Microbiology - Systems Flashcards
Normal (dominant) flora
- Skin
- Nose
- Oropharynx
- Dental plaque
- Colon
- Vagina
- Neonates delivered by C-section
- Skin
- S. epidermidis
- Nose
- S. epidermidis
- Colonized by S. aureus
- Oropharynx
- Viridans group streptococci
- Dental plaque
- S. mutans
- Colon
- B. fragilis > E. coli
- Vagina
- Lactobacillus
- Colonized by E. coli and group B strep
- Neonates delivered by C-section
- Have no flora but are rapidly colonized after birth
Sources of infections of bugs causing food poisoning
- B. cereus
- C. botulinum
- C. perfringens
- E. coli O157:H7
- Salmonella
- S. aureus
- V. parahaemolyticus and V. vulnificus
- B. cereus
- Reheated rice.
- Starts quickly and ends quickly
- “Food poisoning from reheated rice? Be serious!” (B. cereus)
- C. botulinum
- Improperly canned foods (sign is bulging cans)
- C. perfringens
- Reheated meat dishes
- E. coli O157:H7
- Undercooked meat
- Salmonella
- Poultry, meat, and eggs
- S. aureus
- Meats, mayonnaise, custard; preformed toxin
- Starts quickly and ends quickly
- V. parahaemolyticus and V. vulnificus
- Contaminated seafood
- V. vulnificus can also cause wound infections from contact with contaminated water or shellfish
Bugs causing bloody diarrhea (7)
- Campylobacter
- E. histolytica
- Enterohemorrhagic E. coli
- Enteroinvasive E. coli
- Salmonella
- Shigella
- Y. enterocolitica
Bugs causing bloody diarrhea
- Campylobacter
- E. histolytica
- Enterohemorrhagic E. coli
- Enteroinvasive E. coli
- Salmonella
- Shigella
- Y. enterocolitica
- Campylobacter
- Comma- or S-shaped organisms
- Growth at 42°C
- E. histolytica
- Protozoan
- Amebic dysentery
- Liver abscess
- Enterohemorrhagic E. coli
- O157:H7
- Can cause HUS
- Makes Shiga-like toxin
- Enteroinvasive E. coli
- Invades colonic mucosa
- Salmonella
- Lactose (-)
- Flagellar motility
- Has animal reservoir, especially poultry and eggs
- Shigella
- Lactose (-)
- Very low ID50
- Produces Shiga toxin (human reservoir only)
- Bacillary dysentery
- Y. enterocolitica
- Day-care outbreaks
- Pseudoappendicitis
Bugs causing watery diarrhea (6)
- C. difficile
- C. perfringens
- Enterotoxigenic E. coli
- Protozoa
- V. cholerae
- Viruses
Bugs causing watery diarrhea
- C. difficile
- C. perfringens
- Enterotoxigenic E. coli
- Protozoa
- V. cholerae
- Viruses
- C. difficile
- Pseudomembranous colitis.
- Caused by antibiotics.
- Occasionally bloody diarrhea.
