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year 1 > GI - microbiology > Flashcards

GI - microbiology Flashcards

1
Q

what is the first line treatment of gastroenteritis

A

rehydration

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2
Q

what is gastroenteritis

A

inflammation of stomach/intestines

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3
Q

what organisms are the most common cause of infective gastroenteritis

A

viruses

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4
Q

how do bacteria cause GE

A

invade tissues of GI tract and produce toxins

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5
Q

define diarrhoea

A

3+ loose stools in 24 hours

stool holds shape of container

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6
Q

what is considered acute diarrhoea and what is chronic

A

acute < 2 weeks

chronic > 4 weeks

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7
Q

What kind of infection is Giardia Lambia

A

protozoan - single parasite infection
cysts are ingested and hatch into trophozoites
trophozoites colonise upper small bowel mucosa

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8
Q

How is giardia lambia spread

A

cysts in water
travel to areas of contaminated water supply
swimming in ponds

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9
Q

can giardia lambia be spread person-person

A

yes

- also, human only infection

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10
Q

how is giardia lambia diagnosed

A

Lab: stool microscopy for ova/parasites/cysts
3 separate samples
duodenal aspirate is best

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11
Q

what is the treatment for giardia lambia

A

metronidazole 1 week

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12
Q 
diarrhoea (often explosive, foul smelling)
flatulence
anorexia
abdominal cramps
epigastric pain
nausea
vomiting
malabsorption (steatorrhoea, weight loss)
A

symptoms of giardia lambia

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13
Q

give 2 organisms that cause small bowel bacterial overgrowth

A

E.Coli

Bacteriodes (gram negative, anaerobic, bacilli)

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14
Q

how is SBBO diagnosed

A

low cobalamin and high folate
culture on jejunal aspirate obtained by intubation - aerobic +/- anaerobic bacteria present
Schilling test

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15
Q

what is the treatment of SBBO

A

tetracyclines (2-3 weeks)

surgical correction

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16
Q

when is SBBO seen

A 
diverticula
fistulas
strictures related to Crohn's
bypass surgery
functional stasis
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17
Q

diarrhoea
steatorrhoea
macrocytic anaemia

A

symptoms SBBO

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18
Q

what food is scombroid associated with

A 
dark meat/fish in tropical areas
tuna
mahi mahi sushi
tinned tuna
poorly stored fish
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19
Q

Scombroid involves a preformed toxin

true/false

A

true

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20
Q

what is the incubation period of scombroid

A

1-6 hours

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21
Q

what kind of reaction is scombroid poisoning

A

histamine like reaction

rash, headache, shock

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22
Q

what is T1 on the bristol stool chart

A

separate hard lumps like nuts

hard to pass

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23
Q

what is T2 on the bristol stool chart

A

sausage shaped but lumpy

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24
Q

what is T3 on the BSC

A

like a sausage but with cracks on surface

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25
Q

T4 BSC

A

like a sausage or snake

smooth and soft

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26
Q

T5 BSC

A

soft blobs with clear cut edges

passed easily

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27
Q

T6 BSC

A

fluffy pieces with ragged edges, a mushy stool

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28
Q

T7 BSC

A

water, no solid pieces

entirely liquid

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29
Q

what is the incubation period of staph aureus, bacillus cerues

A

1-6 hours

short

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30
Q

what is the incubation period of salmonella, C. perfringens

A

12-48 hours

medium

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31
Q

what is the incubation period of campylobacter, E. Coli 0157

A

2-14 days
long
(16-48 hours usually)

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32
Q

what is the most common cause of diarrhoea in the UK

A

campylobacter

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33
Q

campylobacter is…

A

curved
gram negative
bacilli

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34
Q

what is the source of campylobacter

A 
you CAMP at a farm
farm animals - esp undercooked poultry
milk products
cheese
water
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35
Q

what is a complication of campylobacter

A

gillian barre

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36
Q

what is gillian barre

A

immune system attacks PNS - tingling of feet progresses to paralysis

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37
Q

how are outbreaks of campylobacter caused

A

people exposed to the same source

i.e. not human - human

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38
Q

central abdominal pain
diarrhoea +/- blood
may mimic appendicitis

A

symptoms of campylobacter

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39
Q

how is campylobacter diagnosed

A

stool culture

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40
Q

what is the treatment of campylobacter

A

self limiting
clarithromycin if immunosuppressed
erythromycin or ciprofloxacin if systemic illness

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41
Q

what are some s/s that campylobacter has caused a systemic illness

A

fevers
rigors
flu-like symptoms

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42
Q

salmonella is ….

