYOMAVIRINAE BK virus JC virus "JC: Junky Cerebrum; BK: Bad Kidney" |
DNA NONENVELOPED DS LINEAR ADENOVIRIDAE Adenoviruses * Respiratory tract diseases - Acute febrile pharyngitis Ocular diseases - Pharyngoconjunctival fever - Epidemic keratoconjunctivitis Gastrointestinal diseases - Infantile gastroenteritis |
| DNA ENVELOPED DS HERPESVIRIDAE ALPHAHERPESVIRINAE (herpes simplex group) Herpes Simplex Virus 1 * (HSV-1) Primary HSV-1 infections - Gingivostomatitis - Tonsillitis and pharyngitis - Keratoconjuctivitis - Encephalitis Latent HSV-1 infections - Herpes labialis - "Cold sores" or "fever blisters" Herpes Simplex Virus 2 * (HSV-2) Primary HSV-2 infections Latent HSV-2 infections Varicella-Zoster Virus * (VZV, Chickenpox, Zoster, Shingles) Varicella ("chickenpox") Zoster ("shingles") | DNA ENVELOPED DS HERPESVIRIDAE BETAHERPESVIRINAE (cytomegalovirus group) Cytomegalovirus * (CMV) HCMV infectious mononucleosis Cytomegalic inclusion disease HCMV infection of immunosuppressed transplant recipients HCMV infection of AIDS patients Human Herpesviruses 6 and 7 (HHV-6, HHV-7, Roseola) = Exanthema subitum = Baby Measles Français = Roséole Italien = Sesta malattia |
DNA ENVELOPED DS HERPESVIRIDAE GAMMAHERPESVIRINAE (lymphoproliferative group) Epstein-Barr Virus * (EBV, Infectious Mononucleosis) Infectious mononucleosis (IM) Association with Burkitt lymphoma and other human neoplastic diseases Human Herpesvirus 8 * (HHV-8, KSHV or Kaposi Sarcoma–Associated Herpesvirus) |
DNA ENVELOPED DS POXVIRIDAE Smallpox (Variola) Virus Molluscum Contagiosum Virus Vaccinia virus “Pox is out of the box (nucleus).” RNA viruses All replicate in the cytoplasm (except retrovirus and influenza virus). “Retro flu is outta cyt (sight).” |
| DNA ENVELOPED DS HEPADNAVIRIDAE Hepatitis B Virus * HBV Acute hepatitis Fulminant hepatitis Primary hepatocellular carcinomas (HCC; hepatomas) |
RNA SS - CIRCULAR ENVELOPED Hepatitis D Virus (DELTA) |
RNA SS + NONENVELOPED ICOSAHEDRAL CALICIVIRIDAE Hepatitis E Virus PICORNAVIRIDAE Hepatitis A Virus * Hepatitis A (“infectious hepatitis”) |
RNA SS + ENVELOPED ICOSAHEDRAL FLAVIVIRIDAE Hepatitis C Virus * HCV Hepatitis C |
| RNA SS + NONENVELOPED ICOSAHEDRAL PICORNAVIRIDAE Enterovirus Coxsackievirus * Coxsackievirus infections Enterovirus Echovirus Enterovirus Poliovirus * Poliomyelitis - Flaccid paralysis - Respiratory paralysis Enterovirus Enterovirus Rhinovirus Hepatovirus Hepatitis A virus * - Hepatitis A (“infectious hepatitis”) | RNA SS + NONENVELOPED ICOSAHEDRAL CALICIVIRIDAE Hepatitis E virus Enteric Hepatitis Norwalk virus |
| RNA SS + ENVELOPED ICOSAHEDRAL TOGAVIRIDAE Alphavirus - Chikungunya virus - Eastern and Western equine encephalitis viruses - Venezuelan equine encephalitis virus Rubivirus - Rubella virus * - - German measles - - Congenital rubella Français = Rubéole Italien = Rosolia Spanish = Rubeola | RNA SS + ENVELOPED ICOSAHEDRAL FLAVIVIRIDAE Flavivirus - Dengue fever virus - Japanese encephalitis virus - St. Louis encephalitis virus - Tickborne encephalitis virus - West Nile virus - Yellow fever virus Hepatitis C virus Infectious Hepatitis |
RNA SS + ENVELOPED ICOSAHEDRAL CORONAVIRIDAE Coronavirus |
| RETRO & AIDS RNA SS + ENVELOPED ICOSAHEDRAL RETROVIRIDAE Human immunodeficiency viruses 1 and 2 * - HIV infection - Acquired immune deficiency syndrome (AIDS) Human T-cell lymphotropic viruses 1 and 2 |
