Week 6 - Chemoorganotrophy and fermentation Flashcards

1
Q

Chemoorganotrophs

A

energy, electrons, and carbon all obtained by breaking down organic compounds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Chemoorganotrophs found wherever

A

there is a supply of organic compouds
tend to predominate wherever
a. there is a supply of organic compounds plus oxygen
b. there is a supply of organic compounds and no light (whether oxygen is present or not)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Examples of chemoorganotroph habitats

A

• soil (if light tends to be aerobic, in anaerobic is usually also dark)
• ocean sediments
• our bodies
eg on the skin (plenty of organic compounds, oxygen)
in our guts (may be anaerobic, but also dark)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

All significant pathogens are

A

chemoorganotrophs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Glycolysis

the Embden-Meyerhof pathway

A

Glucose + 2ADP + 2 Pi + 2NAD+
–>
2 pyruvate + 2ATP + 2 NADH + 2H+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Glycolysis is common to

A

respiratory and fermentative metabolism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Glycolysis overall production

A

2 ATP and 2 NADH per glucose molecule

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Significant further oxidation of pyruvate also requires

A

an electron acceptor - eg oxygen

• in the absence of an electron acceptor == fermentation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Fermentation is basically a way of

A

removing excess carbon and electrons in the cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Because of the small amount of energy released by glycolysis

A

not all the carbon and electrons can be used for anabolic reactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Examples of fermentation

A

lactic fermentation
• Streptococcus
• Lactobacillus

ethanolic fermentation
• yeasts
• some bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Lactic fermentation

A

pyruvate –> lactate

NADH –> NAD+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Ethanolic fermentation

A

pyruvate –> acetaldehyde
gives off CO2

acetaldehyde –> ethanol
NADH –> NAD+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Other fermentation pathways lead to production of

A

Propionic acid
• Propionibacterium

Butanediol
• Enterobacter

Butyric acid etc
• Clostridium

Acetic acid + formic acid + ethanol
• many enteric bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Many of the classic tests for bacteria are based on

A

fermentation products

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Fermentation is NOT THE SAME AS

A

anaerobic respiration

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

In aerobic respiration

A

pyruvate is oxidized further

eg the tricarboxylic acid cycle (aka citric acid or Krebs cycle)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Tricarboxylic acid cycle

aka citric acid or Krebs cycle

A

pyruvate is oxidized further

Pyruvate + 4NAD+ + FAD
–>
3CO2 + 4NADH + FADH

1 ATP formed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

After the tricarboxylic acid cycle

A

the NADH and FADH are re-oxidized by the respiratory electron transport chain - located in the plasma membranes of aerobically growing bacteria

eg
2 NADH + O2 + 2H+
–>
2NAD+ + 2 H2O

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

For every NADH oxidized

A

up to 3 molecules of ATP formed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

For every FADH oxidized

A

up to 2 molecules of ATP formed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

For every glucose molecule oxidized

A

38 molecules of ATP form
2 ATP/glucose from fermentatin

glycolysis makes pyruvate
pyruvate through fermentation OR
pyruvate oxidized futher (aerobic respiration - tricarboxylic acid cycle / Krebs / citric acid cycle)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Examples of chemoorganotrophs

A
  • E. coli
  • Pseudomonas sp.
  • Streptococcus pyogenes
  • Mycobacterium tuberculosis
  • Bdellovibrio
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

E. coli is

A

a gram negative eubacterium
• motile - flagella enable it to swim toward food sources
• able to live on a range of sugars etc - aerobic metabolism on the presence of oxygen, but switches to fermentation when oxygen is scarce

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

E. coli’s natural habitat is

A

in the colon of animals
• an enterobacterium
• also found in sewage-polluted water, contaminated food, etc

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

E. coli’s activities in the colon

A

• converts food nutrients into bacterial biomass
• uses oxygen - maintains anaerobic conditions in the lower colon
• produces vitamin K
• may cause disease (occasionally fatal)
- diarrhoea
• septicaemia
• urinary tract infection

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Pathogenic strains of E. coli

A

produce toxins and often have fimbrae
• eg strains responsible for traveller’s diarrhea have genes coding for 2 polypeptide toxins, and genes coding for adhesive fimbrae that allow colonization of the small intestine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

