lab med

Staphylococcus aureus

Diseases: Skin/soft tissue infections, abscesses, pneumonia, sepsis, endocarditis, food poisoning, toxic shock syndrome
Characteristics: Gram-positive cocci in clusters; most isolates are beta-lactamase positive
Habitat: Human skin and mucous membranes (30% nasal carriage)
Transmission: Hands, shared items
Lab Diagnosis: Gram stain (GS), culture & sensitivity (C&S)

Staphylococcus saprophyticus

Diseases: UTI in women
Characteristics: Gram-positive cocci culsters
Habitat: Normal flora (NF) of skin
Transmission: Contact
Lab Diagnosis: GS, culture

Staphylococcus epidermidis

Diseases: Prosthetic implant infections, catheter/shunt infections
Characteristics: Gram-positive cocci clusters
Habitat: NF of skin
Transmission: Contact
Lab Diagnosis: GS, culture

Streptococcus pyogenes (Group A)

Diseases: Pharyngitis, cellulitis, impetigo, scarlet fever, rheumatic fever, glomerulonephritis, necrotizing fasciitis
Characteristics: Gram-positive cocci in chains; beta-hemolytic
Habitat: Human throat and skin
Transmission: Respiratory droplets
Lab Diagnosis: GS, culture, rapid strep test, Lancefield grouping

Streptococcus agalactiae (Group B)

Diseases: Neonatal meningitis, UTI, pneumonia, sepsis
Characteristics: Gram-positive cocci in chains; beta-hemolytic
Habitat: Vagina, male urethra, GI tract
Transmission: Birth, venereal
Lab Diagnosis: GS, culture, urine/CSF antigen

Streptococcus pneumoniae

Diseases: Otitis media, sinusitis, pneumonia, sepsis, adult meningitis
Characteristics: Gram-positive lancet-shaped diplococci; alpha-hemolytic
Habitat: Upper respiratory tract
Transmission: Respiratory droplets
Lab Diagnosis: GS, culture, urine/CSF antigen

Viridans group streptococci

Diseases: Subacute bacterial endocarditis (SBE), dental caries (S. mutans)
Characteristics: Gram-positive cocci in chains; alpha-hemolytic
Habitat: Oropharyngeal NF
Transmission: Opportunistic
Lab Diagnosis: GS, culture

Enterococcus (Group D)

Species: E. faecalis, E. faecium (includes VRE strains)
Diseases: UTI, biliary tract infections, intra-abdominal abscess
Characteristics: Gram-positive cocci in chains; alpha or non-hemolytic
Habitat: Colon, urethra, female genital tract
Transmission: GI/GU procedures, trauma
Lab Diagnosis: GS, culture

Neisseria meningitidis

Diseases: Meningitis, meningococcemia
Characteristics: Gram-negative kidney-bean shaped diplococci; capsulated
Habitat: Upper respiratory tract
Transmission: Respiratory droplets
Lab Diagnosis: GS, culture, CSF antigen, NP swabs

Neisseria gonorrhoeae

Diseases: Gonorrhea, neonatal conjunctivitis, PID, disseminated infection
Characteristics: Gram-negative diplococci; intracellular in PMNs
Habitat: Genitourinary tract
Transmission: Sexual contact, birth
Lab Diagnosis: GS, culture (Thayer Martin media), NAATs

Moraxella catarrhalis

Diseases: Otitis media, sinusitis, bronchitis, pneumonia
Characteristics: Gram-negative diplococci; beta-lactamase positive
Habitat: Pharyngeal NF
Transmission: Respiratory droplets, contact
Lab Diagnosis: GS, culture (chocolate agar)

Clostridium botulinum

Disease(s): Botulism neurotoxin attacks nerves (foodborne, wound, infant)
Characteristics: Anaerobic, gram-positive, spore-forming rod
Habitat & Transmission: Soil, dust, marine sediment; improperly preserved foods
Lab Diagnosis: Toxin detection in food/patient samples; anaerobic culture; CDC serologic/molecular methods

Clostridium tetani

Disease(s): Tetanus (lockjaw, prolonged muscle spasm)
Characteristics: Anaerobic, gram-positive, spore-forming rod
Habitat & Transmission: Soil, intestines of humans/animals; puncture wounds
Lab Diagnosis: Clinical diagnosis; immunization history

Clostridioides difficile

Disease(s): Antibiotic-associated pseudomembranous colitis (PMC)
Characteristics: Anaerobic, gram-positive, spore-forming rod
Habitat & Transmission: GI tract; fecal-oral transmission
Lab Diagnosis: Exotoxin detection in stool (PCR, NAAT); anaerobic culture