| RNA SS - HELICAL ENVELOPED RHABDOVIRIDAE Lyssavirus (rabies virus) * Rabies |
RNA SS - HELICAL ENVELOPED PARAMYXOVIRIDAE PARAMYXOVIRINAE PARAMYXOVIRUS Human parainfluenza viruses types 1 & 3 * RUBULAVIRUS Human parainfluenza viruses types 2 & 4 * Parainfluenza virus 1 2 3 4 hPIV Respiratory tract infections croup, pneumonia, and bronchiolitis "common cold" Mumps virus * Mumps Français = Oreillons Italien = Parotite Epidemica Spanish = MORBILLIVIRUS Measles virus * Postinfectious encephalomyelitis Français = Rougeole Italien = Morbillo Spanish = Sarampión PARAMYXOVIRIDAE PNEUMOVIRINAE PNEUMOVIRUS Respiratory syncytial virus RSV * Respiratory tract infections Bronchiolitis Pneumonia Influenza-like syndrome Severe bronchitis with pneumonia |
RNA SS - HELICAL ENVELOPED ORTHOMYXOVIRIDAE Influenza A B & C Viruses * Influenza (the "flu") Reye syndrome |
RNA SS - HELICAL ENVELOPED FILOVIRIDAE Ebola virus Marburg virus |
RNA SS - HELICAL ENVELOPED BUNYAVIRIDAE Bunyavirus California encephalitis virus LaCrosse encephalitis virus Hantavirus Hantaan viruses |
RNA SS - HELICAL ENVELOPED ARENAVIRIDAE Lymphocytic chorio-meningitis virus Junin virus Machupo virus Lassa virus |
| DS RNA ENVELOPED ICOSAHEDRAL REOVIRIDAE “RepeatO-virus” Rotavirus "ROTAvirus = Right Out The Anus" |
| UNCONVENTIONAL AGENTS PRIONS |
| SYSTEMS |
| NORMAL FLORA | IMMUNOCOMPROMISED | OPPORTUNISTIC INFECTIONS OF HIV Mycobacterium avium complex Streptococcus pneumoniae Mycobacterium tuberculosis Salmonella species Candida species Histoplasma capsulatum Cryptococcus neoformans Pneumocystis jiroveci Cryptosporidium species Toxoplasma gondii Human herpesvirus type 8 (HHV-8) Herpes simplex virus (HSV) JC virus (JCV) Human cytomegalovirus (HCMV) |
RESPIRATORY | COMMUNITY-ACQUIRED PNEUMONIA Streptococcus pneumoniae Haemophilus influenzae Staphylococcus aureus Influenza virus types A and B Parainfluenza viruses Respiratory syncytial virus |
“ATYPICAL” PNEUMONIA Mycoplasma pneumoniae Chlamydia pneumoniae Legionella pneumophila Influenza viruses Respiratory syncytial virus (RSV) Adenovirus |
SINUSITIS (BACTERIAL) Streptococcus pneumoniae Haemophilus influenzae Staphylococcus aureus Anaerobes Moraxella catarrhalis |
| CARDIOVASCULAR | BLOODSTREAM | GI | FOODBORNE ILLNESS (bacterial) Salmonella species Clostridium species Campylobacter jejuni Staphylococcus aureus Shigella species Vibrio species Escherichia coli |
URINARY & REPRODUCTIVE | SEXUALLY TRANSMITTED DISEASES Chlamydia trachomatis Neisseria gonorrhoeae Treponema pallidum Ureaplasma urealyticum Haemophilus ducreyi Candida albicans Trichomonas vaginalis Herpes simplex virus type 2 (HSV-2) Human papillomavirus (HPV) Human cytomegalovirus (HCMV) Human immunodeficiency virus |
URINARY TRACT INFECTIONS Escherichia coli Staphylococcus saprophyticus Other enterobacteria Klebsiella species Proteus species Pseudomonas aeruginosa |
| HEPATITIS Hepatitis B virus Hepatitis A virus Hepatitis C virus Hepatitis D virus Hepatitis E virus | BONES, JOINTS & SKIN | EYE AND EAR | DISEASES OF THE EYE Herpes simplex virus (HSV) Adenovirus Staphylococcus aureus Neisseria gonorrhoeae Chlamydia trachomatis |
OTITIS MEDIA (ACUTE) Streptococcus pneumoniae Haemophilus influenzae Moraxella catarrhalis |
NERVOUS | BACTERIAL MENINGITIS Streptococcus pneumoniae Neisseria meningitidis Haemophilus influenzae Streptococcus agalactiae Listeria monocytogenes |
NOSOCOMIAL |
| CHILDREN | ZOONOTIC |
| ANTIMICROBIALS |
| ANTIBACTERIAL |