A

gram negative
bacillus
enterobacteria

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43
Q

who is at risk of bacteraemia from salmonella

A

HIV
sickle cell
AIDs
recent cryptosporidium

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44
Q

what antigen does salmonella possess

A

O antigen

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45
Q

what is the source of salmonella

A

undercooked poultry
raw eggs
less common due to chicken immunity

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46
Q

what is the treatment of salmonella

A

self limiting

ciprofloxacin 5 days if systemic illness/risk of

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47
Q

what is the incubation period of salmonella

A

12-48 hours

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48
Q

how is salmonella diagnosed

A

stool culture

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49
Q

where does salmonella cause inflammation

A

ileum and colon
salmonella grows in animal gut and multiplies in food - then multiply in gut and cause mucosal damage - decreasing fluid absorption and increasing fluid secretion

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50
Q

where does campylobacter cause inflammation

A

colon and rectum

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51
Q

how does salmonella cause GE

A

invades tissue of GI tract and produces toxin

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52
Q

abdominal pain
diarrhoea (occasionally bloody)
vomiting

A

s/s salmonella

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53
Q

can shigella spread person-person

A

yes

also - human only infection

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54
Q

how is shigella diagnoses

A

stool culture

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55
Q

why is shigella not seen in blood cultures

A

invades intestinal mucosa and causes severe inflammation but no further

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56
Q

what is the treatment of shigella

A

ciprofloxacin if severe

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57
Q

what is a complication of shigella

A

HUS

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58
Q

where is shigella often seen

A

cohorts of children

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59
Q

can salmonella cause outbreaks

A

yes

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60
Q

shigella is…

A

gram negative

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61
Q

what is the incubation period of E. Coli

A

16 - 48 hours

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62
Q

what kind of antigen does E. Coli possess

A

O antigen on surface

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63
Q

E. Coli is …

A

gram negative

coliform

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64
Q

what toxin does E. Coli produce

A

verotoxin (VTEC) (shiga-like toxin)

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65
Q

how does VTEC work

A

binds to cell receptors found on renal and red blood cells

inhibits protein synthesis and causes cell death

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66
Q

what is a major complication of E. Coli

A

HUS

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67
Q

what should be avoided in HUS

A

antibiotics
NSAIDs
anti motility agents

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68
Q

what is HUS

A

haemolytic uraemic syndrome - increased blood urea, red cell haemolysis, thrombocytopaenia
pre-hepatic jaundice

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69
Q

what are some s/s of HUS

A 
abdominal pain
petechiae
fever
pallor
BLOODY DIARRHOEA (e.coli in general)
oliguria
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70
Q

what is petechiae

A

small haemorrhage of blood vessels

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71
Q

what is the source of E. Coli

A 
beef 
minced meat
burgers (not so much steak)
raw milk
soy nut butter
visits to farms
private untreated water sources
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72
Q

can E. coli be spread person - person

A

yes

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73
Q

can E. coli cause outbreaks

A

yes

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74
Q

who is most at risk of HUS

A

children and elderly

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75
Q

E. coli is the commonest cause of renal failure in children <5 in the UK
true/false

A

true

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76
Q

what do the bloods of E.Coli show

A 
increase WCC
low platelets
low Hb
RBC fragments
increased LDH
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77
Q

does e.coli 0104 produce verotoxin

A

yes but less toxic

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78
Q

what does VTEC show in agar

A

agglutination

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79
Q

what is the treatment of E. Coli

A

supportive

NO ABs

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80
Q

what is the cause of enteric fever/typhoid/paratyphoid fever

A

salmonella typhi

salmonella paratyphi A and B

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81
Q 
fever initially then diarrhoea (green)
fever and rigors
headache
rose spots on abdomen
constipation
dry cough
A

s/s enteric fever

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82
Q

what is the treatment for enteric fever

A

depends on sensitivities
azithromycin (uncomplicated)
ceftriaxone IV (severe)
possibly fluoroquinolone e.g. ciprofloxacin but resistance common