E. coli –>

A

diarrhoea

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Infectious diarrhoea

A
  • 3-5 billion episodes yearly
  • major cause of worldwide morbidity and mortality
  • 5 million deaths yearly - 80% are <1 year old
  • major cause of school/work absenteeism
  • major economic burden, especially in developing countries
  • bacteria cause 80% of foodborne diarrhoea
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Infectious diarrhoea

organisms

A

Bacteria
• E. coli, Salmonella, Campylobacter, Vibrio, Yersinia, Clostridium difficle, S. aureus, B. cereus, C. botulinum

Viruses
• Norovirus, Rotavirus, CMV

Parasites
• Giardia, Amoeba, Ascaris

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

These organisms cause diarrhoea through a wide variety of mechanisms

A
pathophysiology
• osmotic
• secretory
• exudation
• abnormal motility
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Daily intake and endogenous secretions are

A

efficiently absorbed by the gastrointestinal tract

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Osmotic diarrhoea

A

increased amounts of poorly absorbed, osmotic active solutes in gut lumen
• interferes with absorption of water
• solutes are ingested (FASTING STOPS DIARRHOEA)
- magnesium sulfate, citrate, or magnesium containing antacids
- sorbitol
- malabsorption of food (variety of infectious organisms, particularly viruses but including E. coli)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Secretory diarrhoea

A

excess excretion of electrolytes and water across mucosal surface
• usually coupled with inhibition of absorption
• clinical features
- stool is very watery
- stool volume large

FASTING DOES NOT STOP DIARRHOEA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Diarrhoea associated with active secretory processes (secretory diarrhoea) can be caused by stimuli from 3 sources

A
  • mucosal/submucosal stimuli
  • blood hormone stimuli
  • liminal stimuli
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q
Secreotry diarrhoea 
(organisms)
A
bacterial or viral enterotoxins
• Vibrio cholerae
• Noncholeraic vibrios
• enterotoxigenic E. coli
• B. cereus
• S. aureus
• others: Rotavirus, Norovirus
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Exudative diarrhoea

A
  • intestinal or colonic inflamed and ulcerated

* the extent and location of bowel involved determines severity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Common syndromes of infectious diarrhoea

A
• food poisoning
• acute watery diarrhoea
 - travelers diarrhoea
 - epidemics
• acute bloody diarrhoea
 - dysentery
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Special circumstances

A
  • outbreaks/food poisoning
  • overseas travel
  • immunocompromised host
  • raw seafood ingestion
  • antibiotic usage
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

E. coli O157:H7

A

1982 - first recognized as a pathogen
1985 - associated with hemolytic uremic syndrome
1990 - outbreak from drinking water
1991 - outbreak from apple cider
1993 - multi-state outbreak from fast food hamburgers
1995 - outbreak from fresh produce
1996 - outbreak in Japan, multi-state outbreak from unpasteurized apple juice

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

E. coli 0157

A

petting zoos

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

E. coli 0157 case history

A
  • onset and duration of diarrhoea
  • timing of exposure to potential pathogens: travel, ingestion history, environment, recent medications (antibiotics), age
  • character of stool: volume, presence of blood, mucus, or pus
  • associated symptoms and signs: abdominal pain, fever, vomiting, dehydration
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

E. coli 0157

physical examination

A
  • vital signs: fever, tachycardia
  • abdominal tenderness or pain
  • signs of dehydration
  • blood, mucus, or pus in stool
44
Q

Type 1

A

separate hard lumps, like nuts (hard to pass)

45
Q

Type 2

A

sausage-shaped but lumpy

46
Q

Type 3

A

like a sausage but with cracks on the surface

47
Q

Type 4

A

like a sausage or snake, smooth and soft

48
Q

Type 5

A

soft blobs with clear-cut edges

49
Q

Type 6

A

fluffy pieces with ragged edges, a mushy stool

50
Q

Type 7

A

watery, no solid pieces, entirely liquid

51
Q

E. coli cow ingestion cycle

A
  1. ingestion of pathogenic E. coli
  2. fecal excretion + contamination of environment
  3. contamination of food + transmission animal to person + transmission person to person
  4. colonization of the large intestine + intimate attachment to epithelial cells
  5. transport of toxin to circulation
  6. bloody diarrhoea + kidney failure
52
Q

Classification

A

chromogenic media

53
Q

E. coli O157 chromogenic media classification

A
  • sorbitol-fermenting bacteria such as most E. coli appear as pink to red colonies
  • on Rainbow Agar O157 or R&F E. coli O157 should appear as black to blue-black colonies
54
Q

