Fiche de Revision 2.4 Digestion and Defense
Case 1:
I. Bacteria
1. Types and Classification of Bacteria
- definition: prokaryote organism (nucloids) whose nutrient cycles releases toxins causing infection
- 2 - 0.2 micrometers (giardia lamblia - 25microm ; plasmodium (malaria) - 5microm)
- composition: nucleoid, capsule, ribosomes, cell membrane, cell wall, flagellum (optional); no
mitochondria/lysosomes/nuclear membrane
- classification: macro/micro appearance, growth/metabolic properties, antigenicity, genotype
- appearance: shape (cocci, coccobacillus, fusiform bacillus, vibrio, spirillum, spirochete, bacillus),
gram- or gram+
- gram negative vs gram positive
- gram positive: purple + rod
- gram negative: pink + circle
- gram + and gram -
- gram + is more sensitive to lysozymes, penicillin activity ; thicker cell wall
- only gram+ produce spores (not all)
- metabolic: anaerobic/aerobic/facultative/capnophilic, requirement for specific nutrients, production
of characteristic metabolic products/enzymes
- methods: experiment-type methods to reveal characteristics
- antigenicity: serotyping to identify characteristic antigens
- genetic: PCR, DNA hybridization
, - examples of bacteria:
- E Coli: commensal, rod, pink, G-, ferments lactose
- Candida albicans: yeast, violet, circle, G+
- pseudomonas aeruginosa: opportunistic pathogen, pink, straight, G-
- staphylococcus aureus: transient skin bacterium, violet, circle, G+
- coagulase negative staphylococcus: skin bacterium, violet, circle, G+
Murray - Medical Microbiology (7th): Chapter 12
2. Commensal Flora
- location: few in stomach/small intestine; many in colon/bowels ; skin
- mouth: straphylococcus aureus
- small intestine: increase of anaerobes (ie bacteroides, clostridium, enterococcus, lactobacillus,
candida)
- colon: E Coli, anaerobes - bifidobacteria, bacteroides, peptococcus, peptostreptococcus,
lactobacillus (least)
- urogenital: staphylococcus epidermis, staphylococcus aureus, propionibacterium
- metabolic activities:
- enterohepatic circulation: metabolites (bile acids) conjugated in liver are deconjugated in the
intestines by the flora
- fiber digestion
- vitamin (K, B12) synthesis
- carbohydrates (indigestible) fermented by bacteria to short chain fatty acids (which can then absorb
other nutrients)
- lactose intolerance: bacteria ferment lactose causing diarrhoea
- composition/distribution:
- mostly anaerobic bacteria (ie. anaerobic streptococci)
- derives from oropharynx
- cover mucosal epithelium
- control: gastric acid, bile acids, peristalsis prevent presence in small intestine; microflora produces
own antibacterial substances
- infection:
- stability prevents pathogens and overgrowth: competition/anti-microbicidial (ie. bactericides, short
chain fatty acids)
- examples:
- phyla: firmicutes, bacteroidetes, actinobacteria, proteobacteria
- bifidobacteria: regulate other bacteria, mediate immune responses, prevent tumour formation,
vitamin synthesis
- E Coli: synthesise vitamin K
, - lactobactilli: vitamin/nutrient production, boost immunity
3. Diarrhea - Bacterial Pathogens
- causes:
- most common: salmonella, shigella, campylobacter
- aeromonas, shigella, campylobacter -> higher incidence in summer/fall
- yersinia -> winter
- risk factors
- use of acid-suppressing medications
- epidemiology
- primary care and emergency department settings
- children < 5yrs
- underdeveloped/developing country
- females have higher incidence of Campylobacter infections and HUS
- yersinia infects only children <1yr ; aeromonas cause it in young children
- symptoms: large daily watery stools
- signs: fecal studies for appearance, volume, frequency, presence of blood, pH, presence of reducing
substances, WBC count ; blood test for serum WBC count
- characteristics to link to a pathogen:
- onset/duration of symptoms ; presence of vomiting ; presence of fever ; presence of abdominal pain
- diet ; water, animal exposure ; travel ; preexisting conditions
- physical findings: dehydration, malnutrition, abdominal pain, borborygmi, perianal erythema
- diagnosis: stool pH, presence of reducing substances, fecal WBC count, anti-listeriolysin O, presence
of pseudomembranes in the colon (C difficile), stool culture
- stool culture method:
- blood agar: aerobic bacteria/yeast
- MacConkey EMB agar: inhibit gram+ organisms
- XLD agar/HE agar: inhibit gram+ organisms and nonpathogenic gram- bacilli
- Skirrow agar: Campylobacter species
- SM agar: enterohemorrhagic E coli
- management
- oral rehydration or IV rehydration
- antimicrobial therapy
- diet: BRAT (banana, rice, applesauce, toast), lean meats, clear fluid