Clostridium perfringens

Disease(s): Cellulitis, gas gangrene, food poisoning
Characteristics: Anaerobic, gram-positive, spore-forming rod
Habitat & Transmission: Soil, water, GI/vaginal flora; contaminated wounds/food
Lab Diagnosis: Gram stain, anaerobic culture of wound/stool

Actinomyces israelii

Disease(s): Actinomycosis (lumpy jaw, pelvic infections, post-surgical abdominal infections)
Characteristics: Anaerobic/facultative, branching gram-positive rod
Habitat & Transmission: Mouth, gut, vagina; trauma, dental disease, IUD
Lab Diagnosis: Gram stain, culture of wound/genital samples

Listeria monocytogenes

Disease(s): Meningitis, sepsis (newborns, immunocompromised), listeriosis
Characteristics: Facultative anaerobe, thin gram-positive, non-spore-forming rod
Habitat & Transmission: Soil, water, milk, vegetables; foodborne or transplacental
Lab Diagnosis: Gram stain, culture of stool, blood, CSF

Corynebacterium diphtheriae

Disease(s): Diphtheria (URI, cutaneous); pseudomembrane on pharynx
Characteristics: Gram-positive rods in V or L shape
Habitat & Transmission: Throat/nasopharynx; respiratory droplets
Lab Diagnosis: Gram stain, selective media culture

Bacillus anthracis

Disease(s): Anthrax (cutaneous, GI, pulmonary); bioterrorism agent
Characteristics: Gram-positive rods in chains, spore-forming
Habitat & Transmission: Soil, infected herbivores; contact/inhalation of spores
Lab Diagnosis: Gram stain, culture of wound/sputum; serologic tests

Mycoplasma pneumoniae

Disease(s): Bronchitis, atypical pneumonia
Characteristics: No cell wall; smallest free-living organism
Habitat & Transmission: Respiratory tract; respiratory droplets
Lab Diagnosis: Serology (IgM/IgG), NAAT, PCR

Chlamydia trachomatis

Disease(s): Urethritis, cervicitis, trachoma, LGV, infant pneumonia
Characteristics: Obligate intracellular; no cell wall
Habitat & Transmission: Eyes, genital tract; sexual, neonatal, hand-to-eye
Lab Diagnosis: NAAT (urine), Giemsa stain for inclusion bodies

Chlamydia psittaci

Disease(s): Psittacosis (pulmonary infection)
Characteristics: Obligate intracellular; no cell wall
Habitat & Transmission: Birds; inhalation of dried feces
Lab Diagnosis: Serologic tests, NAAT

Chlamydophila pneumoniae

Disease(s): Atypical pneumonia, bronchitis (esp. elderly)
Characteristics: Obligate intracellular; no cell wall
Habitat & Transmission: Human respiratory tract; person-to-person
Lab Diagnosis: Serologic tests, NAAT

Rickettsia rickettsii

Disease(s): Rocky Mountain spotted fever (rash on hands/feet)
Characteristics: Obligate intracellular; not seen on Gram stain
Habitat & Transmission: Ticks (dog, deer, rodent); bite transmission
Lab Diagnosis: Serology (IgG, IFA, ELISA), PCR

Escherichia coli

Diseases: UTI, sepsis, neonatal meningitis, traveler's diarrhea, hemorrhagic colitis (E. coli O157:H7)
Characteristics: GNR, lactose fermenting
Habitat & Transmission: Colon; fecal-oral route, birth canal
Lab Dx: Gram stain, culture (stool, urine, CSF, blood), multiplex PCR

Salmonella species

Diseases: Enterocolitis (S. enteritidis), typhoid fever (S. typhi), bacteremia
Characteristics: GNR, non-lactose fermenting
Habitat & Transmission: Enteric tract (humans/animals-turtles), fecal-oral
Lab Dx: Gram stain, culture (stool, blood), PCR

Shigella species

Diseases: Dysentery (enterocolitis)
Characteristics: GNR, NLF, acid-resistant
Habitat & Transmission: Human colon only, fecal-oral, daycare outbreaks
Lab Dx: Gram stain, stool culture, PCR

Campylobacter jejuni

Diseases: Enterocolitis, food poisoning
Characteristics: Curved (comma-shaped) GNR
Habitat & Transmission: Feces (human/animal), fecal-oral
Lab Dx: Gram stain, stool culture on special agar

Helicobacter pylori

Diseases: Gastritis, peptic ulcers, gastric cancer risk
Characteristics: Curved GNR
Habitat & Transmission: Human stomach, ingestion
Lab Dx: Stool antigen, PCR, urea breath test, serology