Serotyping

A

pathgenic E. coli may also be differentiated by serotyping based on antigenic differences in
• the O antigen of the LPS
• in the flagellar or H antigens
• and the fimbral or F antigens

55
Q

EC virotype classification

A

each class falls within a serological subgroup and manifests distinct features in pathogenesis
• ETEC: enterotoxigenic
• EHEC/STEC: enterohaemorrhagic / Shiga toxin
• EIEC: enterinvasive
• EAEC/AEEC: enteoaggrigative / attach effacing
• EPEC: enteropathogic

56
Q

A pathogenic E. coli within each pathotype may be further classified as

A

virotypes, based on the virulence gens that they possess

57
Q

Virotype

A

combination of virulence genes

58
Q

Important virulence factors encoded by these genes include

A
  • fimbrial adhesins
  • enterotoxins
  • cytotoxins
  • capsule
  • lipopolysacccharide (LPS)
59
Q

Virotype/pathotype

ETEC

A
  • watery diarrhoea, travelers diarrhoea

* complications rare

60
Q

Virotype/pathotype
EHEC or STEC
(Shiga toxin 1 and 2)

A
  • bloody diarrhoea

* haemolytic uremic syndrome HUS (mostly O157:H7)

61
Q

Virotype/pathotype

EIEC

A
  • bloody diarrhoea, dysentery

* complications rare

62
Q

Virotype/pathotype

EAEC

A
  • watery diarrhoea or bloody diarrhea, mainly in children

* may be protracted

63
Q

Virotype/pathotype

EPEC or AEEC

A
  • watery, sometimes bloody diarrhoea

* leading cause of infant diarrhoea

64
Q

ET (toxigenic) E. coli produces LT and ST

A
  • produces a heat-labile enterotoxin (LT) similar to the cholera toxin (Ctx)
  • ETEC can also produce a heat stabile toxin (ST) - this causes an increase in cyclic GMP in host cell. ST binds and activates guanylate cyclase on the membranes of host cels. this leads to secretion of fluids and electrolytes resulting in diarrhoea
  • ETEC adhesins are fimbral adhesins - adhere to receptors on the small intestine
  • symptoms ETEC infections include diarrhoea without fever
  • the bacteria colonize the GI tract by means of a fimbral adhesin, and are noninvasive, but produce either LT or ST toxin
65
Q

ETEC process

A
  1. ingestion of pathogenic E. coli
  2. colonization of the jejunum and ileium
  3. water and electrolytes
  4. diarrhea, weight loss, death
66
Q

ETEC

A

surface doesn’t change much, adheres to gut

• delivery of LT or ST enterotoxins

67
Q

EI (invasive) EC

A
  • penetrate and multiply within epithelial cells of the colon causing widespread cell destruction
  • the clinical syndrome is identical to Shigella dysentery and includes a dysentery-like diarrhoea with fever
  • EIEC apparently lack fimbral adhesins but do prossess a specific adhesin that, as in Shigella, is thought to be an outer membrane protein
  • they do not produce LT or ST toxin
68
Q

EIEC

A
surface of host destroyed by toxins, sink and absorbed, horizontal transfer
• invasion
• phagosomal rupture
• intracellular movement
• lateral spread to adjacent cell
69
Q

EP (pathogenic) EC

A

• pathogenesis of EPEC involves
- plasmid-encoded protein referred to as EPEC adherence factor (EAF) that enables localized adherence of bacterial to intestinal cells and
- a non fimbral adhesin designated intimin, whis is an outer membrane protein that mediates the final stages of ahderence
• they do not produce ST or LT toxins
• EPEC strains adhere to the intestinal mucosa, they produce changes in the ultrastructure of the cells
• they cause inflammatory response
• the diarrhoea and other symptoms of EPEC infections are caused by invasion NOT toxins

70
Q

EPEC (picture)

A

adhere (fimbrae), toxins kill flagella, inject agent into cell
• initial adherence via BFP
• intimate attachment
• actin condensation and microvillous effacement

71
Q

EAEC

A
  • strains attach to tissue culture cells in an aggregative manner
  • these strains are associated with persistent diarrhoea in young children
  • they resemble ETEC strains in that the bacteria adhere to the intestinal mucosa and cause non-bloody diarrhoea without invading or causing inflammation
  • the organisms produce an enterotoxin. a heat-labile plasmid-encoded toxin has been isolated from these strains, called the EAST (EnteroAggregative ST) toxin
  • they also produce a haemolysin related to the haemolysin prooduced by E. coli strains involved in urinary tract infections
  • the role of the toxin and the haemolysin in virulence has not been proven, the significance of EAEC strains in humans is controversial
72
Q

