Tuesday, March 29, 2016

Introduction to Medically Important Bacteria

Introduction to Medically Important Bacteria
Updated: 08/07/2016
Types of Therapy
  • Prophylactic Therapy – treatment initiated to prevent an infection that has not yet developed
    • Ex. Antibiotic “prophy” to prevent opportunistic bacterial infections
    • Ex. Antibiotics while on a trip to Mexico
    • Ex. Antibiotics before surgery or dental procedures to prevent bacterial endocarditis
  • Empiric Therapy
    • Empiric – relies solely on observation or practical experience.
    • Therapy initiated to treat serious infections until test results are available; or therapy for minor infections (URI’s, UTI’s) because causative organisms are predictable and their susceptibility to available antibiotics is known
  • Definitive Therapy
    • Start broad spectrum antibiotics before the culture and sensitivity results are reported. When they become reported, you know what will kill the bug in vitro and can tailor the therapy making it less broad and more definitive.
    • The hospital antibiogram can assist with empiric or definitive therapies.
  • Antibiogram
    • The cumulative results of hospital performed bacterial susceptibility testing organized into a summary table which may be used by clinicians, pharmacists, infection control personnel and microbiologists as a reference guide to community or hospital-specific resistance patterns.

How to Read an Antibiogram
Coming soon….

Bacterial Taxonomy
  • Two part names: Genus – species
    • E.g. Staphylococcus aureus
  • Grouped according to morphology and biochemical/metabolic differences
    • E.g. staining, oxygen use, growth req’s, enzymes, etc.
  • We cannot name the organism until we
    • Visualize it
    • Describe its features
  • Early descriptions of a microbe’s morphologic features and metabolic characteristics are helpful

Selected Medically Important Bacteria
    • Gram (+) Facultative Anaerobic Cocci
      • (Catalase +) – ALL staphylococcus spp.
        • Staphylococcus aureus (Coagulase +)
        • Staphylococcus epidermidis
        • Staphylococcus saprophyticus
      • Alpha-hemolytic
        • Streptococcus pneumoniae
      • Beta-hemolytic
        • Streptococcus pyogenes (Group A)
        • Streptococcus agalactiae (Group B)
    • Gram (+) Anaerobic Spore-forming Rod
      • Clostridium difficile
    • Gram (+) Facultative Non-spore forming Anaerobic Rod
      • Listeria monocytogenes (intracellular parasite)
    • Gram (-) Anaerobic Rods
      • The “Non-Enterics”
        • Haemophilus influenzae
        • Legionella pneumophila
        • Pasteurella multocida
        • Pseudomonas aeruginosa (Oxidase +)
      • Gram (-) Facultative Anaerobic Rods (generally, the “Enterics”)
        • Escherichia coli
        • Campylobacter jejuni
        • Helicobacter pylori (Urease +)
        • Salmonella
        • Shigella
        • Klebsiella pneumoniae
    • Gram (-) Aerobic Diplococci
      • (Catalase + and Oxidase +)
        • Moraxella catarrhalis
        • Neisseria gonorrhoeae
        • Neisseria meningitidis
    • Gram (-) Coccobacillus
      • Haemophilus ducreyi
    • Gram (-) Spirochete
      • Treponema pallidum
    • Mycoplasmas
      • Mycoplasma pneumoniae
      • Ureaplasma urealyticum
    • Chlamydiae
      • Chlamydia pneumoniae
      • Chlamydia trachomatis
    • Aerobic Acid-Fast Rod
      • Mycobacterium tuberculosis