- C. perfringens
- Also causes gas gangrene
- Enterotoxigenic E. coli
- Travelers’ diarrhea
- Produces heat-labile (LT) and heat-stable (ST) toxins
- Protozoa
- Giardia
- Cryptosporidium (in immunocompromised)
- V. cholerae
- Comma-shaped organisms
- Rice-water diarrhea
- Often from infected seafood
- Viruses
- Rotavirus, norovirus
Common causes of pneumonia
- Neonates (<4 wk)
- Children (4 wk - 18 yr)
- Adults (18-40 yr)
- Adults (40-65 yr)
- Elderly
- Neonates (<4 wk)
- Group B streptococci
- E. coli
- Children (4 wk - 18 yr)
- Viruses (RSV)
- Mycoplasma
- C. trachomatis (infants–3 yr)
- C. pneumoniae (school-aged children)
- S. pneumoniae
- Runts May Cough Chunky Sputum
- Adults (18-40 yr)
- Mycoplasma
- C. pneumoniae
- S. pneumoniae
- Adults (40-65 yr)
- S. pneumoniae
- H. influenzae
- Anaerobes
- Viruses
- Mycoplasma
- Elderly
- S. pneumoniae
- Influenza virus
- Anaerobes
- H. influenzae
- Gram-negative rods
Causes of special groups
- Alcoholic/IV drug user
- Aspiration
- Atypical
- Cystic fibrosis
- Immunocompromised
- Nosocomial (hospital acquired)
- Postviral
- Alcoholic/IV drug user
- S. pneumoniae, Klebsiella, Staphylococcus
- Aspiration
- Anaerobes
- Atypical
- Mycoplasma, Legionella, Chlamydia
- Cystic fibrosis
- Pseudomonas, S. aureus, S. pneumoniae
- Immunocompromised
- Staphylococcus, enteric gram-negative rods, fungi, viruses, P. jirovecii (with HIV)
- Nosocomial (hospital acquired)
- Staphylococcus, Pseudomonas, other enteric gram-negative rods
- Postviral
- Staphylococcus, H. influenzae, S. pneumoniae
Common causes of meningitis
- Newborn (0-6 mo)
- Children (6 mo - 6 yr)
- Adults (6-60 yr)
- Elderly (60 yr+)
- Treatment
- Viral causes
- In HIV
- Incidence of H. influenzae meningitis
- Newborn (0-6 mo)
- Group B streptococci
- E. coli
- Listeria
- Children (6 mo - 6 yr)
- S. pneumoniae
- N. meningitidis
- H. influenzae type B
- Enteroviruses
- Adults (6-60 yr)
- S. pneumoniae
- N. meningitidis (#1 in teens)
- Enteroviruses
- HSV
- Elderly (60 yr+)
- S. pneumoniae
- Gram-negative rods
- Listeria
- Treatment
- Give ceftriaxone and vancomycin empirically
- Add ampicillin if Listeria is suspected
- Viral causes
- Enteroviruses (esp. coxsackievirus), HSV-2 (HSV-1 = encephalitis), HIV, West Nile virus, VZV.
- In HIV
- Cryptococcus, CMV, toxoplasmosis (brain abscess), JC virus (PML).
- Incidence of H. influenzae meningitis
- Has decreased greatly with introduction of the conjugate H. influenzae vaccine in last 10–15 years.
- Today, cases are usually seen in unimmunized children.
CSF findings in meningitis
- For each
- Opening pressure
- Cell type
- Protein
- Sugar
- Bacterial
- Fungal / TB
- Viral
- Bacterial
- Opening pressure: increased
- Cell type: increased PMNs
- Protein: increased
- Sugar: decreased
- Fungal / TB
- Opening pressure: increased
- Cell type: increased lymphocytes
- Protein: increased
- Sugar: decreased
- Viral
- Opening pressure: normal / increased
- Cell type: increased lymphocytes
- Protein: normal / increased
- Sugar: normal
Osteomyelitis
- Causes of risk factors
- Assume if no other information is available
- Sexually active
- Diabetics and IV drug users
- Sickle cell
- Prosthetic joint replacement
- Vertebral involvement
- Cat and dog bites
- Most osteomyelitis occurs in…
- Diagnosis
- Risk factors & cause(s)
- Assume if no other information is available
- S. aureus (most common overall)
- Sexually active
- Neisseria gonorrhoeae (rare)
- Septic arthritis (more common)
- Diabetics and IV drug users
- Pseudomonas aeruginosa
- Serratia
- Sickle cell
- Salmonella
- Prosthetic joint replacement
- S. aureus
- S. epidermidis
- Vertebral involvement
- Mycobacterium tuberculosis (Pott disease)
- Cat and dog bites
- Pasteurella multocida
- Assume if no other information is available
- Most osteomyelitis occurs in children.
- Diagnosis
- Elevated CRP and ESR observed but nonspecific.