- bacteria specific
- aeromonas: cefixime, 3rd or 4th generation cephalosporins
- bacillus: none necessary for self-limited gastroenteritis ; vancomycin, clindamycin for severe
disease
- E. Coli: TMP-SMX if moderate/severe diarrhea ; systemic complications needs a parenteral
2nd/3rd generation cephalosporin
, - Salmonella: none for nontyphoid/uncomplicated diarrhea ; ampicillin or TMP-SMX,
fluoroquinolones, 3rd generation cephalosporins
- Shigella: none for mild infections ; ampicillin/drug-sensitive strain, TMP-SMX for
moderate/severe cases ; fluoroquinolones for resistant organisms
- campylobacter: erythromycin
- C difficile: discontinuance of causative antibiotics -> oral metronidazole -> vancomycin
- clostridium perfringens: none
- listeria: none unless invasive disease -> ampicillin and trimethoprim-sulfamethoxazole
- vibrio cholera: tetracycline -> TMP-SMX, erythromycin, doxycycline, chloramphenicol,
furazolidone
http://emedicine.medscape.com/article/176400-overview#a6
4. UTI - Pathogens
- types
- lower urinary tract = bladder infection (cystitis)
- upper urinary tract = kidney infection (pyelonephritis) -> see other notes
- cause
- most -> least common: E. Coli -> Staphylococcus saprophyticus -> viral, fungal infection
- healthcare-associated UTI involve more pathogens: E. Coli, klebsiella, pseudomonas, candida
albicans, enterococcus
- other: staphylococcus aureus is 2ndry to blood-borne infections
- risk factors:
- female anatomy (smaller urethra), sexual intercourse, diabetes, obesity, family history
- symptoms:
- pain on urination, frequent urination, feeling the need to urinate (despite empty bladder)
- diagnosis:
- in young women: based on symptoms alone
- urine culture (nitrites, WBC, leukocyte esterase), urine microscopy (RBCs, WBCs, bacteria)
- differential diagnosis: cervicitis, vaginitis, urethritis, prostatitis
- treatment
- uncomplicated cases: antibiotics (nitrofurantoin, trimethoprim/sulfamethoxazole)
- no antibiotics needed in patients with bacteria/WBC in urine but no symptoms
- antibiotic-resistance may exacerbate the condition
- complicated cases: long course antibiotics or IV antibiotics
- palliative: phenazopyridine
5. Skin Infection - Pathogens
- causes: Staphylococcus aureus, streptococcus pyogenes, enterococci, pseudomonas aeruginosa
- treatment
Case 1:
I. Bacteria
1. Types and Classification of Bacteria
- definition: prokaryote organism (nucloids) whose nutrient cycles releases toxins causing infection
- 2 - 0.2 micrometers (giardia lamblia - 25microm ; plasmodium (malaria) - 5microm)
- composition: nucleoid, capsule, ribosomes, cell membrane, cell wall, flagellum (optional); no
mitochondria/lysosomes/nuclear membrane
- classification: macro/micro appearance, growth/metabolic properties, antigenicity, genotype
- appearance: shape (cocci, coccobacillus, fusiform bacillus, vibrio, spirillum, spirochete, bacillus),
gram- or gram+
- gram negative vs gram positive
- gram positive: purple + rod
- gram negative: pink + circle
- gram + and gram -
- gram + is more sensitive to lysozymes, penicillin activity ; thicker cell wall
- only gram+ produce spores (not all)
- metabolic: anaerobic/aerobic/facultative/capnophilic, requirement for specific nutrients, production
of characteristic metabolic products/enzymes
- methods: experiment-type methods to reveal characteristics
- antigenicity: serotyping to identify characteristic antigens
- genetic: PCR, DNA hybridization
, - examples of bacteria:
- E Coli: commensal, rod, pink, G-, ferments lactose
- Candida albicans: yeast, violet, circle, G+
- pseudomonas aeruginosa: opportunistic pathogen, pink, straight, G-
- staphylococcus aureus: transient skin bacterium, violet, circle, G+
- coagulase negative staphylococcus: skin bacterium, violet, circle, G+
Murray - Medical Microbiology (7th): Chapter 12
2. Commensal Flora
- location: few in stomach/small intestine; many in colon/bowels ; skin
- mouth: straphylococcus aureus
- small intestine: increase of anaerobes (ie bacteroides, clostridium, enterococcus, lactobacillus,
candida)
- colon: E Coli, anaerobes - bifidobacteria, bacteroides, peptococcus, peptostreptococcus,
lactobacillus (least)
- urogenital: staphylococcus epidermis, staphylococcus aureus, propionibacterium
- metabolic activities:
- enterohepatic circulation: metabolites (bile acids) conjugated in liver are deconjugated in the
intestines by the flora
- fiber digestion
- vitamin (K, B12) synthesis
- carbohydrates (indigestible) fermented by bacteria to short chain fatty acids (which can then absorb
other nutrients)
