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Flashcards in Microbiology - Systems Deck (38):
1

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

2

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

3

Bugs causing bloody diarrhea (7)

  • Campylobacter
  • E. histolytica
  • Enterohemorrhagic E. coli
  • Enteroinvasive E. coli
  • Salmonella
  • Shigella
  • Y. enterocolitica

4

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

5

Bugs causing watery diarrhea (6)

  • C. difficile
  • C. perfringens
  • Enterotoxigenic E. coli
  • Protozoa
  • V. cholerae
  • Viruses

6

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

7

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

8

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

9

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.

10

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

11

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
  • 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].

12

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.

13

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.
  • Diagnostic markers
    • (+) Leukocyte esterase = bacterial.
    • (+) Nitrite test = gram-negative bugs.
    • (+) Urease test = urease-producing bugs (e.g., Proteus, Klebsiella).
    • (-) Urease test = E. coli, Enterococcus.

14

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
  • Trichomoniasis
    • Signs and symptoms
      • Inflammation
      • Frothy, grey-green, foul-smelling discharge
    • Lab findings
      • Motile trichomonads
      • pH > 4.5
    • Treatment
      • Metronidazole
      • Treat sexual partner
  • Candida vulvovaginitis
    • Signs and symptoms
      • Inflammation
      • Thick, white, “cottage cheese” discharge
    • Lab findings
      • Pseudohyphae
      • pH normal (4.0–4.5)
    • Treatment
      • -azoles

15

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.

16

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

17

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

18

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

19

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

20

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

21

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

22

Agents of red rashes of childhood (7)

  • Coxsackievirus type A
  • HHV-6
  • Measles virus
  • Parvovirus B19
  • Rubella virus
  • Streptococcus pyogenes
  • VZV

23

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

24

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

25

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

26

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

27

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

28

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

29

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

30

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
  • Gonorrhea
    • Clinical features: Urethritis, cervicitis, PID, prostatitis, epididymitis, arthritis, creamy purulent discharge
    • Organism: Neisseria gonorrhoeae

31

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)
  • 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

32

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).
  • 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.

33

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.

34

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

35

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

36

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)

37

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)

38

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

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