Proteus mirabilis/vulgaris

Diseases: UTI, urosepsis, wound infections
Characteristics: GNR, NLF, highly motile
Habitat & Transmission: Colon, soil/water; catheter contamination
Lab Dx: Gram stain, culture (urine, blood)

Pseudomonas aeruginosa

Diseases: Wound infections, UTI, pneumonia, CF infections, sepsis, endocarditis in IV drug users
Characteristics: GNR, NLF, virulent
Habitat & Transmission: Soil/water, human colon/skin; aerosols, water sources
Lab Dx: Gram stain, culture (wound, sputum, urine, blood)

Vibrio species

Diseases: Cholera (V. cholerae), cellulitis/sepsis (V. vulnificus)
Characteristics: Comma-shaped GNR
Habitat & Transmission: Cholerae, colon/shellfish; Vulnificus,  seawater/shellfish
Lab Dx: Gram stain, culture (stool, blood)

Bacteroides fragilis

Diseases: Abdominal abscesses, peritonitis, PID, sepsis
Characteristics: GNR, strict anaerobe, human flora
Habitat & Transmission: GI tract; bowel rupture
Lab Dx: Gram stain, anaerobic culture (wound, blood, genital)

Eikenella corrodens

Diseases: Bite wounds, periodontal infections, head/neck cancer
Characteristics: GNR, facultative anaerobe
Habitat & Transmission: Oral, intestinal, genital flora; bites
Lab Dx: Gram stain, wound culture

Pasteurella multocida

Diseases: Bite wound infections, cellulitis
Characteristics: GNR, facultative anaerobe
Habitat & Transmission: Animal oropharynx (cats/dogs); bites
Lab Dx: Gram stain, wound culture

Bartonella hensalae

Diseases: Cat scratch disease, bacillary angiomatosis
Characteristics: Fastidious GNR
Habitat & Transmission: Cat mouth; scratch/bite
Lab Dx: PCR, biopsy (BA)

Borrelia burgdorferi

Diseases: Lyme disease
Characteristics: Gram-negative spirochete (not seen on Gram stain)
Habitat & Transmission: White-footed mouse; Ixodes tick bite
Lab Dx: ELISA/IFA + Western blot, PCR, IgM/IgG

Klebsiella pneumoniae

Diseases: Pneumonia, UTI, sepsis (esp. alcoholics, COPD)
Characteristics: GNR, LF, capsule
Habitat & Transmission: Respiratory/enteric tracts; droplets, aspiration, NF
Lab Dx: Gram stain, culture (sputum, urine, blood)

Haemophilus influenzae

Diseases: Otitis media, sinusitis, pneumonia, epiglottitis, meningitis
Characteristics: Gram-negative coccobacilli, capsule
Habitat & Transmission: Upper respiratory tract; droplets, NF
Lab Dx: Gram stain, culture (sputum, CSF), chocolate agar

Legionella pneumophila

"Diseases: Legionnaires' disease (atypical pneumonia)
Characteristics: GNR, stains poorly, hard to culture
Habitat & Transmission: Environmental water; aerosol
Lab Dx: Serology, urine antigen"

Bordetella pertussis

Diseases: Whooping cough
Characteristics: GNR, toxin-producing
Habitat & Transmission: Human respiratory tract; droplets
Lab Dx: Gram stain, NP culture (Bordet-Gengou media), PCR

Entamoeba histolytica

Type: Parasite
Disease: Amoebiasis – asymptomatic colonization, invasive colitis, liver/pleural abscesses
Habitat & Transmission: Human reservoir; fecal-oral via contaminated food, water, hands, or sexual contact
Lab Diagnosis: Stool O&P for cysts; EIA, PCR, GI pathogen panel

Giardia lamblia

Type: Parasite
Disease: watery diarrhea, abdominal pain, nausea, malabsorption
Habitat & Transmission: Fecal-contaminated water/food; animal reservoirs; person-to-person
Lab Diagnosis: Stool O&P; ELISA or DFA for antigen; PCR

Cryptosporidium parvum

Type: Parasite
Disease: watery diarrhea, severe in immunocompromised
Habitat & Transmission: Fecal-contaminated food/water; domestic/farm animals; person-to-person
Lab Diagnosis: Modified acid-fast stain; ELISA antigen; PCR

Trichomonas vaginalis

Type: Parasite
Disease: vaginitis, cervicitis, urethritis, prostatitis, epididymitis
Habitat & Transmission: Sexual contact; birth canal in infants, humans only host
Lab Diagnosis: Wet mount; PAP smear; DNA probe, PCR, NAAT