Staining and Morphology
  • Staining
    • Gram Positive = Violet/blue
      • Ex. Staphylococcus aureus
    • Gram Negative = Red (Safranin dye)
      • Ex. Escherichia coli
  • Morphologies
    • Straight rod – Escherichia
    • Spore forming rod – Clostridium
    • Spiral forms – spirochaeta
    • Coccus – staphylococcus
    • Diplococcus – Neisseria
    • Chain – Streptococcus
    • Cluster – Staphylococcus
    • Bacillus = rod
  • Peptidoglycan Layer Differences
    • E. Coli – gram negative
      • Thick outer membrane
    • Staph aureus – gram positive
      • Thick peptidoglycan layer
  • Other ID Tests
    • KOH – dissolves host cells and bacteria; only fungal elements survive
      • Hyphae, spores
    • Acid Fast Stain – Mycobacterium spp., e.g Tuberculosis
      • Waxy mycolic layer surrounding cell wall; heat fix smear
    • India Ink Stain – “negative stain”; organism white, background black;
      • E.g. Cryptococcus
    • “Atypicals” - Lack characteristic structural components (cell wall) or metabolic capabilities. This separates them from the larger group of typical bacteria.
      • Mycoplasmas, Chlamydia, Rickettsias
      • Stain poorly, require special stains, or don’t stain
  • Metabolic Characteristics (oxygen use, growth req)
    • Aerobes: require O2 for energy and growth
      • Mainly at top of tube
    • Anaerobes: require no O2. Produce energy by fermentative pathways.
      • Mainly at bottom of tube
    • Facultative anaerobes: organism that preferentially use O2 for energy and growth, but may rely on anaerobic respiration depending on amount of O2 or fermentable material in environment
      • Mainly dispersed at top of tube, but some throughout rest
    • Aerotolerant anaerobes: strictly fermentative. Growth unaffected by the presence of O2.
      • Dispersed evenly throughout tube
  • Hemolytic Properties (Streptococcal spp)
    • Alpha = partial hemolysis (oxidation of iron in Hgb -> green color)
    • Gamma = no hemolysis
    • Beta = complete hemolysis
  • Normal Flora (commensals)
    • Location: skin, eyes, GI tract, nose, mouth, throat, upper respiratory tract, external GU tract
    • Problems arise when host defenses are compromised or bacteria migrate from the surface into sterile areas. In these cases, colonization may progress into invasion, infection and/or intoxication. Balance is key.
    • It is important to consider the status of your human host when collecting a history.
      • Is their immune status competent or incompetent?
      • Temporarily compromised?
      • What unusual exposure have they encountered?
        • Occupational – healthcare, TB
        • Recreational – travel, malaria
        • Pets – dog bites, cat bites
        • Social – IV drug use, skin popping  -> cellulitis, endocarditis
        • Sexual partners – one or many?
        • Exchange sex for drugs or money?
    • Benefits?
      • Minimize survival of invaders
      • Secrete antimicrobial substances (GI)
      • Stimulus for development of immunity
      • Source of nutrients in the gut (vitamin k)
    • When does friend become foe?
      • Microbe is displaced from “home” and enters sterile site (IVDU – staph epidermidis)
      • Loss of balance – populations of harmless bacteria are reduced and lose their competitive advantage
      • Impaired immunity of host

Bacterial Pathogenesis
  • Entry to host/evasion of primary defenses
  • Adhesion of microbe to host cell
  • Propagation of the microbe
  • Damage to host by toxins; evoke inflammatory response
  • Evasion of host's secondary defenses
    • Evasion of immune system (surface antigen switching)

Bacterial Culture & Sensitivity
  • Why? Identifying microorganisms that cause disease and evaluating their susceptibilities allows us to tailor (narrow) therapy
  • What do we send? Body fluids or tissue
  • What do we get back? Identification of organisms – a preliminary report of morphology (24h), followed by a specific microbe (48-72h) along with a list of drugs that may or may not kill it (sensitivity or susceptibility report)
  • What’s the most important part of the process when evaluating and considering treatment of bacterial infection? The patient’s H&P!
  • The single most important source to consult when investigating an infectious disease problem is? The patient!

Catalase Testing
  • Hydrogen peroxide + bacteria
  • Bubbles and fizzing = oxygen release = catalase positive

Coagulase Testing
  • Coagulase (bacteria) + Prothrombin (in rabbit plasma) = activation of protease
  • = fibrinogen to fibrin = fibrin clot!

Oxidase Testing
  • Useful for identifying some aerobic organisms, e.g. Moraxella, Neisseria, & Pseudomonas spp.
  • Use cytochrome oxidase in their respiratory chains. Oxidase reagent is oxidized to dark blue or violet within 20 seconds of contact with reagent.

Urease Testing
  • Enzymes may enhance survival of the microbe.
    • E.g. helicobacter pylori
  • High protein foods are rich – especially meats
  • Breath test: swallow urea rich solution (pretest); 10-30 minutes later, exhale into a bag to detect CO2 levels; Cut off parameters between pre- and post- levels confirm the presence of H. Pylori

Gram Positive Staph Species

Gram (+/-)
Staph. Aureus
Fac anaerobic cocci in clusters
Bone – Osteomyelitis
Heart – Endocarditis
Skin & soft tissue – Cellulitis
SSSS (Staphylococcal Scalded Skin Syndrome) – Nikolsky’s sign
Staph. Epidermidis
Fac anaerobic cocci in clusters
CONs (Coagulase Negative staph)
Central lines & indwelling catheters
Prosthetic valve endocarditis (biofilms)
Nosocomial sepsis
Staph. saprophyticus
Fac anaerobic cocci in clusters

