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Mycobacteria Tuberculosis (morphology)
Peptidoglycan similar to GP bacteria
Unique: waxy coat of mycolic acids and lipoarabinomannan (LAM) - hydrophobic
- Limits nutrient entry (slow clumpy growth on plates)
- Prevents gram staining
Confers acid-fast (AF) staining properties, resist acid decolorization
Mycobacteria Tuberculosis (reservoir)
Active human cases
Mycobacteria Tuberculosis (transmission)
Aerosol (low infectious dose)
Risk factors:
- Prolonged exposure
- Immunocompromised (extremes of age, AIDS, anti-TNF-alpha therapy)
Most cases from high burden countries
Mycobacteria Tuberculosis (clinical)
Primary TB (initial exposure)
- Sometimes mild, asymptomatic
- Can spontaneously heal
Latent TB (majority of cases)
- Infection contained but not cleared
- Asymptomatic, non-infectious
Secondary TB (5-10% latent cases)
- Reactivation of latent TB into acute TB
Active infections (primary or secondary)
- Cough, hemoptysis, fever, malaise, dyspnea
- Cachexia (wasting)
- Top 10 causes of death
Extrapulmonary spread (uncommon but greater risk if immunocompromised)
- Spinal TB (Pott’s disease)
- Miliary TB
Spinal TB (Pott’s disease)
- Infection of 2 contiguous vertebrae
- Nutrient supply to IVD lost
- Microbial toxins leach into IVD
- IVD degenerates
- Leads to outward curvature of spine (kyphosis)
Miliary TB
- Widely disseminated TB
- Lung and tissues covered with white nodules (like millet seeds)
Pulmonary TB
- Bacteria from infected person is inhaled
- Lung macrophages phagocytose bacteria
- Problem: bacteria has virulence factors that evade macrophage killing
- Solution: wall it off in a granuloma
Outcome of granuloma formation: latent TB
- Infection is contained
Problem: waning containment (granuloma collapses, bacteria released leading to secondary TB)
Mycobacteria Tuberculosis (virulence)
Host evasion: multiple virulence factors allow survival in macrophages (waxy coat protects bacteria, inhibits phagolysosome fusion and maturation)
Inhibits production of ROS
Secretes siderophores to compete for Fe
- Macrophage attempts to starve for Fe using a pump in phagosome membrane
Bacteria secrete siderophores to get Fe
Mycobacteria Tuberculosis (diagnosis)
Clinical: cough, fever, weight loss, hemoptysis
Chest radiograph
Sputum: culture, acid fast stain (gram won’t work)
Tuberculin skin test: mantoux test or PPD
- Mantoux: screening, bacteria proteins injected intradermally, mechanism: delayed-type hypersensitivity to bacteria antigens (delayed because it involves Th cells, not Abs)
- If positive, additional tests to distinguish latent TB from active infection
Delayed-type hypersensitivity
- Delayed kinetics (T-cell mediated rather than Ab)
- Mechanism: memory Th cells activate local macrophages at injection site
Interferon gamma release assays
- Blood test detects latent TB
Measures interferon gamma release from patient’s T. cells in response to bacteria antigens (not present in BCG vaccine)
Mycobacteria Tuberculosis (treatment/prevention)
Long-term treatment
- Multiple drug combinations
- MDR-TB emerging
Prevention:
- SDOH (healthcare access)
BCG vaccine: attenuated strain, only used in countries with high prevalence (variable effectiveness, false + on TB skin test)
Mycobacteria leprae (morphology)
Similar waxy coat to Mycobacterium tuberculosis
Reduced genome: lacks genes for essential biosynthetic functions
Obligate intracellular pathogen
Mycobacteria leprae (reservoir)
Human cases
Mycobacteria leprae (transmission)
Skin breaks, respiratory
Low infectivity
