GI - microbiology Flashcards
1
Q
what is the first line treatment of gastroenteritis
A
rehydration
2
Q
what is gastroenteritis
A
inflammation of stomach/intestines
3
Q
what organisms are the most common cause of infective gastroenteritis
A
viruses
4
Q
how do bacteria cause GE
A
invade tissues of GI tract and produce toxins
5
Q
define diarrhoea
A
3+ loose stools in 24 hours
stool holds shape of container
6
Q
what is considered acute diarrhoea and what is chronic
A
acute < 2 weeks
chronic > 4 weeks
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
8
Q
How is giardia lambia spread
A
cysts in water
travel to areas of contaminated water supply
swimming in ponds
9
Q
can giardia lambia be spread person-person
A
yes
- also, human only infection
10
Q
how is giardia lambia diagnosed
A
Lab: stool microscopy for ova/parasites/cysts
3 separate samples
duodenal aspirate is best
11
Q
what is the treatment for giardia lambia
A
metronidazole 1 week
12
Q
diarrhoea (often explosive, foul smelling) flatulence anorexia abdominal cramps epigastric pain nausea vomiting malabsorption (steatorrhoea, weight loss)
A
symptoms of giardia lambia
13
Q
give 2 organisms that cause small bowel bacterial overgrowth
A
E.Coli
Bacteriodes (gram negative, anaerobic, bacilli)
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
15
Q
what is the treatment of SBBO
A
tetracyclines (2-3 weeks)
surgical correction
16
Q
when is SBBO seen
A
diverticula fistulas strictures related to Crohn's bypass surgery functional stasis
17
Q
diarrhoea
steatorrhoea
macrocytic anaemia
A
symptoms SBBO
18
Q
what food is scombroid associated with
A
dark meat/fish in tropical areas tuna mahi mahi sushi tinned tuna poorly stored fish
19
Q
Scombroid involves a preformed toxin
true/false
A
true
20
Q
what is the incubation period of scombroid
A
1-6 hours
21
Q
what kind of reaction is scombroid poisoning
A
histamine like reaction
rash, headache, shock
22
Q
what is T1 on the bristol stool chart
A
separate hard lumps like nuts
hard to pass
23
Q
what is T2 on the bristol stool chart
A
sausage shaped but lumpy
24
Q
what is T3 on the BSC
A
like a sausage but with cracks on surface
25
T4 BSC
like a sausage or snake
| smooth and soft
26
T5 BSC
soft blobs with clear cut edges
| passed easily
27
T6 BSC
fluffy pieces with ragged edges, a mushy stool
28
T7 BSC
water, no solid pieces
| entirely liquid
29
what is the incubation period of staph aureus, bacillus cerues
1-6 hours
| short
30
what is the incubation period of salmonella, C. perfringens
12-48 hours
| medium
31
what is the incubation period of campylobacter, E. Coli 0157
2-14 days
long
(16-48 hours usually)
32
what is the most common cause of diarrhoea in the UK
campylobacter
33
campylobacter is...
curved
gram negative
bacilli
34
what is the source of campylobacter
```
you CAMP at a farm
farm animals - esp undercooked poultry
milk products
cheese
water
```
35
what is a complication of campylobacter
gillian barre
36
what is gillian barre
immune system attacks PNS - tingling of feet progresses to paralysis
37
how are outbreaks of campylobacter caused
people exposed to the same source
| i.e. not human - human
38
central abdominal pain
diarrhoea +/- blood
may mimic appendicitis
symptoms of campylobacter
39
how is campylobacter diagnosed
stool culture
40
what is the treatment of campylobacter
self limiting
clarithromycin if immunosuppressed
erythromycin or ciprofloxacin if systemic illness
41
what are some s/s that campylobacter has caused a systemic illness
fevers
rigors
flu-like symptoms
42
salmonella is ....
gram negative
bacillus
enterobacteria
43
who is at risk of bacteraemia from salmonella
HIV
sickle cell
AIDs
recent cryptosporidium
44
what antigen does salmonella possess
O antigen
45
what is the source of salmonella
undercooked poultry
raw eggs
less common due to chicken immunity
46
what is the treatment of salmonella
self limiting
| ciprofloxacin 5 days if systemic illness/risk of
47
what is the incubation period of salmonella
12-48 hours
48
how is salmonella diagnosed
stool culture
49
where does salmonella cause inflammation
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
50
where does campylobacter cause inflammation
colon and rectum
51
how does salmonella cause GE
invades tissue of GI tract and produces toxin
52
abdominal pain
diarrhoea (occasionally bloody)
vomiting
s/s salmonella
53
can shigella spread person-person
yes
| also - human only infection
54
how is shigella diagnoses
stool culture
55
why is shigella not seen in blood cultures
invades intestinal mucosa and causes severe inflammation but no further
56
what is the treatment of shigella
ciprofloxacin if severe
57
what is a complication of shigella
HUS
58
where is shigella often seen
cohorts of children
59
can salmonella cause outbreaks
yes
60
shigella is...