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83
Q

what are some complications of enteric fever

A

GI bleeding
GI perforation
encephalopathy
bone/joint infection - osteomyelitis

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84
Q

how is enteric fever diagnosed

A

blood culture

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85
Q

what is the incubation period of salmonella type/paratyphi

A

14-21 days

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86
Q

when is enteric fever seen in the UK

A

when imported from india, SE asia, far/middle east, Africa

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87
Q

how is enteric fever spread

A

person-person
- human only infection
drinking/eating contaminated food/water
poor sanitation

88
Q

where does bacteria stay in chronic carriers of enteric fever

A

gall bladder

89
Q

what causes cholera

A

vibrio cholerae

90
Q

vibrio cholerae is…

A

gram negative
small
bacillus

91
Q

what is a BUZZWORD symptom of cholera

A

rice water stools - profuse water diarrhoea

92
Q

what does the toxin of cholera cause

A

release of water from small intestine cells

93
Q

when is cholera seen

A

water/disasters

refugee camps

94
Q

cholera causes outbreaks

true/false

95
Q

what is the incubation period of cholera

96
Q

what is the treatment of cholera

A

fluid/electrolyte replacement

no ABs

97
Q

what organism commonly causes infection in CREAM BUNS

A

staph aureus

98
Q

staph aureus infection involves a preformed toxin

true/false

A

true - food contaminated and left - allowed bacterial replication and exotoxin production

99
Q

where does the toxin of staph aureus work

A

vagus nerve and vomiting centre

100
Q

what is the incubation period of staph aureus

101
Q

s/s staph aureus

A

diarrhoea NO BLOOD

102
Q

clostridium perfringens is…

A

gram positive
large
bacillus
anaerobic

103
Q

C. perfringens infection involves a preformed toxin

true/false

104
Q

what is c. perfringens associated with

A

poorly refrigerated/re-heated MEAT GRAVY

105
Q

how does C. perfringens cause infection

A

produces cooking resistant spores that grow after cooking and produce enterotoxin

106
Q

what is the incubation period of c. perfringens

A

medium

12-48 hours

107
Q

what organism is associated with poorly refrigerated/reheated RICE (starchy food)

A

bacillus cereus

108
Q

what is a s/s of bacillus cereus

A

diarrhoea NO BLOOD

109
Q

bacillus cereus is …

A

gram positive
large
aerobic bacillus

110
Q

bacillus cereus infection involves a preformed toxin

true/false

111
Q

how does bacillus cereus cause infection

A

exotoxin ingested or produced by bacteria in gut after infection - spores survive cooking, sporulate and produce exotoxin

112
Q

what kind of organism is cryptosporidium

A

protozoan - single organism infection

113
Q

how does cryptosporidium cause infection

A

ingested cysts hatch into trophozoites which invade small intestinal enterocytes

114
Q

what is the source of cryptosporidium

A

domestic animals esp. calves

contaminated water - swimming pools (cysts are chlorine resistant)

115
Q

can cryptosporidium be spread person-person

116
Q

how is cryptosporidium diagnosed

A

duodenal aspirate / stool sample

cryptosporidium stains with Ziehl Neelsen

117
Q

s/s cryptosporidium

A

diarrhoea

particularly bad in HIV

118
Q

how is trypanasoma cruzi transmitted

american trypanosomiasis - Chaga’s Disease

A

kissing bug - Triatome

119
Q

what does trypanasoma cruzi cause

A

parasympathetic denervation - affects colon and oesophagus –> megaoesophagus

120
Q

What kind of infection is enterobius vermicularis

A

thread worms

tiny white worms in stool

121
Q

where are thread worms seen

A

families - children infect family

122
Q

where do thread worm eggs hatch

123
Q

where do thread worm eggs live

A

caecum/colon

124
Q

where do the adult female threadworms lay eggs

A

perianal skin at night

125
Q

how are the thread worm eggs ingested

A

perianal itch - fingers infected - mouth

126
Q

what is the treatment of threadworms

A

oral mebendazole
often treat all members of family

sounds like Me - bend - over (perianal area)