Skin-Furuncles or Carbuncles
Staphylococcus aureus
Uncomplicated: afebrile, outpatient, boils >5 cm
  • TMP/SMX or Clinda or Doxy
Complicated: febrile, fluctuant/draining, multiple lesions, IVDU
  • TMP/SMX + Rifampin (outpatient) or Linezolid (inpatient)
Bone = osteomyelitis
Endocarditis - native heart valves
Staphylococcal Scalded Skin Syndrome - exotoxin
Staphylococcus aureus
Staphylococcus epidermidis (CONs)
Indwelling lines or catheters: Vancomycin or Nafcillin
Prosthetic heart valves: Vancomycin + Rifampin + Gentamicin
Bone, heart, skin: Vancomycin + Nafcillin or Penicillin
Bacteremia/Sepsis: add Clindamycin

Gram Positive STREP Species
Hemolytic Properties
  • Alpha hemolytic – green, partial hemolysis
    • Pneumoniae - Pneumonia, meningitis, otitis, sinusitis
  • Beta hemolytic – clear, complete hemolysis
    • Pyogenes (Group A) “GAS” - pharyngitis, cellulitis/NF (exotoxins)
    • Agalactiae (Group B) “GBS” - meningitis (neonates)
  • Gamma hemolytic – responsible for hospital acquired infections in immunocompromised hosts
    • NF – necrotizing fasciitis
  • Bacteria fit into 1 of 12 Lancefield classes based on CHO and antigens present in their cell walls
    • Medically important strep is classified according to hemolytic properties

Endogenous vs. Exogenous Infections
  • Endogenous infection: occurs in carriers whose immune system becomes weakened
  • Exogenous infection: droplets from the nasopharynx of healthy carriers to those who have weakened immune systems

Rapid Latex Agglutination
  • Latex particles clump together in the presence of GAS antigen
    • Ex. “Rapid strep test”
  • How will S. agalactiae or S. pneumo. Respond to latex antigen Test?
    • Negative = no agglutination = no GAS antigen;
    • Only strep pyogenes will test positive

Gram (+/-)
Hemolytic Properties
Strep pneumoniae
Cocci in chains or pairs

Young children, elderly, chronic disease -  Pneumonia, meningitis, otitis, sinusitis
Commonly found in nasopharynx of healthy individuals
Strep pyogenes (Group “A” Strep)
Exotoxin producing bacteria (like staph aureus) cocci in chains

Strep throat – pharyngitis, tonsillitis
Cellulitis, erysipelas
Streptococcal Toxic Shock Syndrome
Impetigo (strep + staph)
Bacteremia or sepsis
Strep Agalactiae (Group “B” Strep)
Cocci in chains
Meningitis (neonates)

CAP = Community Acquired Pneumonia
  • Pneumonia in a previously healthy person who acquired the infection outside the hospital or other healthcare setting
  • Setting matters – risk for acquiring certain types of PNA vary by location. Staph aureus PNA more common in hospital.
  • Location influences treatment – resistance patterns
    • Patients with comorbidity have less robust immune response
Acute Bacterial Meningitis
  • Most common causative pathogens in patients 1 month – 50 years include:
    • Strep. Pneumoniae
    • N. meningitidis
  • Which individuals are at greatest risk for strep pneumo meningitis?
    • Very young or those with comorbid conditions
Strep agalactiae (Group B strep)
  • Acute Neonatal Bacterial Meningitis (< 1 month old)
    • 49% S. agalactiae (“GBS”)
    • Colonize vagino-cervical tract of women and expose infants during birth
    • GBS swabs are obtained 35-37 weeks gestation during labor and if +, antibiotics are started before delivery
    • This practice has reduced neonatal GBS sepsis by 90%

Bacterial Meningitis
At-Risk Groups
Preferred Treatment
<1 month old
Strep agalactiae (GBS)
E. coli
L. monocytogenes
3rd Generation + Ampicillin*
*Prolonged nursery stay - Vancomycin instead of Ampicillin
1 month - 50 years
Strep pneumoniae
N. meningitis**
Ceftriaxone + Vancomycin
**Consider contact exposure, give meningococcal meningitis prophylaxis = ceftriaxone
>50 years, alcoholics, immunocompromised
Strep pneumoniae
L. monocytogenes
H. influenzae
S. auerus
3rd Generation + Vancomycin + Ampicillin