Rare zoonotic outbreaks
Mycobacteria leprae (clinical)
Major signs are cutaneous
Tuberculoid leprosy
- Bacteria contained in granulomas
- Flat, anesthetic skin lesions
- Neurovascular granulomas with rare acid fast bacilli
Lepromatous leprosy
- Poor containment due to weak immune response
- Widespread skin lesions
- neurovascular granulomas with many acid fast bacilli visible
- permanent damage to skin, nerves, limbs, eyes
common cause of crippled hands
Mycobacteria leprae (virulence)
Obligate intracellular pathogen
- avoids intracellular killing
- slow growth progressing over years
Preferentially infects Schwann cells
- trigger neurovascular granulomas
nerves swell
Mycobacteria leprae (diagnosis)
Clinical: skin lesions with patchy anesthesia
Skin biopsy: acid fast rods, neurovascular granulomas
Unculturable
Mycobacteria leprae (treatment/prevention)
Curable with multidrug regimens
Non-tuberculous mycobacteria (reservoir)
Environmental
Opportunistic pathogens
Non-tuberculous mycobacteria (transmission)
Recent outbreak in tattoo parlors
E. coli (morphology)
GN Enteric bacteria
Reside in GI
E. coli (reservoir)
Lower GI commensals of animals/humans
Environment
- Fecal coliforms (test used to screen aquatic environments)
UTIs: GI tract
Enterotoxigenic E. coli (ETEC)
- Infected humans
STEC
- Animals colonized by STEC
E. coli (transmission)
Fecal contamination
UTIs: ascending infections via urethra, hematogenous dissemination to kidney
Enterotoxigenic E. coli (ETEC)
- Fecal-oral (high infectious dose)
STEC:
- Food outbreaks
- Low infectious dose
Serotype: O157:H7
E. coli (clinical)
UTIs
- Infection of urinary track
- Cystitis (lower UTI) - most cases (symptoms due to bladder infection)
- Pyelonephritis (upper UTI) - symptoms due to kidney infection (risk of bacteremia)
- Prevalence: reproductive years (50:1, female to male)
- Elderly (2:1, female to male due)
Uncomplicated UTIs (uUTIs): confined to bladder
- Toxin-mediated bladder damage and inflammation
- Dysuria, hematuria, urgency, frequency, cloudy urine, suprapubic pain
Complicated UTIs
- Additional signs/symptoms
- Fever, chills, nausea, dropping bp, flank pain, CVA tenderness (pyelonephritis)
- UTI associated with foreign bodies (catheters)
UTI risk factors:
- Reduced urine flow (obstruction, neurogenic bladder, urologic surgery, pregnancy), chronic dehydration (nursing homes, voluntarily avoiding bathroom visits)
- Females
- Aging (both sexes)
- Immunocompromise
- Obesity
- Sexual activity
- Urinary catheters (biofilms)
Urinary tract defenses:
- Mechanical flushing
- Uromodulin (Tamm-Horsfall protein): most abundant protein in normal urine, from epithelium of thick ascending limb, decoy receptor for E. coli pili (blocks adhesion, allows flow to clear)
Neonatal meningitis
- Second most common cause
- Exposure to pathogenic strain during delivery
- Rare in adults
Diarrhea
- Non-infectious: inflammation mediated
- Infectious: inflammation and toxin-mediated
Infectious diarrhea:
- Secretory diarrhea: toxins and inflammation drive epithelial hypersecretion
- Bloody diarrhea: secretory component, damage component (loss of epithelial barrier, damage to underlying vessels)
Diarrhea causing E. coli
- Enterotoxigenic E. coli (ETEC)
- Shiga toxin-producing E. coli (STEC)
Enterotoxigenic diarrhea E. coli (ETEC)
- Most frequent cause of traveler’s diarrhea (secretory diarrhea)
STEC: hemolytic uremic syndrome (HUS)
- Systemic toxin damages ECs in kidney triggering microthrombi
- Thrombocytopenia, hemolytic anemia
- Renal damage: fluid/electrolyte imbalance, uremia, hematuria