127
Q

thread worms are a human only infection

true/false

128
Q

what are the s/s of thread worms

A

worms in stool

perianal itch

129
Q

length of presenting complaint of helminths tends to be much longer
true/false

130
Q

what immune cells are involved in helminth infection

A

eosinophils

131
Q

how are helminth infections diagnosed

A

worms/eggs in stool

132
Q

what are nematodes

A

round worms

133
Q

what kind of nematodes infect the intestine

A

ascariasis

134
Q

what kind of nematodes infect the tissues/lymph

A

filariasis

135
Q

what are trematodes

136
Q

how does one catch schistosomiasis (type of fluke)

A

fresh water exposure

137
Q

what are some s/s chronic schistosomiasis infection

A

hepatomegaly
liver fibrosis
portal hypertension

138
Q

give an example of a liver fluke and where are they seen

A

clonorchis
Fasciola
SE asia

139
Q

what are cestodes

A

tape worms

140
Q

what food is taenia solium associated with (cestode)

what is another way of infection

A

undercooked pork
autoinnoculation
human faeces

141
Q

what food is saginatum associated with (cestode)

A

undercooked beef

142
Q

how do cestodes cause infection

A

larval cysts in undercooked meat

143
Q

what do the eggs of taenia solium cause

A

cysticercosis - tissue cysts in muscle/brain

144
Q

what virus is the cause of the winter vomiting disease

145
Q

what are some s/s of norovirus

A

explosive diarrhoea and vomiting

146
Q

who does norovirus affect

147
Q

can norovirus cause outbreaks

A

yes - family/community outbreaks

CRUISE SHIPS

148
Q

how is norovirus diagnosed

A

PCR on vomit swab or faeces specimen

149
Q

how long does PCR usually take

150
Q

what is the treatment of norovirus

A

rehydration

151
Q

what is the route of spread of norovirus

A

faecal-oral
waterborne (droplet)
shellfish

152
Q

what is the incubation period of norovirus

A

short, often < 24 hours

153
Q

how long should you stay off work after symptoms of norovirus stop

154
Q

norovirus survives on fomites for days-weeks

true/false

155
Q

what is the most common cause of D and V in children under 3 years

156
Q

what is the route of spread of rotavirus

A

person-person

faecal oral

157
Q

what are some s/s of rotavirus

A

diarrhoea NO BLOOD

158
Q

how is rotavirus diagnosed

A

PCR of faeces

159
Q

what is the treatment of rotavirus

A

rehydration (orally where possible)

160
Q

what kind of vaccine is available for rotavirus and when is it given

A

live attenuated
oral
2 doses at 2/3 months old

161
Q

what kind of infection is amoebiasis

162
Q

what causes amoebiasis

A

entamoeba histolytica

163
Q

where is amoebiasis seen

A

areas of poor sanitation

164
Q

what is the treatment of amoebiasis

A

metronidazole

+ diloxanide furoate/paromomycin to clear gut

165
Q

what is the route of spread of amoebiasis

A

faecal oral

by ill/asymptomatic carrier

166
Q

acute bloody diarrhoea
fever
abdominal pain
may mimic acute colitis

A

s/s amoebiasis

167
Q

how is amoebiasis diagnosed

A

hot stool microscopy/culture for ova/cysts

168
Q

what is a complication of amoebiasis

A

amoebic liver abscess

169
Q

amoebic liver abscess is more common in males

true/false

170
Q 
fever
cough
aching abdominal pain
hepatomegaly
raised RHD on CXR
large opacity over right lung base
abnormal LFTs
A

s/s amoebic liver abscess

171
Q

what are some investigations done for amoebic liver abscess

A

serology

U/S, CT, CXR, LFTs

172
Q

what should be done before drug use in amoebic liver abscess

173
Q

what are some other complications of amoebiasis

A

colitis
perforation
peritonitis

174
Q

C. diff is …

A

gram positive
anaerobic
bacillus
spore forming (innoculum 10 spores)