Skin - Cellulitis and Impetigo
Streptococcus pyogenes
Uncomplicated: afebrile, outpatient
  • PCN V or Cephalexin or TMP/SMX
Complicated: febrile, facial, diabetic legs/feet
  • Vancomycin
Non-bullous Impetigo
Streptococcus pyogenes
Mupirocin ointment
Bullous Impetigo
Streptococcus pyogenes +/- Staph aureus (MSSA or MRSA)
Cephalexin +/- Mupirocin
If MRSA - TMP/SMX, Clindamycin, or Doxycycline + Mupirocin

Conjunctivitis of the newborn
N. gonorrhea, C. trachomatis, viral
1. Erythromycin 0.5% ointment prophylaxis (1st hour)
2. Ceftriaxone IV, days 2-4, GC?
3. Erythromycin PO, days 4-10, ?CT
Suppurative Conjunctivitis
Staph auerus, Strep pneumo, H. flu
Ophthalmic FQ (Levo 0.5% or Moxi 0.5%)
Granular Conjunctivitis
C. trachomatis
1. Tetracycline (Erythromycin) or Azithromycin

Aerobic Gram Negative Rods (Non-Enterics)

Gram (+/-)
Haemophilus influenza (Hib) B
Unencapsulated (type B) rod
Otitis media, sinusitis, bronchitis, pneumonia

Disseminated spread to distant sites - meningitis, epiglottitis, septic arthritis
Legionella pneumophila
Large central AC systems, evaporative coolers, nebulizers, humidifiers, whirlpool spas, hot water systems, room-air humidifiers, ice making machines, misting equipment
Intracellular parasite
“Aerobic, non-enteric, gram negative rod”
Chlorine-tolerant rod
Legionnaire’s disease (atypical lobar pneumonia), rare 5% of CAP
HX: recent vent in ICU or known outbreak
Pasteurella multocida
Animal flora/bites
Aerobic gram negative non-enteric rod
Painful cellulitis
Pseudomonas aeruginosa
Skin-skin, hospitals, urinary and respiratory tract
Encapsulated motile rod
Oxidase (+)
Hospitalized patients with comorbidities, immunocompromised (diabetic, chemotherapy)
Moraxella catarrhalis

Aerobic diplococci
Oxidase (+)
URI (bronchitis, sinusitis), otitis media
Neisseria gonorrhoeae
Skin-skin, mucous membrane secretions
Aerobic intracellular diplococci
Oxidase (+)
Gonococcal urethritis
Pharyngitis, cervicitis, urethritis
Neisseria meningitidis
Young healthy adults in close quarters (military barracks, schools, college dorms) in winter and early spring
Aerobic diplococci
Oxidase (+)
Acute bacterial meningitis

Acute Otitis Externa (Swimmer’s Ear)
Pseudomonas aeruginosa +/- MSSA*
Fluoroquinolone drops +/- steroids
*If MRSA suspicious, add oral Bactrim or Doxycycline (CI in patients <8, causing permanent tooth staining)
Acute Otitis Media
Strep pneumo (49%)
H. flu (29%)
M. catarrhalis (28%)
1. Penicillin (amoxicillin)
2. Augmentin, for resistant strep
PCN allergy: 2nd Gen Cephalosporin (Cefuroxime) or Bactrim
“Strep” (Exudative) Pharyngitis/tonsillitis
Strep pyogenes
1. PCN G Benzathine 1.2 M units x 1 or PCN V (PO) x 10 days
Alternative: Clindamycin x 5 days
Gonococcal Pharyngitis/tonsillitis
N. gonorrhoeae
1. Ceftriaxone 250 mg IM x 1 +
Azithromycin 1 gm PO x 1 (covers CT)
No alternatives

Respiratory Pathogens
  • Presence of capsule = virulence factor; causes serious invasive disease, esp. in children
  • Haemophilus influenzae
    • Hib vaccination series – 2,4,6, & 12-15 months has decreased “H. flu” related disease dramatically, esp. Meningitis
  • Legionella pneumophila – intracellular parasite
    • Chlorine tolerant aquatic organism
    • Pontiac Fever” – mild flu-like URTI
    • Legionnaire’s disease” – atypical lobar pneumonia
    • Incidence of CAP – Strep pneumo, Atypicals, Viruses, H. Flu, Staph aureus, Legionella
Opportunistic Pathogen
  • Pseudomonas aeruginosa – encapsulated motile rod
    • Ubiquitous in nature; most are colonized; Oxidase (+)
    • Grows in distilled water and hot water baths – pseudomonas folliculitis
      • Identified by: Oxidase ++ test
Animal Flora
  • Pasteurella multocida – humans are accidental hosts
    • Acute painful cellulitis develops within 24 hours of an animal bite or scratch
Gram (-) Aerobic Diplo-cocci (Catalase + and Oxidase +) – usually associated with PMN’s (pus producing)
  • Moraxella catarrhalis (M. cat)
    • URI’s (bronchitis, sinusitis) & otitis media
  • Neisseria gonorrhoeae
    • Gonococcal urethritis (Gonorrhea)
    • Pharyngitis, Cervicitis, Urethritis – attaches easily to columnar epithelium on mucosal surfaces; copious purulent bright green active discharge
  • Neisseria meningitidis
    • Meningococcal meningitis (acute bacterial meningitis) – VACCINATE; rapidly fatal; strikes young healthy adults in close quarters;
      • Vaccines: Menomune (MCV4), Menactra (MPSV)
      • Meningococcal rash (hemorrhagic) – very important sign of meningococcemia sepsis that accompanies meningitis