Plasmodium species

Type: Parasite
Disease: Malaria – fever, chills, anemia, splenomegaly
Habitat & Transmission: Female Anopheles mosquito; blood transfusion; congenital
Lab Diagnosis: Thin/thick blood smears; Giemsa stain; rapid antigen tests

Babesia microti

Type: Parasite
Disease: Babesiosis – malaria-like symptoms; often asymptomatic
Habitat & Transmission: Ixodes scapulairs tick bite; blood transfusion; rodent reservoir
Lab Diagnosis: Blood smears; IFA or IgM titers; PCR

Toxoplasma gondii

Type: Parasite
Disease: body fluids affects brain, eye, muscles; severe in immunocompromised or congenital
Habitat & Transmission: Cat feces; transplacental; blood transfusion
Lab Diagnosis: IgG/IgM serology; IFA; PCR

Trypanosoma cruzi

Type: Parasite
Disease: Chagas Disease – cardiac and intestinal complications
Habitat & Transmission: no person to person Triatomine insect bite; congenital; transfusion
Lab Diagnosis: Giemsa-stained blood smear; ELISA, IFA, PCR

Taenia saginata/ Taenia solium

Type: Parasite(Cestodes-flatworm/tapeworm)
Disease: Taeniasis(intestinal)-GI symptoms and Cysticercosis(solium only)– seizures, headaches, muscle/brain cysts
Habitat & Transmission: Undercooked,contiminated beef/pork; fecal-oral ingestion of eggs
Lab Diagnosis: Stool O&P; serology; PCR; MRI/CT

Diphyllobothrium latum

Type: Parasite
Disease: abdominal pain, resdies in small intestine, diarrhea, B12 deficiency
Habitat & Transmission: Raw/undercooked freshwater fish
Lab Diagnosis: Stool O&P; PCR

Necator americanus / Ancylostoma duodenale

Type: Parasite(hookworms)
Disease: Hookworm disease – rash, anemia due to GI, growth delay
Habitat & Transmission: No person to person, Soil contaminated with feces; skin penetration, larvae can infect lungs
Lab Diagnosis: Stool O&P; ELISA antigen

Ascaris lumbricoides

Type: Parasite(Round Worms)
Disease: intestinal obstruction, pneumonia
Habitat & Transmission: Ingestion of eggs from contaminated soil
Lab Diagnosis: Stool O&P; ELISA antigen

Enterobius vermicularis

Type: Parasite(Pinworms)
Disease: anal itching
Habitat & Transmission: Fecal-oral(ingestion of eggs); eggs on bedclothes
Lab Diagnosis: Scotch tape test; visible worms

Strongyloides stercoralis

Type: Parasite(Threadworms)
Disease: GI and pulmonary symptoms; septicemia in immunocompromised
Habitat & Transmission: Soil contaminated with feces; skin penetration, cats and dogs 
Lab Diagnosis: Stool O&P; EIA antibody

Candida species

Type: Fungus
Disease: thrush, vaginitis, systemic infections
Habitat & Transmission: Normal flora; overgrowth after antibiotics
Lab Diagnosis: Fungal culture; serologic IgG

Cryptococcus neoformans

Type: Fungus
Disease: pulmonary and meningitis
Habitat & Transmission: Inhalation of yeast from pigeon droppings
Lab Diagnosis: Fungal culture; latex antigen; India ink prep

Pneumocystis jiroveci

Type: Fungus
Disease: severe in immunosuppressed
Habitat & Transmission: Airborne; reservoir unknown
Lab Diagnosis: Lung biopsy/washings; IFA; PCR, cannot be cultured

Aspergillus fumigatus

Type: Fungus
Disease: pulmonary, CNS, GI;
Habitat & Transmission: Inhalation of spores; environmental mold
Lab Diagnosis: Fungal culture; biopsy; CT scan; PCR

Histoplasma capsulatum

Type: Fungus
Disease: TB-like pulmonary disease; can disseminate
Habitat & Transmission: inhalation Bird/bat droppings in soil; Ohio/Mississippi River valleys
Lab Diagnosis: Fungal culture; urine antigen; immunodiffusion

Coccidioides immitis

Type: Fungus
Disease: pulmonary infection; meningitis, Valley Fever
Habitat & Transmission: Soil in southwestern US; airborne spores
Lab Diagnosis: Fungal culture; biopsy; IgM/IgG serology

Blastomyces dermatitidis

Type: Fungus
Disease: pulmonary, skin, joints, CNS
Habitat & Transmission: Moist soil, decomposing wood/leaves; airborne spores. No person to person
Lab Diagnosis: Fungal culture; blood/urine EIA; IgM/IgG