- Can be subtle on radiographs (arrow in [A])
- Same lesion more easily seen on MRI [B].

Urinary tract infections
- Cystitis
- Pyelonephritis
- Gender
- Predisposing factors
- Diagnostic markers
- Cystitis
- Presents with dysuria, frequency, urgency, suprapubic pain, and WBCs (but not WBC casts) in urine.
- Primarily caused by ascension of microbes from urethra to bladder.
- Males— infants with congenital defects, vesicoureteral reflux.
- Elderly—enlarged prostate.
- Pyelonephritis
- Ascension to kidney results in pyelonephritis
- Presents with fever, chills, flank pain, costovertebral angle tenderness, hematuria, and WBC casts.
- Gender
- Ten times more common in women (shorter urethras colonized by fecal flora).
- Predisposing factors
- Obstruction, kidney surgery, catheterization, GU malformation, diabetes, and pregnancy.
- Diagnostic markers
- Leukocyte esterase test (+) = bacterial UTI
- Nitrite test (+) = gram-negative bacterial UTI.
UTI bugs
- Species & features (9)
- Diagnostic markers
- (+) Leukocyte esterase
- (+) Nitrite test
- (+) Urease test
- (-) Urease test
- Species & features
- Escherichia coli
- Leading cause of UTI.
- Colonies show green metallic sheen on EMB agar.
- Staphylococcus saprophyticus
- 2nd leading cause of UTI in sexually active women.
- Klebsiella pneumoniae
- 3rd leading cause of UTI.
- Large mucoid capsule and viscous colonies.
- Serratia marcescens
- Some strains produce a red pigment
- Often nosocomial and drug resistant.
- Enterobacter cloacae
- Often nosocomial and drug resistant.
- Proteus mirabilis
- Motility causes “swarming” on agar
- Produces urease
- Associated with struvite stones.
- Pseudomonas aeruginosa
- Blue-green pigment and fruity odor
- Usually nosocomial and drug resistant.
- Escherichia coli
- Diagnostic markers
- (+) Leukocyte esterase = bacterial.
- (+) Nitrite test = gram-negative bugs.
- (+) Urease test = urease-producing bugs (e.g., Proteus, Klebsiella).
- (-) Urease test = E. coli, Enterococcus.
Common vaginal infections
- For each
- Signs and symptoms
- Lab findings
- Treatment
- Bacterial vaginosis
- Trichomoniasis
- Candida vulvovaginitis
- Bacterial vaginosis
- Signs and symptoms
- No inflammation
- Thin, white discharge with fishy odor
- Lab findings
- Clue cells
- pH > 4.5
- Treatment
- Metronidazole
- Signs and symptoms
- Trichomoniasis
- Signs and symptoms
- Inflammation
- Frothy, grey-green, foul-smelling discharge
- Lab findings
- Motile trichomonads
- pH > 4.5
- Treatment
- Metronidazole
- Treat sexual partner
- Signs and symptoms
- Candida vulvovaginitis
- Signs and symptoms
- Inflammation
- Thick, white, “cottage cheese” discharge
- Lab findings
- Pseudohyphae
- pH normal (4.0–4.5)
- Treatment
- -azoles
- Signs and symptoms
ToRCHeS infections
- Microbes
- Transmission
- Nonspecific signs common to many ToRCHeS infections
- ToRCHeS infectious agents
- Other important infectious agents
- Microbes
- May pass from mother to fetus.
- Transmission
- Transplacental in most cases, or via delivery (especially HSV-2).
- Nonspecific signs common to many ToRCHeS infections
- Hepatosplenomegaly, jaundice, thrombocytopenia, and growth retardation.
-
ToRCHeS infectious agents
- Toxoplasma gondii, Rubella, CMV, HIV, Herpes simplex virus-2, Syphilis
- Other important infectious agents
- Include Streptococcus agalactiae (group B streptococci), E. coli, and Listeria monocytogenes—all causes of meningitis in neonates.
- Parvovirus B19 causes hydrops fetalis.