Acute Bronchitis & Rhinosinusitis
Usually Viral
Strep pneumo (33%)
H. flu (32%)
M. cat (9%)
If no relief after 10-14 days with symptomatic TX → ABX
Fever, chills, comorbidity → ABX
1. Amoxicillin HD or Augmentin
2. Bactrim or Macrolide (Azithromycin)
3. Severe: Fluoroquinolone (Levofloxacin)
Community Acquired Pneumonia (CAP)
No Comorbidity: S. pneumo + Atypicals (Mycoplasma, Chlamydia)
Comorbidity*: S. pneumo, H. flu, Staph aureus, K. pneumoniae**
*COPD, CF, IVDU, Heart, Kidney or Liver disease, Alcoholism**
No Comorbidity
1. Macrolide (Azithromycin) - do not use beta-lactams or cell wall synthesis inhibitors for young people, atypicals do not have cell walls
Alternate: Doxycycline
1. Respiratory Fluoroquinolone (Levofloxacin or Moxifloxacin)
Alternate: Macrolide (Azithromycin or Clarithromycin) + HD Amoxil or Augmentin
***Hospitalize, if advanced age
Legionella pneumophila
1. Fluoroquinolone (Levofloxacin)
Alternative: Macrolide (Azithromycin)
Hospital Acquired Pneumonia (HAP)
S. pneumo (? resistant)
S. auerus
P. aeruginosa
E. coli & Klebsiella
1. B-lactam (Ceftriaxone or Unasyn) + Respiratory Fluoroquinolone (Levofloxacin or Moxifloxacin)
PCN allergy? Respiratory FQ + Aztreonam
Pseudomonas? Resp FQ + Zosyn
Ventilator Associated Pneumonia (VAP)
Pseudomonas aeruginosa
1. Antipseudomonal PCN (Zosyn)
Healthcare-associated Pneumonia (HCAP)
Pseudomonas aeruginosa
1. Antipseudomonal PCN (Zosyn)
Skin (ears, feet, follicles)
Hospitals (wounds, ICU)
Urinary tract
Respiratory tract (vent)
Pseudomonas aeruginosa
Immunocompromised at risk
  1. Hospitalize, antibiogram
  2. Antipseudomonal PCN (Zosyn) or 4th generation cephalosporin (Cefipime)
Do not use carbapenems (imipenem or meropenem) empirically
Painful cellulitis
Pasteurella multocida
1. Augmentin

Enteric Gram Negative Anaerobic Rods
Gram (+/-)
E. Coli
Contaminated water or food
Facultative-anaerobic rod, plasmids
Lactose (+)
Neonatal sepsis/meningitis
UTI: urethritis, cystitis, pyelonephritis
Diarrheal illness
  • ETEC
  • EPEC
  • EHEC
GI tract of animals and fowl
Facultative anaerobic rods
Very young and old
S. typhimurium or enteritidis
Human-human (poor hygiene, improper food handling, exposure to contaminated raw milk or poultry, especially eggs)
Facultative anaerobic rods
Gastroenteritis (“food poisoning”)
S. typhi
Swallowing water contaminated with human feces or food washed in contaminated water
Facultative anaerobic rods
“Enteric fever”
Spreads to liver, spleen, bone → bacteremia
Fecal-oral (poor sanitation or overcrowding)
Facultative anaerobic rods
Very young and old
Inflammatory diarrhea
Campylobacter jejuni
Fecal-oral (contaminated meat or water)
Facultative anaerobic “S-shaped” rods
Food-borne illness (acute enteritis)
Helicobacter pylori
Person-person (NOT from food/water)
Flagellated, Facultative anaerobic rods
Urease (+)
Acute gastritis, PUD, duodenal ulcers
Klebsiella Pneumoniae
Aspiration of GI contents
Facultative anaerobic rods
Aspiration pneumonia
Immunocompromised - DM, COPD, alcoholics

