Organisms associated with a healthy microbiome
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Bacteroides (GI tract)
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Lactobacillus (Vagina)
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Staphylococcus epidermidis (Skin)
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Head
- Meningitis: Differentiate by age (newborn, adult, elderly) and by “septic” (culture +) vs “aseptic” (culture negative – usually virus, prior antibiotics, or drug-induced).
- Bacteria:
- Neonate: E. coli, Group B Strep, Listeria
- Infant: Neisseria meningitidis, Strep pneumo, Haemophilus
- Young Adult: Neisseria meningitidis, Strep pneumo
- Elderly: Strep pneumo, Listeria
- Aseptic bacterial causes (routine culture negative): Spirochetes (Treponema, Borrelia, Leptospira), Mycobacterium tuberculosis, and fungi
- Others: Bacillus anthracis, B. cereus (Wool-sorters and bioterrorism)
- Viruses (aseptic):
- Enteroviruses: most common (including Coxsackievirus, Echovirus, Poliovirus)
- Herpes simplex (HSV-2, but increasing HSV-1)
- Others: HIV, West Nile, St. Louis Encephalitis, Mumps, Lymphocytic choriomeningitis (LCM), Lassa, etc
- Fungi: Cryptococcus, Coccidioidomycosis/Coccidioides, etc
- Parasites: Naegleria (free-living amoeba), Angiostrongylus (eosinophilic meningitis)
- Bacteria:
- Encephalitis: Herpes simplex (esp. HSV-1), HIV, Rabies, ARBO Viruses, JC virus, Prions, Listeria, Trypanosoma
- CNS Nodules and Cavities: neurocysticercosis, toxoplasmosis (in immune suppressed), bacterial brain abscess (polymicrobial anaerobes, Strep, Staph, Nocardia).
- Eye
- Conjunctivitis:
- Viruses: Adenovirus, Measles, Herpes simplex (dendritic ulcerative keratitis), Coxsackie,
- Bacteria: Strep pneumo, neonatal conjunctivitis (Gonococcus or Chlamydia, also called inclusion conjunctivitis), Chlamydia trachomatis, Leptospira.
- Parasites: Acanthamoeba, Loa loa/”eye worm”
- Periorbital infection or swelling: Mucormycosis (in DKA), onchocerciasis (nodules), trichinosis, Chagas’s Disease (Romaña’s sign). (Non-infectious causes include allergies, nephrotic syndrome, cavernous sinus thrombosis, and superior vena cava syndrome).
- Retinitis: CMV, HIV, Toxoplasma (less likely Toxocara, TB, syphilis, Candida, onchocerciasis)
- Conjunctivitis:
- Ear: Otitis media/mastoiditis (S. pneumoniae, H. influenzae, M. catarrhalis (big three for otitis media), Gp A Strep, Staph aureus, many viruses), Otitis externa (Pseudomonas), Parotitis (Mumps, Staph aureus)
- Sinuses: Respiratory viruses (Rhinoviruses, Adenovirus, Coronavirus, Influenza), Strep pneumo, Haemophilus, Moraxella, Mucormycosis/Zygomycosis, Aspergillus
- Facial cellulitis: Group A Strep, Erythema infectiosa (Fifth’s Disease/Parvovirus)
- Pharyngitis/Epiglottitis:
- Common: Group A Strep, EBV, and respiratory viruses (Rhinoviruses, Adenovirus, etc)
- Less Common: Enteroviruses/Coxsackie (Herpangina or Hand, Foot & Mouth disease), CMV, Group C & G Strep, STDs (HSV, HIV, Gonorrhea), and Candida
- Rare, but important: Diphtheria (Corynebacterium), Fusobacterium, Epiglottitis (H. influenzae)
- Non-infectious causes: Allergies, Smoking, GERD
- Dental Infections: Strep viridans, Strep anginosus, mixed anaerobes (Fusobacterium, Prevotella)
- Dental Cavities: Streptococcus mutans
- TORCH: Toxoplasmosis, Others (syphilis, varicella-zoster, Parvovirus B19), Rubella, Cytomegalovirus (CMV most common), Herpes simplex/HIV.