ToRCHeS infections:
Toxoplasma gondii
- Mode of transmission
- Maternal manifestations
- Neonatal manifestations
- Mode of transmission
- Cat feces or ingestion of undercooked meat
- Maternal manifestations
- Usually asymptomatic
- Lymphadenopathy (rarely)
- Neonatal manifestations
- Classic triad: chorioretinitis, hydrocephalus, and intracranial calcifications
ToRCHeS infections:
Rubella
- Mode of transmission
- Maternal manifestations
- Neonatal manifestations
- Mode of transmission
- Respiratory droplets
- Maternal manifestations
- Rash, lymphadenopathy, arthritis
- Neonatal manifestations
- Classic triad: PDA (or pulmonary artery hypoplasia), cataracts, and deafness +- “blueberry muffin” rash
ToRCHeS infections:
CMV
- Mode of transmission
- Maternal manifestations
- Neonatal manifestations
- Mode of transmission
- Sexual contact, organ transplants
- Maternal manifestations
- Usually asymptomatic
- Mononucleosis-like illness
- Neonatal manifestations
- Hearing loss, seizures, petechial rash, “blueberry muffin” rash
ToRCHeS infections:
HIV
- Mode of transmission
- Maternal manifestations
- Neonatal manifestations
- Mode of transmission
- Sexual contact, needlestick
- Maternal manifestations
- Variable presentation depending on CD4+ count
- Neonatal manifestations
- Recurrent infections, chronic diarrhea
ToRCHeS infections:
Herpes simplex virus-2
- Mode of transmission
- Maternal manifestations
- Neonatal manifestations
- Mode of transmission
- Skin or mucous membrane contact
- Maternal manifestations
- Usually asymptomatic
- Herpetic (vesicular) lesions
- Neonatal manifestations
- Encephalitis, herpetic (vesicular) lesions
ToRCHeS infections:
Syphilis
- Mode of transmission
- Maternal manifestations
- Neonatal manifestations
- Mode of transmission
- Sexual contact
- Maternal manifestations
- Chancre (1°) and disseminated rash (2°) are the two stages likely to result in fetal infection
- Neonatal manifestations
- Often results in stillbirth, hydrops fetalis
- If child survives, presents with facial abnormalities [A] (notched teeth [B], saddle nose, short maxilla), saber shins, CN VIII deafness

Agents of red rashes of childhood (7)
- Coxsackievirus type A
- HHV-6
- Measles virus
- Parvovirus B19
- Rubella virus
- Streptococcus pyogenes
- VZV
Red rashes of childhood:
Coxsackievirus type A
- Associated syndrome / disease
- Clinical presentation
- Associated syndrome / disease
- Hand-foot-mouth disease
- Clinical presentation
- Vesicular rash on palms and soles [A]
- Vesicles and ulcers in oral mucosa

Red rashes of childhood:
HHV-6
- Associated syndrome / disease
- Clinical presentation
- Associated syndrome / disease
- Roseola
- Clinical presentation
- A macular rash over body appears after several days of high fever
- Can present with febrile seizures
- Usually affects infants
Red rashes of childhood:
Measles virus
- Associated syndrome / disease
- Clinical presentation
- Associated syndrome / disease
- Measles (rubeola)
- Clinical presentation
- A paramyxovirus
- Beginning at head and moving down
- Rash is preceded by cough, coryza, conjunctivitis, and blue-white (Koplik) spots on buccal mucosa
Red rashes of childhood:
Parvovirus B19
- Associated syndrome / disease
- Clinical presentation
- Associated syndrome / disease
- Erythema infectiosum (fifth disease)
- Clinical presentation
- “Slapped cheek” rash on face [B]
- Can cause hydrops fetalis in pregnant women

Red rashes of childhood:
Rubella virus
- Associated syndrome / disease
- Clinical presentation
- Associated syndrome / disease
- Rubella
- Clinical presentation
- Rash begins at head and moves down
- –> fine truncal rash