- lactose intolerance: bacteria ferment lactose causing diarrhoea
- composition/distribution:
- mostly anaerobic bacteria (ie. anaerobic streptococci)
- derives from oropharynx
- cover mucosal epithelium
- control: gastric acid, bile acids, peristalsis prevent presence in small intestine; microflora produces
own antibacterial substances
- infection:
- stability prevents pathogens and overgrowth: competition/anti-microbicidial (ie. bactericides, short
chain fatty acids)
- examples:
- phyla: firmicutes, bacteroidetes, actinobacteria, proteobacteria
- bifidobacteria: regulate other bacteria, mediate immune responses, prevent tumour formation,
vitamin synthesis
- E Coli: synthesise vitamin K
, - lactobactilli: vitamin/nutrient production, boost immunity
3. Diarrhea - Bacterial Pathogens
- causes:
- most common: salmonella, shigella, campylobacter
- aeromonas, shigella, campylobacter -> higher incidence in summer/fall
- yersinia -> winter
- risk factors
- use of acid-suppressing medications
- epidemiology
- primary care and emergency department settings
- children < 5yrs
- underdeveloped/developing country
- females have higher incidence of Campylobacter infections and HUS
- yersinia infects only children <1yr ; aeromonas cause it in young children
- symptoms: large daily watery stools
- signs: fecal studies for appearance, volume, frequency, presence of blood, pH, presence of reducing
substances, WBC count ; blood test for serum WBC count
- characteristics to link to a pathogen:
- onset/duration of symptoms ; presence of vomiting ; presence of fever ; presence of abdominal pain
- diet ; water, animal exposure ; travel ; preexisting conditions
- physical findings: dehydration, malnutrition, abdominal pain, borborygmi, perianal erythema
- diagnosis: stool pH, presence of reducing substances, fecal WBC count, anti-listeriolysin O, presence
of pseudomembranes in the colon (C difficile), stool culture
- stool culture method:
- blood agar: aerobic bacteria/yeast
- MacConkey EMB agar: inhibit gram+ organisms
- XLD agar/HE agar: inhibit gram+ organisms and nonpathogenic gram- bacilli
- Skirrow agar: Campylobacter species
- SM agar: enterohemorrhagic E coli
- management
- oral rehydration or IV rehydration
- antimicrobial therapy
- diet: BRAT (banana, rice, applesauce, toast), lean meats, clear fluid
- bacteria specific
- aeromonas: cefixime, 3rd or 4th generation cephalosporins
- bacillus: none necessary for self-limited gastroenteritis ; vancomycin, clindamycin for severe
disease
- E. Coli: TMP-SMX if moderate/severe diarrhea ; systemic complications needs a parenteral
2nd/3rd generation cephalosporin
, - Salmonella: none for nontyphoid/uncomplicated diarrhea ; ampicillin or TMP-SMX,
fluoroquinolones, 3rd generation cephalosporins
- Shigella: none for mild infections ; ampicillin/drug-sensitive strain, TMP-SMX for
moderate/severe cases ; fluoroquinolones for resistant organisms
- campylobacter: erythromycin
- C difficile: discontinuance of causative antibiotics -> oral metronidazole -> vancomycin
- clostridium perfringens: none
- listeria: none unless invasive disease -> ampicillin and trimethoprim-sulfamethoxazole
- vibrio cholera: tetracycline -> TMP-SMX, erythromycin, doxycycline, chloramphenicol,
furazolidone
http://emedicine.medscape.com/article/176400-overview#a6
4. UTI - Pathogens
- types
- lower urinary tract = bladder infection (cystitis)
- upper urinary tract = kidney infection (pyelonephritis) -> see other notes
- cause
- most -> least common: E. Coli -> Staphylococcus saprophyticus -> viral, fungal infection
- healthcare-associated UTI involve more pathogens: E. Coli, klebsiella, pseudomonas, candida
albicans, enterococcus
- other: staphylococcus aureus is 2ndry to blood-borne infections
- risk factors:
- female anatomy (smaller urethra), sexual intercourse, diabetes, obesity, family history
- symptoms:
- pain on urination, frequent urination, feeling the need to urinate (despite empty bladder)
- diagnosis:
- in young women: based on symptoms alone
- urine culture (nitrites, WBC, leukocyte esterase), urine microscopy (RBCs, WBCs, bacteria)
- differential diagnosis: cervicitis, vaginitis, urethritis, prostatitis
- treatment
- uncomplicated cases: antibiotics (nitrofurantoin, trimethoprim/sulfamethoxazole)
- no antibiotics needed in patients with bacteria/WBC in urine but no symptoms
- antibiotic-resistance may exacerbate the condition
- complicated cases: long course antibiotics or IV antibiotics
- palliative: phenazopyridine
5. Skin Infection - Pathogens
- causes: Staphylococcus aureus, streptococcus pyogenes, enterococci, pseudomonas aeruginosa
- treatment