Chest
- Bronchitis/Pneumonia
- Hemoptysis: TB, necrotizing pneumonia (Staph aureus/Pneumococcus, etc), bronchitis, coccidioidomycosis, aspergilloma (fungus ball in pre-existing cavity), paragonimiasis (lung fluke), (other non-infectious causes such as lung cancer, lung infarct, lung vasculitis)
- Bronchitis: pertussis/“whooping cough” (Bordetella pertussis), H. influenzae, Moraxella
- Wheezing: bronchiolitis (RSV, parainfluenza, influenza, etc), allergic bronchopulmonary aspergillosis (ABPA), parasites with lung migration (Ascaris, hookworm, Strongyloides, filaria)
- Lobar Pneumonia: Streptococcus pneumoniae/pneumococcus, Klebsiella, etc.
- Diffuse Alveolar: Pneumocystis (late), Hanta virus, Pseudomonas (esp. cystic fibrosis pts)
- Interstitial: viruses (influenza, metapneumovirus, RSV), Mycoplasma/Chlamydia, Pneumocystis (early)
- Nodular/Cavitary Disease: mycobacteria, coccidioidomycosis, paragonimiasis, Echinococcus, etc
- Pericarditis: mostly viruses (e.g. Enteroviruses/Coxsackie), TB
- Myocarditis: viruses (esp. Enteroviruses/Coxsackie), diphtheria, Chagas, trichinosis, toxoplasmosis,
- Endocarditis: acute and subacute: Strep viridans, Enterococcus, Staph, Candida, rheumatic fever
- Mediastinitis: anthrax (Bacillus anthracis), Post-op Staph, Strep
Abdomen
- Gastritis/Gastric ulcers: Helicobacter pylori (H. pylori)
- Gastroenteritis/Colitis
- Food poisoning: Staph aureus, Clostridium perfringens, Bacillus cereus, Listeria, EHEC (causes HUS)
- Non-Dysentery (watery diarrhea)
- Enteroviruses, Norovirus (cruise ships), Rotavirus (children in winter)
- Enterotoxigenic E. coli (ETEC causes most traveler’s diarrhea), Enteropathogenic E. coli (EPEC), cholera (Haiti, Africa, other travel), Vibrio parahaemolyticus (clam/shellfish), Yersinia
- Giardia (camping/travel), Cryptosporidium (especially severe in HIV/AIDS), Cyclospora
- Dysentery (fever, blood, and diarrhea): Shigella, Salmonella, Campylobacter, enteroinvasive E. coli (EIEC), Shiga toxin-producing E. coli (STEC, also called enterohemorrhagic E. coli/EHEC, causes 90% of hemolytic uremic syndrome/HUS in children – e.g. E. coli O157; H7), Clostridium difficile, amebiasis (Entamoeba histolytica)
- Bowel obstruction: Ascaris
- Perianal itching and “itchy butt”: Enterobius (pinworms) and Strongyloides
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Liver
- Liver Disease
- Hepatitis (increase AST/ALT) /Cirrhosis/Portal hypertension
- Hepatitis A and E (oral exposure) – acute only
- Hepatitis B and C (parenteral exposure) – mostly chronic hepatitis →cirrhosis (acute uncommon)
- Hepatitis Delta (Hep D can only co-infect a person with active Hep B, thus exacerbating hepatitis)
- Epstein-Barr virus (EBV) and Cytomegalovirus (CMV)
- Other uncommon: Yellow Fever, Leptospirosis, Herpes simplex, Visceral Leishmaniasis
- Schistosoma mansoni or japonicum – Hepatic schistosomiasis causes portal hypertension, but no hepatocellular injury (i.e. no true hepatitis)
- Infiltrative Disease of Liver/Spleen: Visceral Leishmaniasis, Miliary TB, Brucellosis,
- Obstructive Biliary Disease (increased Alkaline Phosphatase and Bilirubin)
- Ascending Cholangitis: Fever and RUQ abdominal pain from obstructed biliary tree, usually choledocholithiasis (stones in common duct), but also liver flukes (Clonorchis, Fasciola, Fasciolopsis), or round worms (Ascaris).