175
Q

C. diff spores are resistant to disinfectant

true/false

176
Q

what is the route of spread of C. diff

A

faecal oral

177
Q

how is C. diff infection caused

A

part of normal flora

broad spectrum ABs destroys bowel flora allowing C. diff to predominate

178
Q

who is at risk of getting C. Diff infection

A 
>65
previous CDI
hospitalised
immunosuppressed
PPI use / H1RA use
chronic renal disease
chemotherapy
IBD
179
Q

what are some complications of C diff

A

pseudo-membranous colitis
bowel perforation
bowel dilation
peritonitis

180
Q

what toxins does C diff produce

A 
toxin A (enterotoxin)
toxin B (cytotoxin)
181
Q

how is C. diff diagnosed

A

stool toxin test

182
Q

what are some s/s of c diff infection

A

diarrhoea +/- blood

abdominal pain

183
Q

what are the 3 stages of lab diagnosis of c diff

A

screening test for presence of organism (GDH)
test for presence of toxin
culture can be done if strain needs to be typed - not routine

184
Q

screening test positive

toxin test positive

A

positive c diff

185
Q

screening test positive

toxin test negative

A

indeterminant

send repeat specimen

186
Q

screening test negative

toxin test positive

187
Q

how can c diff infection be prevented

A

reduce 4 Cs
prompt isolation and treatment
hand washing - not alcohol gel

188
Q

what 3 things are taken into account in a severity test of C diff

A

suspected pseudomembranous colitis/colonic dilation > 6cm/toxic megacolon/ileus
WCC > 15
high creatinine

189
Q

what are the 4 Cs associated with C diff infection

A

Clindamycin
Ciprofloxacin (quinolones)
Co-amoxiclav
Cephalosporins e.g. ceftriaxone

190
Q

what is the treatment of C Diff

A

mild - metronidazole
severe - Vancomycin PO/NG + metronidazole

1st recurrence - fidaxomycin

191
Q

define travellers diarrhoea

A

3 loose stools in 24 hours

192
Q

how is travellers diarrhoea diagnosed

A

stool culture

stool wet prep

193
Q

what is travellers diarrhoea caused by

A

enterotoxigenic E. Coli (not enterohaemorrhagic)

campylobacter
salmonella
shigella
norovirus
rotavirus
194
Q

what is the treatment of travellers diarrhoea

A

early symptomatic - single dose ciprofloxacin
ST antidiarrhoeals
fluid replacement

195
Q

what do all stools automatically get tested for

A 
salmonella
shigella
campylobacter
e coli 0157
cryptosporidium
c.diff if > 15
196
Q

what kind of medium should be selected if the infective cause is unknown

A

enrichment medium

197
Q

how can different types of salmonella be detected

A

agglutination in lab - serogrouping

198
Q

how is malaria transmitted

199
Q

what does malaria cause

A

haemolytic jaundice

200
Q

what is the most common GI group of E. coli

A

enterohaemorrhagic

0157 is most toxic

201
Q

what kind of typing is used for E. Coli

A

EHEC
McKonkey agar
antisera serotypes
ELISA test

202
Q

what are 3 types of antidiarrhoeals

A

anti motility agents
antisecretory agents
absorbents

203
Q

give 2 examples of anti motility agents

A

opiates

loperamide

204
Q

when should anti-motility agents be avoided

A

dysenteric symptoms - fever, abdominal pain, bloody diarrhoea

205
Q

empirical treatment of GE

A

ciprofloxacin 500mg BD 3-5 days

206
Q

what 4 organisms should you think of if there is blood in the stool

A

e coli 0157
campylobacter
c. perfringens
salmonella

207
Q

what is dysentery

A

blood/mucus in stool

- E. Coli / shigella

208
Q 
diarrhoea
steatorrhoea
weight loss
nausea
anorexia
anaemia
A

tropical sprue s/s

209
Q

what is the treatment for tropical sprue

A

tetracycline + folic acid

210
Q

how is tropical sprue diagnosed

211
Q

what causes Whipple’s disease

A

tropheryma whipplei

212
Q

how is whipple’s disease diagnosed

A

tissue microscopy

213
Q

what is the treatment of whipple’s disease

A

ceftriaxone

trimethoprim-sulfamethoxazole

214
Q

what is meant by the ‘source/reservoir’ of an infection

A

original source e.g. animal gut

215
Q

what is meant by ‘vehicle’ of an infection

A

how it is transmitted e.g. food

216
Q

what is the source of E. Coli

A

cattle gut

217
Q

what is the vehicle of E. Coli

A

undercooked burger

year 1 (45 decks)

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