- Postauricular lymphadenopathy
Red rashes of childhood:
Streptococcus pyogenes
- Associated syndrome / disease
- Clinical presentation
- Associated syndrome / disease
- Scarlet fever
- Clinical presentation
- Erythematous, sandpaper-like rash with fever and sore throat
Red rashes of childhood:
VZV
- Associated syndrome / disease
- Clinical presentation
- Associated syndrome / disease
- Chickenpox
- Clinical presentation
- Vesicular rash begins on trunk
- Spreads to face and extremities with lesions of different ages
Sexually transmitted diseases
- For each
- Clinical features
- Organism
- Aids
- Chancroid
- Chlamydia
- Condylomata acuminata
- Genital herpes
- Gonorrhea
- AIDS
- Clinical features: Opportunistic infections, Kaposi sarcoma, lymphoma
- Organism: HIV
- Chancroid
- Clinical features: Painful genital ulcer, inguinal adenopathy
-
Organism: Haemophilus ducreyi
- It’s so painful, you “do cry”
- Chlamydia
- Clinical features: Urethritis, cervicitis, conjunctivitis, reactive arthritis, PID
- Organism: Chlamydia trachomatis (D–K)
- Condylomata acuminata
- Clinical features: Genital warts, koilocytes
- Organism: HPV-6 and -11
- Genital herpes
-
Clinical features: Painful penile, vulvar, or cervical vesicles and ulcers
- Can cause systemic symptoms such as fever, headache, myalgia
- Organism: HSV-2, less commonly HSV-1
-
Clinical features: Painful penile, vulvar, or cervical vesicles and ulcers
- Gonorrhea
- Clinical features: Urethritis, cervicitis, PID, prostatitis, epididymitis, arthritis, creamy purulent discharge
- Organism: Neisseria gonorrhoeae
Sexually transmitted diseases
- For each
- Clinical features
- Organism
- Hepatitis B
- Lymphogranuloma venereum
- 1° syphilis
- 2° syphilis
- 3° syphilis
- Trichomoniasis
- Hepatitis B
- Clinical features: Jaundice
- Organism: HBV
- Lymphogranuloma venereum
-
Clinical features: Infection of lymphatics
- Painless genital ulcers, painful lymphadenopathy (i.e., buboes)
- Organism: C. trachomatis (L1–L3)
-
Clinical features: Infection of lymphatics
- 1° syphilis
- Clinical features: Painless chancre
- Organism: Treponema pallidum
- 2° syphilis
- Clinical features: Fever, lymphadenopathy, skin rashes, condylomata lata
- Organism: Treponema pallidum
- 3° syphilis
- Clinical features: Gummas, tabes dorsalis, general paresis, aortitis, Argyll Robertson pupil
- Organism: Treponema pallidum
- Trichomoniasis
- Clinical features: Vaginitis, strawberry cervix, motile in wet prep
- Organism: Trichomonas vaginalis
Pelvic inflammatory disease
- Top bugs
- Manifestations
- Top bugs
- Chlamydia trachomatis (subacute, often undiagnosed)
- The most common bacterial STD in the United States.
- Neisseria gonorrhoeae (acute).
- Chlamydia trachomatis (subacute, often undiagnosed)
- Manifestations
- Cervical motion tenderness (chandelier sign), purulent cervical discharge [A].
- PID may include salpingitis, endometritis, hydrosalpinx, and tubo-ovarian abscess.
- Can lead to Fitz- Hugh–Curtis syndrome—infection of the liver capsule and “violin string” adhesions of peritoneum to liver [B].
- Salpingitis is a risk factor for ectopic pregnancy, infertility, chronic pelvic pain, and adhesions.

Nosocomial infections
- Candida albicans
- Risk factor
- CMV, RSV
- Risk factor
- E. coli, Proteus mirabilis
- Risk factor
- Notes
- HBV
- Risk factor
- Legionella
- Risk factor
- Notes
- Pseudomonas aeruginosa
- Risk factor
- Notes
- Candida albicans
- Risk factor: Hyperalimentation
- CMV, RSV
- Risk factor: Newborn nursery
- E. coli, Proteus mirabilis
- Risk factor: Urinary catheterization
- Notes: The 2 most common causes of nosocomial infections are E. coli (UTI) and S. aureus (wound infection).