Enteric Gram (-) Rods; Facultative anaerobe
Intra and Extra Intestinal Disease
  • Escherichia coli
    • Ferment lactose (Lac+) – produces acid and gas in presence of CHO
    • Neonatal sepsis & meningitis
      • Newborns lack immunity – increases susceptibility
      • <1 month – S. agalactiae, E. coli, L. monocytogenes
    • Diarrheal illness
      • EnteroToxigenic (ETEC): contaminated food/water; small intestine; watery stool
        • Traveler’s diarrhea; abx okay (Bactrim, Alt: FQ)
      • EnteroPathogenic (EPEC): common in infants exposed at birth; affects small intestine; watery stool
        • Newborn diarrhea; abx okay (Bactrim, Alt: FQ)
      • EnteroHemorrhagic (EHEC): “0157:H7”
        • Cattle.
        • Hemorrhagic diarrhea
        • EXOTOXIN binds to cells in large intestine causing hemorrhagic colitis.
        • NO ANTIBIOTICS → hydration and watchful waiting
        • Abx increases risk for Hemolytic Uremic Syndrome (HUS) – hospitalize, hydrate with electrolyte solution, no antimotility agents.
          • HUS = hemolysis, anemia, renal failure
  • Salmonella
    • Facultative anaerobe
    • Most risk: very young and very old
  • S. typhimurium or enteritidis (GI tract of animals and fowl)
    • Gastroenteritis – “food poisoning”
    • Human-human transmission: poor hygiene, improper food handling
    • Exposure to contaminated raw milk or poultry product, especially eggs.
    • Invade enterocytes of sm & lg intestine -> N/V/D/cramps 10-14 hour after ingestion; resolves ~7d. Can be a severe, potentially fatal dehydrating illness in very young or old.
    • Wash hands, disinfect surfaces, thoroughly cook meat
    • Antibiotics: Fluoroquinolones
  • S. typhi (pathogenic to humans only)
    • Enteric fever (Typhoid fever); rare in US
    • Swallowing water contaminated with human feces; eating food washed with contaminated water;
    • Underdeveloped countries; crowded conditions
    • Invade macrophages of intestinal lymphoid tissues (Peyer’s patches); incubate/replicate 1-3 weeks; spreads to liver, spleen, bone; bacteremia can result
    • Severe, life threatening febrile systemic illness can occur
    • Vaccine available (PO, IM); 70% effective
    • Chronic carriers – Typhoid Mary (NYC -1910)
    • Antibiotics: Fluoroquinolones

Intra-intestinal disease only
  • Shigella
    • Fecal-oral transmission - Very low infectious dose
    • Secondary cases are common in areas of poor sanitation or overcrowding
    • Shiga-toxin: cytotoxic properties; destroys superficial layers of colon mucosa
    • Inflammatory diarrhea – blood, mucus, painful cramps
    • Most severe in very young & old; potentially fatal dehydration
    • Prevention: hygiene, clean food/water
    • Antibiotics: Fluoroquinolones (Ciprofloxacin) or Azithromycin
  • Campylobacter jejuni
    • Widely distributed; colonizes gut of mammals/fowl
    • Fecal-oral transmission: direct exposure to contaminated meat or water
    • Leading cause of foodborne disease in US
    • Acute enteritis (dysentery) – ulcerative inflammatory lesions of J, I, or colon
    • Mild or severe with intestinal and/or systemic symptoms
    • Prevention: hygiene, clean food/water, cook meat thoroughly
    • Antibiotics: Azithromycin
  • Helicobacter pylori – flagellated; Urease (+)
    • Person:person transmission; not isolated from food/water
    • H/o: gastric or duodenal ulcer?
      • (+) culture on endoscopy, (+) antibody testing, (+) breath test
    • Invades mucosal layer of GI epithelium
      • Urease cleaves urea → CO2 + NH3; neutralizes pH for H. pylori survival
      • NH3 cytotoxic to mucous producing cells
    • Sequential Therapy
      • Amoxicillin x 5 days
      • Macrolide x 5 days
      • Metronidazole x 5 days + PPI for 15 days

Extra-intestinal disease only
  • Klebsiella pneumonia
    • Necrotizing lobar pneumonia; “aspiration pneumonia
    • Immunocompromised (DM, COPD, alcoholism)
    • Aspiration of GI contents
    • Cultured in 29% of cases