- Cholangiocarcinoma: (esp. Clonorchis/Opisthorchis)
- Hepatitis (increase AST/ALT) /Cirrhosis/Portal hypertension
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Genitourinary tract/Sexually transmitted infections
- Cystitis/Pyelonephritis: E. coli, Enterococcus, Proteus, Klebsiella, Staph saprophyticus, Pseudomonas, TB, Schistosoma hematobium (hematuria)
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Vagina
- Vaginitis: bacterial vaginosis (Gardnerella), Candida, Trichomonas
- Cervicitis/Urethritis/PID: Neisseria gonorrhea, Chlamydia, Herpes simplex, HPV, Trichomonas
- Genital Ulcers: Syphilis/Treponema pallidum, Herpes simplex, Chancroid/Haemophilus ducreyi, etc.
- Genital Itching: Candida, dermatophyte/tinea cruris, pediculosis/public lice, scabies
Extremities
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Muscles
- Myalgia/Arthralgias: Influenza, Dengue, Chikungunya, Trichinella spiralis
- Cellulitis: Group A Strep, Staph, Pasteurella multocida (cat/dog bite), Capnocytophaga (dog bite)
- Necrotizing fasciitis: Group A Streptococcus, plus mixed anaerobes
- Myonecrosis: Staph aureus and Clostridium (gas gangrene)
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Joints
- Septic arthritis: Staph aureus (MSSA/MRSA), GC, Lyme/Borrelia burgdorferi, TB, (reactive arthritis from Campylobacter, Campylobacter, etc.)
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Lymphatics
- Group A Strep, Staph aureus, Pasteurella, tularemia/Francisella tularensis, lymphatic filariasis/esp. Wuchereria, Plague/Yersinia pestis, lymphocutaneous syndrome (Sporothrix, Nocardia, Mycobacterium marinum, cutaneous leishmaniasis), cat scratch fever/Bartonella henselae
- Group A Strep, Staph aureus, Pasteurella, tularemia/Francisella tularensis, lymphatic filariasis/esp. Wuchereria, Plague/Yersinia pestis, lymphocutaneous syndrome (Sporothrix, Nocardia, Mycobacterium marinum, cutaneous leishmaniasis), cat scratch fever/Bartonella henselae
Skin
- Vascular Reactive: e.g. erythema nodosum (assoc. with certain bacteria, viruses, fungi), erythema multiforme, hives
- Dermatitis/Eczema: e.g. impetigo (Gp A Strep, Staph aureus), folliculitis, erythema migrans (Borrelia), Tinea/dermatophytes, Candida, cutaneous larva migrans, onchocerciasis, injection drug use (e.g. MSSA/MRSA, Clostridium, Eikenella, Pseudomonas)
- Vesiculobullous: bullous impetigo, staphylococcal scalded skin, Herpes simplex, Herpes zoster, Enterovirus/Coxsackie (hand-foot and mouth disease or herpangina)
- Maculopapular: Measles/rubeola, rubella, roseola (Human herpesvirus 6 – HHV-6), Molluscum, HPV, etc.
- Papulosquamous: rarely infection related – Psoriasis, Lichen planus
- Ulceronodular: syphilis, chancroid/Chlamydia trachomatis), tularemia, sporotrichosis, Nocardia, atypical mycobacteria, disseminated blastomycosis, coccidioidomycosis, onchocerciasis, cutaneous leishmaniasis. Mixed organisms (diabetic foot ulcers). Kaposi sarcoma papules, nodules or plaques (HHV-8).
Systemic and/or sepsis
- Bacteria: Endocarditis, Meningococcemia, Pneumococcemia in asplenic pt, Gram-negative sepsis (usually urinary, biliary or GI source), Neonatal sepsis (Group B Strep/Streptococcus agalactiae), Line sepsis, Toxic Shock (Group A Strep or Staph aureus), Tetanus, Botulism (Clostridium botulinum)
- Atypical Bacteria (not taking a Gram stain): Rickettsia (RMSF, Typhus,) Spirochetes (Leptospirosis, Syphilis/Treponema, Lyme/Borrelia burgdorferi, Relapsing Fever/Borrelia recurrentis, etc.)
- Viruses: HIV, Dengue, Ebola, Marburg, etc
- Fungus: Candida line sepsis, disseminated coccidioidomycosis, histoplasmosis, blastomycosis, etc.
- Parasites: Malaria/Plasmodium, Babesia, Trypanosoma brucei, Strongyloides hyper-migration