Common cause of acute renal failure in children
E. coli (virulence)
Uropathogenic virulence:
- Adhesion/colonization: nearby rectal flora colonize perineum, if dislodged: adhere to urethra (pili) through intercourse, catheters, post-partum
- Motility (flagella, pili)
- Exotoxin release (damage to epithelium - inflammation)
ETEC
- Adhesion
- Enterotoxin secretion (hypersecretion of GI epithelium watery diarrhea)
STEC
- Adhesion
- T3SS injects VFs into cell (creates permissive niche)
- Exotoxin secretion (damages tissue)
Shiga toxin:
- AB5 toxin acquired by HGT from shigella dysenteriae
MOA: GI epithelium endocytoses toxin A subunit exits to cytoplasm, poisons ribosomes epithelial cell dies, exposing underlying blood vessels (bloody diarrhea)
E. coli (diagnosis)
uUTIs
- POC dipstick leukocyte esterase (pyuria), nitrites (bacterial metabolites), protein (tissue damage), hematuria (tissue damage)
cUTIs
- CVA tenderness
- Vitals
Imaging
- Urine culture
ETEC
- Not tested (self limited)
STEC
Molecule testing (replace stool culture)
- Specialized lab testing
E. coli (treatment/prevention)
uUTIs: empiric ABX, without urine culture (assume E. coli)
cUTIs: empiric ABX initially, ABX narrowed following urine culture/ID/susceptibility profile
Emerging: ABX cause GI microbiome dysbiosis
Prevention:
- Frequent hydration/voiding
- Catheter care
- Vaccines: in development (target adhesion, siderophores, toxins)
ETEC:
- Oral fluids
- Prevention: well-cooked food, bottled water
STEC:
- Oral rehydration
- ABX not favored evidence that they increase production of shiga toxin by bacteria
Prevention: hand washing, cook food to internal temp. in excess of 155 F
Shigella dysenteriae (reservoir)
Humans (infected or carriers)
Shigella dysenteriae (transmission)
Fecal-oral
Low infectious dose
Developed countries: pediatric disease
Developing countries: poor sanitation
Shigella dysenteriae (clinical)
Shigellosis:
- Dysentery:
- Fever, cramping, bloody diarrhea with mucus and inflammatory cells
- Severe, but resolves within a week
- HUS risk:
- S.dysenteriae has the highest risk due to prevalence of Stx
Shigella dysenteriae (virulence)
Acid resistant
Facultative intracellular pathogen that tricks M cells into internalizing them
- Bind to M cells in colon
- Uses T3SS to inject VFs into the M cells (triggers endocytosis of bacteria)
Invasive spread within epithelium
- Escapes endocytic vacuole
- Actin polymerization promotes lateral spread
Shiga toxin
Destruction of epithelium and underlying tissue bloody diarrhea
Shigella dysenteriae (diagnosis)
NAAT for Stx in stool
Stool culture - hektoen enteric agar (being replaced by molecular tests)
HUS suspected if classic triad of signs
- Thrombocytopenia
- Hemolytic anemia
- Renal damage (clogged glomeruli)
Shigella dysenteriae (treatment/prevention)
Oral rehydration
ABX avoided except in severe cases
Prevention: sanitation, insect control (raw sewage)
Salmonella enterica serovar typhimurium (resorvoir)
Animals and humans
Salmonella enterica serovar typhimurium (transmission)
Outbreaks (from food and environment)
Salmonella enterica serovar typhimurium (clinical)
Acute gastroenteritis
- Diarrhea, fever, abdominal cramps after a meal
- Difficult to distinguish from other pathogens
- Lasts about a week
Salmonella enterica serovar typhimurium (virulence)
Children <5 most at risk
- Acid sensitive
- T3SS like Shigella, tricks M cell endocytosis (but no lateral spread through comet tails), transcytosed all the way through to underlying tissue