EAEC

A

knocked out all flagella, sits on surface, toxin goes into cell
• aggregative adherence
• mucus biofilm
• delivery of cytotoxin

73
Q

STEC / EH (haemohorrhagic) EC

A
  • EHEC causes bloody diarrhoea, which can progress to the potentially fatal haemolytic uremic syndrome (HUS)
  • EHEC are characterized by the production of verotoxin or Shiga toxins (Stx). Although Stx1 and Stx2 are most often implicated in human illness, several variants of Stx2 exist
  • O157:H7 is the prototypic EHEC and most often implicated in illness worldwide
  • the infectious dose for O157:H7 is 10-100 cells
  • EHEC infections are mostly food or water borne
74
Q

STEC Edema disease

A
  1. ingestion of pathogenic E. coli
  2. colonization of the jejunum and ileum
  3. transport of toxin to circulation
  4. edema, ataxia, death
75
Q

EHEC

A

toxin through cell to blood stream –> kills you
• Shiga toxin kills flagella, shiga toxin through cell –> blood
• intimate attachment of bacteria
• actin condensation and microvillous effacement
• delivery of shiga toxin

76
Q

EcL approach to identification of pathogenic E. coli

Sample analysis

A
  • sample
  • enrichment (over night)
  • multiplex PCR
  • rapid evaluation of the virulence potential of the sample (pathotype)
77
Q

EcL approach to identification of pathogenic E. coli

Isolate analysis

A
  • E. coli isolates
  • agar plates
  • virotyping (multiplex PCR or colony hybridization)
  • serotyping
  • pulse typing (PFGE)
  • identification and virotyping of the isolate
78
Q

Alcohol gels are NOT effective against E. coli in the presence of

A

feces

79
Q

Pseudomonas - versatile, ecologically important

A
  • Pseudomonas species are aerobic
  • gram negative rods
  • motile because of flagellae
  • significant in the environment and also the cause of plant and animal diseases
  • opportunistic infections
  • versatile metabolism - able to use many different organic compounds as carbon and energy sources
80
Q

Pseudomonas - versatile metabolism

A

able to use many different organic compounds as carbon and energy sources

81
Q

Example of versatility

Pseudomonas aeroginosa

A
  • primarily a soil microbe

* is also a serious opportunistic pathogen - infects wounds, abcesses, burns, etc

82
Q

Streptococcus pyogenes

A
  • gram positive
  • forms chains
  • can grow aerobically or anaerobically
  • responsible for numerous infections
83
Q

Erysipelas

A
  • infection of the dermal layer of the skin with Streptococcus pyogenes
  • produces toxins and breaks down host tissue
84
Q

Respiratory diseases

A
  • infections of the upper respiratory system are the most common type of infection
  • pathogens that enter the respiratory system can infect other parts of the body
85
Q

Tuberculosis

A

• bacterial disease of the lower respiratory system

86
Q

Tuberculosis

pathogenesis

A

M. tuberculosis can remain viable for long periods in aerosol drops
• 3 types of tuberculosis
- primary tuberculosis - initial case of tuberculosis disease
- secondary tuberculosis - reestablished tuberculosis
- disseminated tuberculosis - tuberculosis involving multiple systems