Uncomplicated urethritis & cystitis
Escherichia coli
Staph saprophyticus
Outpatient: depends on resistance patterns
  • <20% E. coli resistance to bactrim → Bactrim
  • >20% E. coli resistance to bactrim → Ciprofloxacin
  • Sulfa-allergy: Nitrofurantoin
Recurrent Uncomp UTI: Nitrofurantoin prophylaxis

Gram Positive Anaerobic Rods
Gram (+/-)
Clostridia spp.
Contaminated soil, puncture wounds, antibiotic overuse (ampicillin, amoxicillin, cephalosporins, clindamycin)
Spore forming rods
C. perfringens (gas gangrene)
C. botulinum (botulism)
C. tetani (tetanus)
C. difficile (pseudomembranous colitis)
Listeria monocytogenes
Anaerobic rods
Non-spore forming
Febrile enteritis = inoculated and healthy
Bacteremia or meningitis = inoculated and vulnerable

Clostridia spp. (toxin producing)
  • C. perfringens (gas gangrene) ->myonecrosis
  • C. Botulinum (botulism) ->flaccid paralysis
  • C. tentani (tetanus) -> sustained m. contraction
  • C. difficile -> pseudomembranous colitis (PMC)
    • Normal, but minor component of intestinal flora
    • Spores contaminate environment (bleeding, toilets, dust); hearty!
    • Risk: age, colonized carrier, Ab’s
    • Overgrowth may occur with antibiotics (AAC)
      • Toxin A = inflammatory colitis (CDC)
      • Toxin B (cytotoxin) = PMC
    • Pseudomembranes on endoscopy – exudate (mucus, fibrin, cellular debris overlying ulcerated colon)
    • Abx Culprits: Ampicillin, amoxicillin, cephalosporins, clindamycin
      • Occasionally: other PCNs, Erythromycin, Sulfonamides (Bactrim), Quinolones (Levaquin)
      • Rarely/Never: Tetracyclines, Vancomycin, Metronidazole, Aminoglycosides
    • Treatments: Metronidazole + Probiotics (Lactobacillus + Saccharomyces)
      • Alternative: Vancomycin PO

Listeria monocytogenes
  • Widespread among animals
  • Infection foodborne
  • Risk: old, young, immunocompromised, pregnant
  • Prevention: Safe food handling, storage, and prep
  • Enters cells by phagocytosis & releases listeriolysin
    • Listeriosis: febrile enteritis or invasive disease (sepsis)
  • Soft cheeses in pregnancy
    • Infection, transplacental migration, meningitis  
  • 3rd most common cause of neonatal bacterial meningitis
  • Antibiotics
    • Mild = Bactrim DS (PO)
    • Severe: Ampicillin + Gentamicin (IV)
Other Gram Negatives

Gram (+/-)
Haemophilus Ducreyi
Break in skin
Gram stain: “school of fish”
Painful chancroid on genitals
Treponema Pallidum
Sexual transmission
Spirochete, stains poorly
Dark field: long, slender, flexible, spiral rod, highly motile
Obligate internal parasite with cytoplasmic inclusion bodies
Giemsa staining or direct immunofluorescence
Syphilis - painless genital chancre or rash

Non-gonococcal cervicitis, trachoma (conjunctivitis), LGV (lymphogranuloma venereum)

Haemophilus ducreyi
  • Gram stain: “school of fish” appearance
  • Opportunistic pathogen – enters via breaks in skin
  • Treatment: azithromycin or ceftriaxone
  • “Chancroid” on genitals
    • Painless, hard raised edge
  • Soft ragged edge with pus; very painful

Treponema Pallidum – a Spirochete
  • Gram (-), but stains poorly
  • Dark field microscopy – reveals long, slender, flexible, spiral rod that is highly motile
  • Obligate internal parasite: primary, secondary, and tertiary stages of disease
    • Primary and secondary stages highly contagious (syphilis)
  • Syphilis – painless genital chancre & or rash
    • “The great imitator”
    • Treatment: Benzathine G or Azithromycin
      • Doxy or 3rd generation cephalosporin

Atypicals and Mycobacterium
Gram (+/-)
Chlamydia pneumoniae
Respiratory droplets
School aged children

Community acquired pneumonia, pharyngitis, laryngitis, bronchitis
Chlamydia trachomatis
Sexual transmission
Obligate intracellular parasite
Cervicitis, urethritis, LGV
Droplet of respiratory or GU tract secretions
No cell wall - insensitive to antibiotics that interfere with cell wall synthesis
Smallest free-living prokaryotic cells; evade and pass through bacteriological filters

Ureaplasma urealyticum
Sexually active adults
Microbe of exclusion
“Genital mycoplasma””
Non-gonococcal urethritis: urethritis (M>F), endometritis
Mycoplasma pneumoniae
Young adults without comorbidities