Inhibits macrophage phagolysosome fusion (bacteria released, cause local damage and bloody diarrhea)
Salmonella enterica serovar typhimurium (diagnosis)
NAATs, stool culture (becoming rare)
Salmonella enterica serovar typhimurium (treatment/prevention)
Self limited
- Fluid/electrolytes
- ABX only in severe cases
Prevention: proper food handling, hand-washing
Salmonella enterica serovar typhi (reservoir)
Human specific (chronic carriers)
Healthy carriers
- Gallbladder colonized by S. Typhi in chronic carriers
- Forms gall stone biofilms and enter gall bladder epithelium, chronic shedding into GI
Salmonella enterica serovar typhi (transmission)
Fecal-oral
Salmonella enterica serovar typhi (clinical)
Typhoid fever
- Severe systemic illness
- Fever due to chronic bacteremia
- Weakness, headache, loss of appetite, abdominal discomfort
- Persistent bacteremia seeds to other organs
Chronic infection can lead to hemorrhage from intestinal perforations
Salmonella enterica serovar typhi (virulence)
Exploits M cell transcytosis like S. typhimurium
- Transported to lamina propria
Evasion of macrophage killing
- Blocks phagolysosome fusion and oxidative burst
- Infected macrophages don’t die, spread bacteria
Systemic infection
Salmonella enterica serovar typhi (diagnosis)
NAAT, blood/stool culture
Serology for public health monitoring
Salmonella enterica serovar typhi (treatment/prevention)
ABX
Prevention: hand-washing, vaccine (not 100% effective)
Vibrio cholerae (morphology)
GN, curved rods, motile (flagella)
Vibrio cholerae (reservoir)
Free-living bacteria in warm coastal brackish waters (reproduce slowly, not all are toxigenic)
Vibrio cholerae (transmission)
Environmental strains (shellfish, oysters)
Epidemic strains: obtained cholera toxin gene by HGT
Cause: present in environment, poor water/sewage treatment infrastructure
Vibrio cholerae (clinical)
Rapid onset (days)
Abdominal fullness/discomfort, vomiting
Rushes of peristalsis, voluminous stools (watery, almost odorless, mucous flecks)
Dehydration is life threatening (low bp, weakness, dizziness, confusion, electrolyte imbalance)
Vibrio cholerae (virulence)
Adhesion to GI epithelium
Motility (single polar flagellum, colonizes intestinal crypts)
Cholera toxin (AB5 toxin):
- ADP ribosylates membrane-associated adenylate cyclase
- Locks adenylate cyclase in “on” position
- cAMP activates ion efflux channels
- Ion buildup in GI draws water from tissues
- Greatest effect is small intestine
Advantage of cholera toxin
- Fitness increases spread
- Increases luminal concentrations of some nutrients that support bacterial growth
Flushes competing bacteria from the gut
Vibrio cholerae (diagnosis)
Clinical: signs and symptoms, appropriate epidemiologic setting
Laboratory: stool culture
Vibrio cholerae (treatment/prevention)
Oral rehydration therapy (self-limiting, resolves with hydration)
Severe cases: rehydration and ABX
Prevention: bottled water, peel fruits/vegetables, avoid raw shellfish
Vaccines: vaxchora (live, attenuated, deleted Ctx gene), dukoral (killed whole cell and B subunit)
Vibrio vulnificus (reservoir)
Warm, brackish water, coastal shellfish (oysters)
Vibrio vulnificus (transmission)
Food, skin breaks
Increased risk: coastal disasters
Vibrio vulnificus (clinical)
Blistering cellulitis/necrotizing fasciitis
Vibrio vulnificus (virulence)
Multiple toxins
Campylobacter jejuni (morphology)
Short corkscrew-shaped GNRs
Single polar flagellum
Campylobacter jejuni (reservoir)
GI tracts of animals
Campylobacter jejuni (transmission)
Contaminated food - most cases are chicken
Most common cause of diarrhea in U.S.