- HBV
- Risk factor: Work in renal dialysis unit
- Legionella
- Risk factor: Water aerosols
- Notes: Think Legionella when water source is involved.
- Pseudomonas aeruginosa
- Risk factor: Respiratory therapy equipment
- Notes: Presume Pseudomonas “airuginosa” when air or burns are involved.
Bugs affecting unimmunized children:
Dermatologic:
Rash
- Findings / labs and associated pathogens (2)
- Beginning at head and moving down with postauricular lymphadenopathy
- Rubella virus
- Beginning at head and moving down; rash preceded by cough, coryza, conjunctivitis, and blue-white (Koplik) spots on buccal mucosa
- Measles virus
Bugs affecting unimmunized children:
Neurologic:
Meningitis
- Findings / labs and associated pathogens (2)
- Microbe colonizes nasopharynx
- H. influenzae type B
- Can also lead to myalgia and paralysis
- Poliovirus
Bugs affecting unimmunized children:
Respiratory
- Epiglottitis
- Findings / labs
- Associated pathogen
- Pharyngitis
- Findings / labs
- Associated pathogen
- Epiglottitis
- Fever with dysphagia, drooling, and difficulty breathing due to edematous “cherry red” epiglottis; “thumbprint sign” on X-ray
- H. influenzae type B (also capable of causing epiglottitis in fully immunized children)
- Pharyngitis
- Grayish oropharyngeal exudate (“pseudomembranes” may obstruct airway); painful throat
- Corynebacterium diphtheriae (elaborates toxin that causes necrosis in pharynx, cardiac, and CNS tissue)
Bug hints
- Asplenic patient (due to surgical splenectomy or autosplenectomy, e.g., chronic sickle cell anemia)
- Branching rods in oral infection, sulfur granules
- Chronic granulomatous disease
- “Currant jelly” sputum
- Dog or cat bite
- Facial nerve palsy
- Fungal infection in diabetic or immunocompromised patient
- Health care provider
- Neutropenic patients
- Asplenic patient (due to surgical splenectomy or autosplenectomy, e.g., chronic sickle cell anemia)
- Encapsulated microbes, especially SHiN (S. pneumoniae >> H. influenzae type B > N. meningitidis)
- Branching rods in oral infection, sulfur granules
- Actinomyces israelii
- Chronic granulomatous disease
- Catalase (+) microbes, especially S. aureus
- “Currant jelly” sputum
- Klebsiella
- Dog or cat bite
- Pasteurella multocida
- Facial nerve palsy
- Borrelia burgdorferi (Lyme disease)
- Fungal infection in diabetic or immunocompromised patient
- Mucor or Rhizopus spp.
- Health care provider
- HBV (from needle stick)
Bug hints
- Neutropenic patients
- Organ transplant recipient
- PAS (+)
- Pediatric infection
- Pneumonia in cystic fibrosis, burn infection
- Pus, empyema, abscess S
- Rash on hands and feet
- Sepsis/meningitis in newborn
- Surgical wound
- Traumatic open wound
- Neutropenic patients
- Candida albicans (systemic), Aspergillus
- Organ transplant recipient
- CMV
- PAS (+)
- Tropheryma whipplei (Whipple disease)
- Pediatric infection
- Haemophilus influenzae (including epiglottitis)
- Pneumonia in cystic fibrosis, burn infection
- Pseudomonas aeruginosa
- Pus, empyema, abscess
- S. aureus
- Rash on hands and feet
- Coxsackie A virus, Treponema pallidum, Rickettsia rickettsii
- Sepsis/meningitis in newborn
- Group B strep
- Surgical wound
- S. aureus
- Traumatic open wound
- Clostridium perfringens