“Walking pneumonia”
Mycobacterium tuberculosis

Aerobic, acid-fast, long, slender, non-motile rod
Active TB, latent TB, miliary TB

  • Chlamydia pneumoniae
    • Incidence unknown; respiratory droplets
    • Common in school aged children – wash hands!
    • Community Acquired Respiratory Pathogen (CAP)
    • Pharyngitis, laryngitis, bronchitis, pneumonia
    • Treatment: doxycycline or azithromycin, quinolone
  • Chlamydia trachomatis
  • Obligate intracellular parasite
  • Cytoplasmic inclusion bodies
  • Requires Giemsa staining or direct immunofluorescence
  • Nongonococal cervicitis, trachoma (conjunctivitis), LGV (lymphogranuloma venereum)
  • Treatment: treat partner(s) or encourage treatment; doxycycline or azithromycin; treat GC at same time

Opthalmia Neonatorum
  • Causative organisms: chlaymdia or gonorrhea
  • Corneal scarring, iritis, blindness
  • Prophylaxis with E-mycin 0.5% ointment to all infants within 30 minutes of delivery

  • No cell wall - insensitive to antibiotics that interfere with cell wall synthesis
  • Smallest known free-living prokaryotic cells, capable of evading and passing through bacteriological filters
  • Commensals exist in mouth and GU tract of humans
  • Droplet transmission of respiratory or GU tract secretions

Ureaplasma urealyticum
  • “genital mycoplasma”
  • Most sexually active adults are colonized; microbe of exclusion
  • Nongonococcal urethritis (NGU)
  • Urethritis (M > F) & endometritis
    • All NGU treated like chlamydia unless proven otherwise
  • Doxycycline or azithromycin
  • Quinolone

Mycoplasma pneumoniae
  • Common culprit in young adults (“walking pneumonia”)
    • 2nd to strep pneumo as common cause of CAP – esp. in those without comorbidities
  • Gradual onset: nonspecific symptoms “not feeling well” followed by h/a, fever, chills, earache, persistent cough, minimal sputum; rarely debilitating
  • CXR: patchy, diffuse infiltrates
  • Micro ID difficult (8-15 days)
  • If suspicious, treat it!
  • Treatment: macrolides (azithromycin, clarithromycin) if no comorbidity; quinolone if comorbidity present
  • Incidence of CAP (community acquired pneumonia)
    • Strep pneumo – 60%
    • Atypicals (mycoplasma/chlamydia)
    • Viruses – 12%
    • H. Flu – 11%
    • Staph aureus
    • Legionella

Mycobacterium tuberculosis
  • Aerobic, acid-fast, long, slender, non-motile rod
  • Active but quiescent – productive granulomatous lesion (tubercles)
  • Chronic bacterial infection in humans; leading cause of ID related death worldwide
  • Tubercles “arrest” (fibrotic, calcified) or break-down and disseminate via lymphatics (miliary TB)
    • Vancomycin (Gram + organisms) – primarily MRSA, cellulitis, or PNA; C. difficile colitis (PO)
    • If used empirically to cover MRSA but culture reveals MSSA, switch to anti-staph PCN or 1st generation Cephalosporin (more effective)

Chlamydia (cervicitis, urethritis, LGV)
Chlamydia trachomatis
1. Doxycycline or Azithromycin (single dose)
Gonorrhea (cervicitis, urethritis, pharyngitis)
Neisseria gonorrhoeae
1. Ceftriaxone IM x 1
Genital Mycoplasma (Urethritis & Endometritis)
Ureaplasma urealyticum
1. Doxycycline or Azithromycin
Haemophilus ducreyi
1. Ceftriaxone IM x 1
2. Azithromycin x 1
Treponema pallidum
1. PCN G (Bicillin LA) 2.4 M units IM x 1
ALT: Doxycycline BID x 14-28 days

Question 1: Which of the following tests are useful for identifying Moraxella, Neisseria, and Pseudomonas sp?
  1. Catalase testing
  2. Coagulase testing
  3. Oxidase testing
  4. Urease testing

Question 2: Which bacteria does not have a cell wall and spreads through droplet transmission?
  1. Staph pyogenes
  2. Mycoplasma pneumonia
  3. Shigella
  4. Pasteurella multocida

Answer 1: C
Answer 2: B



  1. I would be awesome if I could get a version of this that is printable! Is that possible?? I just to the PACKRAT and see that my pathogen skills are lacking, this would be the perfect study material. Thank!

    1. Thanks! I appreciate the feedback. I will consider publishing this in the future as a free PDF.


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