Campylobacter jejuni (clinical)
Abdominal discomfort a few days of exposure
Watery diarrhea that may become bloody
Usually resolves within a weak
Sequalae:
Post-infectious Guillain-Barre syndrome
- Rare complication of campylobacteriosis
- Demyelinating neuropathy (weakness/tingling in both legs, spreading to arms and upper body)
Similar mechanism to acute rheumatic fever
Campylobacter jejuni (virulence)
Adhesion
Invasion of GI epithelial lining cells
Toxins (secretory diarrhea, bloody diarrhea if cells are killed)
Campylobacter jejuni (diagnosis)
PCR/stool culture
Campylobacter jejuni (treatment)
Usually not treated unless severe
Prevention: cook chicken well, wash hands after handling meat
Helicobacter pylori (morphology)
GN curved rods, polar flagella
Helicobacter pylori (reservoir)
Humans (increases with age, life-long)
Helicobacter pylori (transmission)
Fecal-oral (contaminated food/water)
Mouth-to-mouth contact
Helicobacter pylori (clinical)
Infects stomach mucosa
Gastritis (nausea, vomiting, abdominal pain)
Gastritis can ulcerate lining (risk for bleeding)
Helicobacter pylori (virulence)
Periplasmic urease (hydrolyzes urea in gastric juice into ammonium, facilitates survival in low pH until they can swim down to where pH is higher)
Motility
Uses a T3SS to inject toxins into the cell
- Damages epithelium
- Some toxigenic strains linked to gastric cancer
Damages epithelium as it grows
Helicobacter pylori (diagnosis)
Urea breath tests (patient ingests capsule with 13C-labeled urea if urea is in stomach, urea will be broken down, releasing 13C as part of Co2 in breath
Stool tests
Helicobacter pylori (treatment/prevention)
ABX for patients with evidence of ulcers
(not treated if no ulcers)
Proton pump inhibitor (raises pH to promote healing)
Mycoplasma pneumoniae (morphology)
Phylogenetically related to GP
- No cell wall, just a membrane: pleomorphic (all kinds of shapes)
- Smallest of free-living bacteria
In a separate class: mollicutes (soft skin)
Mycoplasma pneumoniae (reservoir)
Humans (especially children)
Mycoplasma pneumoniae (transmission)
Inhaling respiratory droplets
Dies quickly due to lack of cell wall Rapid person-to-person spread
Any crowded place
Common tissue culture contaminant
Mycoplasma pneumoniae (clinical)
Walking pneumonia
- Fever, cough, shortness of breath
- Most are tracheobronchitis (not lungs), can progress to pneumonia
Smoldering infection
- Incubation period can be weeks (vs. viral pneumonia)
Mycoplasma pneumoniae (virulence)
Adhesion: requires a specialized attachment organelle
Motility
- Lack flagella, attachment organelle functions in gliding motility
- Facilitates colonization of airway
- Mechanism: inchworm or centipede-like (catch-release)
Host evasion
- Surface antigenic variation
Damages mucociliary escalator
- CARDS toxin (community acquired respiratory distress syndrome toxin)
Causes cough
Mycoplasma pneumoniae (diagnosis)
Overlaps with other respiratory infections
- Slow onset is big clue
Sputum sample/throat swab
- No gram stain
- Slow growth in culture
NAA tests
Mycoplasma pneumoniae (treatment/prevention)
Most infections are mild/self-limited
ABX in severe situations
No vaccines
Rickettsia rickettsii (morphology)
GNR
Obligate intracellular bacterium
Rickettsia rickettsii (reservoir)
Ticks (vector)
Seasonal infection
Rickettsia rickettsii (clinical)
Within a week of tick bite
- Fever, headache, vomiting, joint pain
- Petechial rash (centripetal pattern, hands and feet spreading to trunk)
May progress to DIC (disseminated intravascular coagulation)
Rickettsia rickettsii (virulence)
Tick introduces bacteria into blood
Obligate intracellular bacterium
- Endocytosed by cells
- Escapes phagosome and grows in cytoplasm
Targets endothelial cells
- Triggers vasculitis
- Increased vascular permeability (hypovolemia)
Hypercoagulopathy (petechiae)
Rickettsia rickettsii (diagnosis)
History of tick bite
Clinical signs/symptoms: spotted rash that expands centripetally
Serology/PCR
Unculturable on solid medium
Rickettsia rickettsii (treatment/prevention)
Treatment:
- Mortality from vascular collapse if untreated
- Vascular damage can be permanent, requiring amputation
Empiric ABX
Prevention:
- Avoid ticks
- Frequent de-ticking in infested areas
No vaccine
Rickettsia prowazeki (morphology)
GN coccobacillus
Rickettsia prowazeki (reservoir)
Humans (most cases)
Flying squirrels
Rickettsia prowazeki (transmission)
Vector-borne
- Body lice acquire bacterium by biting an infected human and transmit to other humans