87
Q

Primary tuberculosis

A

initial case of tuberculosis disease

88
Q

Secondary tuberculosis

A

reestablished tuberculosis

89
Q

Disseminated tuberculosis

A

tuberculosis involving multiple systems

90
Q

Tuberculosis epidemiology

A
  • immunocompromised individuals are most at risk

* tuberculosis is the leading killer of IHV+ individuals

91
Q

The pathogenesis of tuberculosis

A
  1. tubercle bacilli that reach the alveoli of the lung are ingested by macrophages, but often some survive. Infection is present, but no symptoms of disease
  2. Tubercle bacilli multiplying in macrophages cause a chemotactic response that brings additional macrophages and other defensive cells to the area. These form a surrounding layer and, in turn, an early tubercle. Most of the surrounding macrophages are not successful in destroying bacteria but release enzymes and cytokines that cause a lung-damaging inflammation
  3. after a few weeks, disease symptoms appear as many of the macrophages die, releasing tubercle bacilli and forming a caseous center in the tubercle. the aerobic tubercle bacilli do not grow well in this location. However, many remain dormant (latent TB) and serve as a basis for later reactivation of the disease. The disease may be arrested at this stage, and the lesions become calcified.
  4. In some individuals, disease symptoms appear as a mature tubercle is formed. The disease progresses as the caseous center enlarges in the process called liquefaction. The caseous center now enlarges and forms an air-filled tuberculous cavity in which the aerobic bacilli multiply outside the macrophages
  5. Liquefaction continues until the tubercle ruptures, allowing bacilli to spill into a bronchiole and thus be disseminated throughout the lungs and then to the circulatory and lymphatic systems
92
Q

Mycobacterium tuberculosis VNTR typing

A
  • the ability to link related cases of tuberculosis (TB) infection and exclude unrelated cases in important for epidemiologiology
  • various methods can be used to track spread of infection and DNA typing of M. tuberculosis cases has recently focused on Variable Number Tandem Repeat (VNTR) DNA sequences as markers in the genome that show variation between unrelated strains
  • VNTR- PCR amplification is a method that involves amplifying the DNA using PCR primers in the sequences flanking this region to detectable levels. The number of tandem repeat units can be determined from the size of the PCR product using various methods (including automated fragment analysis and gel electrophoresis)
93
Q

Various methods can be used to track spread of infection and DNA typing of M. tuberculosis cases has recently focused on

A

Variable Number Tandem Repeat (VNTR) DNA sequences as markers in the genome that show variation between unrelated strains

94
Q

VNTR-PCR amplification is a method that involves

A
  • amplifying the DNA using PCR primers in the sequences flanking this region to detectable levels
  • the number of tandem repeat units can be determined from the size of the PCR product using various methods (including automated fragment analysis and gel electrophoresis)
95
Q

TB

A
  • about 1/3 of the world’s population is infected with Mycobacterium tuberculosis
  • it is estimated that currently there are about 10 million new cases of TB every year with 3 million deaths occurring world-wide
  • death from TB comprise 25% of all avoidable deaths in developing countries
  • in India TB has the greatest incidence
96
Q

About 1/3 of the world’s population is infected with

A

Mycobacterium tuberculosis

97
Q

It’s estimated that currently there are about

A

10 million new cases of TB every year with 3 million deaths occurring world-wide

98
Q

death from TB comprise

A

25% of all avoidable deaths in developing countries

99
Q

Benefits of TB genotyping

A

When combined with epidemiologic data
Confirm epidemiologic links
• outbreaks detected earlier - controlled more rapidly
• detect unsuspected transmission
• transmission between patients living in different jurisdictions are detected more readily
• detect or confirm false positive cultures
• able to monitor progress toward the elimination of TB transmission

100
Q

The biggest bacterial killer of all Homo sapiens

A

Mycobacterium tuberculosis

1.5-3 million deaths per year

101
Q

Mycobacterium tuberculosis

x deaths per year

A

1.5-3 million deaths per year

102
Q

Mycobacterium tuberculosis

A
  • 1-5 - 3 million deaths per year
  • gram-positive
  • aerobic eubacterium
  • first isolated and identified as the cause of tuberculosis by Robert Koch (1880s) - Nobel Prize 1905
103
Q

M. tuberculosis invades lung tissue

A

• cells often survive being engulfed by macrophages
and can grow and divide inside macrophage cells
• destruction of lung tissue can eventually lead to death
• infection spread from individual to individual by coughing (infection can also be contracted from contaminated milk)
• treatment with a cocktail of chemotherapeutic agents and antibiotics
• but resistant strains are an increasing problem in some regions - high rate of spontaneous mutations
• genome now sequenced - hope for development of new chemotherapeutic agents

104
Q

M. tuberculosis - infection spread from individual to individual by

A

coughing

• infection can also be contracted from contaminated milk

105
Q

M. tuberculosis - resistant strains

A

an increasing problem in some regions

• high rate of spontaneous mutation

106
Q

Bdellovibrio bacteriovorus

A
  • gram-negative
  • aerobic
  • curved rod
  • with a flagellum
  • small, highly motile cells
  • widespread in soil and water
  • bacterial predator - enters the periplasm of other bacteria, eats them from the inside, reproduces in the carcass
107
Q

Enters the periplasm of other bacteria, eats them from the inside, reproduces in the carcass

A

Bdellovibrio bacteriovorus