- Contact with flying squirrels (rare)
World outbreaks: war, famine, poverty, aid workers
Rickettsia prowazeki (clinical)
Fever with neurological manifestations of stupor and confusion
Similar to RMSF (rocky mountain sided fever)
- RMSF: tick-borne, rash on palms/soles spreads centripetally
- Epidemic typhus: Louse-borne, centrifugal rash (trunk to extremities)
Both diseases may be fatal due to vascular collapse
Rickettsia prowazeki (virulence)
Obligate intracellular pathogen (infects ECs)
Lives in clothing and bedding, not body
Louse feces laden with this bacteria —> person scratches infected excrement into skin
RMSF vs. typhus
- RMSF: tick is the reservoir, transmitted by bite
Epidemic typhus: humans are reservoir, louse is vector (acquires bacterium from infected humans)
Rickettsia prowazeki (diagnosis)
Serology
ABX
Louse control
Pseudomonas aeruginosa (morphology)
GN rods
Prolific biofilm producer
Pseudomonas aeruginosa (reservoir)
Widespread humid environmental bacterium
Pseudomonas aeruginosa (transmission)
Airborne droplets
Contact with contaminated surfaces (biofilms)
Pseudomonas aeruginosa (clinical)
Potent opportunistic pathogen:
- Lung infections
- Skin infections
- Eye infections
Many tissues affected
- Urinary tract
- CNS
- GI tract
- Ears
- Bones and joints
- Heart
Lung infections (pneumonia)
- Life threatening
- At risk: CF patients, immunocompromised, patients on ventilators (biofilms)
Skin infections:
- Mild: hot tub rash (pseudomonas folliculitis) thrives in hot-tub temperatures, transmission: contact with contaminated water, treatment not necessary
- Green snail syndrome (more prevalent in cooks and dishwashers, treatment: topical ABX)
- Severe: Problem in burn units
Eye infections:
Pseudomonas keratitis: most common cause of corneal infection associated with contact lenses contaminated solutions, eye trauma caused by lens insertion/removal or debris
Pseudomonas aeruginosa (virulence)
- Forms in response to host environment to protect bacteria
- Overproduces biofilm rich in alginate (polysaccharide)
Neutrophil defenses against Pa
- H202: causes oxidative damage to bacteria
- LL-37: antimicrobial protein (AMP), damages bacterial membranes
Biofilms contain a mix of two variants
- Mucoid variants (make alginate): block entry of LL-37, but not H202, unable to make catalase
- Nonmucoid variants (don’t make alginate): produces catalase to neutralize H202
- Protected from LL-37 by alginate
Toxin production
- Pyocyanin: oxidative damage to human cells
- Tissue damaging enzymes: proteases, elastase
- T3SS inject toxins that impair phagocytosis
Fe acquisition
- Secretes pyoverdine (siderophore)
Motility
- Flagellum (swimming in liquid) - gets it to a surface
Twitching motility: crawling on surfaces (mucosa and biofilms) catch pull release mechanism involving type IV villi
Pseudomonas aeruginosa (diagnosis)
Culture
Pseudomonas aeruginosa (treatment/prevention)
ABX
- Notorious for acquiring resistance by mutations
- ABX selection pressure can drive LOF mutations in MutS (involved in DNA damage/repair, creates a hypermutator phenotype: allows massive mutations)
Prevention:
- Reduced hospital stays
- Sanitation of surfaces, hot tubs, contact lenses
No vaccine
Legionella pneumophila (morphology)
GN rods (some longer filaments)
Motile
Facultative intracellular pathogen
Legionella pneumophila (reservoir)
Biofilms in aquatic environments
Legionella pneumophila (transmission)
Inhalation of aerosols (mists)
- Contain bacteria released from biofilms
No evidence of PtP
Incidence is increasing
- Aging infrastructure (older plumbing and cooling)
- Climate change
- Vulnerable population
Legionella pneumophila (clinical)
Severe
- Legionnaires’ disease (legionellosis)
- Severe pneumonia: headache, fever, chills, dry cough, chest pain
Mild
- Pontiac fever
Resolve without treatment
Legionella pneumophila (virulence)
Biofilm formation in wet environments
Evades macrophage killing
- Inhibits phagolysosome fusion and maturation
- Recruits ER membrane to pathogen-containing vacuole (PCV) resembles an organelle
Multiplies in phagosome
Legionella pneumophila (diagnosis)
Clinical manifestations are non-specific
- Requires lab testing
Urinary antigen test
PCR on sputum
Culture requires specialized media
Legionella pneumophila (treatment/prevention)
Treatment:
- ABX with high intracellular potential
- No vaccine
Prevention
- Sanitation and hyperchlorination of water systems
- Superheating of stagnant water
- Copper - silver disinfection of pipes