gram negative
61
what is the incubation period of E. Coli
16 - 48 hours
62
what kind of antigen does E. Coli possess
O antigen on surface
63
E. Coli is ...
gram negative
| coliform
64
what toxin does E. Coli produce
verotoxin (VTEC) (shiga-like toxin)
65
how does VTEC work
binds to cell receptors found on renal and red blood cells
| inhibits protein synthesis and causes cell death
66
what is a major complication of E. Coli
HUS
67
what should be avoided in HUS
antibiotics
NSAIDs
anti motility agents
68
what is HUS
haemolytic uraemic syndrome - increased blood urea, red cell haemolysis, thrombocytopaenia
pre-hepatic jaundice
69
what are some s/s of HUS
```
abdominal pain
petechiae
fever
pallor
BLOODY DIARRHOEA (e.coli in general)
oliguria
```
70
what is petechiae
small haemorrhage of blood vessels
71
what is the source of E. Coli
```
beef
minced meat
burgers (not so much steak)
raw milk
soy nut butter
visits to farms
private untreated water sources
```
72
can E. coli be spread person - person
yes
73
can E. coli cause outbreaks
yes
74
who is most at risk of HUS
children and elderly
75
E. coli is the commonest cause of renal failure in children <5 in the UK
true/false
true
76
what do the bloods of E.Coli show
```
increase WCC
low platelets
low Hb
RBC fragments
increased LDH
```
77
does e.coli 0104 produce verotoxin
yes but less toxic
78
what does VTEC show in agar
agglutination
79
what is the treatment of E. Coli
supportive
| NO ABs
80
what is the cause of enteric fever/typhoid/paratyphoid fever
salmonella typhi
| salmonella paratyphi A and B
81
```
fever initially then diarrhoea (green)
fever and rigors
headache
rose spots on abdomen
constipation
dry cough
```
s/s enteric fever
82
what is the treatment for enteric fever
depends on sensitivities
azithromycin (uncomplicated)
ceftriaxone IV (severe)
possibly fluoroquinolone e.g. ciprofloxacin but resistance common
83
what are some complications of enteric fever
GI bleeding
GI perforation
encephalopathy
bone/joint infection - osteomyelitis
84
how is enteric fever diagnosed
blood culture
85
what is the incubation period of salmonella type/paratyphi
14-21 days
86
when is enteric fever seen in the UK
when imported from india, SE asia, far/middle east, Africa
87
how is enteric fever spread
person-person
- human only infection
drinking/eating contaminated food/water
poor sanitation
88
where does bacteria stay in chronic carriers of enteric fever
gall bladder
89
what causes cholera
vibrio cholerae
90
vibrio cholerae is...
gram negative
small
bacillus
91
what is a BUZZWORD symptom of cholera
rice water stools - profuse water diarrhoea
92
what does the toxin of cholera cause
release of water from small intestine cells
93
when is cholera seen
water/disasters
| refugee camps
94
cholera causes outbreaks
| true/false
true
95
what is the incubation period of cholera
1-9 days
96
what is the treatment of cholera
fluid/electrolyte replacement
| no ABs
97
what organism commonly causes infection in CREAM BUNS
staph aureus
98
staph aureus infection involves a preformed toxin
| true/false
true - food contaminated and left - allowed bacterial replication and exotoxin production
99
where does the toxin of staph aureus work
vagus nerve and vomiting centre
100
what is the incubation period of staph aureus
1-6 hours
101
s/s staph aureus
diarrhoea NO BLOOD
102
clostridium perfringens is...
gram positive
large
bacillus
anaerobic
103
C. perfringens infection involves a preformed toxin
| true/false
true
104
what is c. perfringens associated with
poorly refrigerated/re-heated MEAT GRAVY
105
how does C. perfringens cause infection
produces cooking resistant spores that grow after cooking and produce enterotoxin
106
what is the incubation period of c. perfringens
medium
| 12-48 hours
107
what organism is associated with poorly refrigerated/reheated RICE (starchy food)
bacillus cereus
108
what is a s/s of bacillus cereus
diarrhoea NO BLOOD
109
bacillus cereus is ...
gram positive
large
aerobic bacillus
110
bacillus cereus infection involves a preformed toxin
| true/false
true
111
how does bacillus cereus cause infection
exotoxin ingested or produced by bacteria in gut after infection - spores survive cooking, sporulate and produce exotoxin
112
what kind of organism is cryptosporidium
protozoan - single organism infection
113
how does cryptosporidium cause infection
ingested cysts hatch into trophozoites which invade small intestinal enterocytes
114
what is the source of cryptosporidium
domestic animals esp. calves
| contaminated water - swimming pools (cysts are chlorine resistant)
115
can cryptosporidium be spread person-person
yes
116
how is cryptosporidium diagnosed
duodenal aspirate / stool sample
| cryptosporidium stains with Ziehl Neelsen
117
s/s cryptosporidium
diarrhoea
| particularly bad in HIV
118
how is trypanasoma cruzi transmitted
| american trypanosomiasis - Chaga's Disease
kissing bug - Triatome
119
what does trypanasoma cruzi cause
parasympathetic denervation - affects colon and oesophagus --> megaoesophagus
120
What kind of infection is enterobius vermicularis
thread worms
| tiny white worms in stool
121
where are thread worms seen
families - children infect family
122
where do thread worm eggs hatch
intestine
123
where do thread worm eggs live
caecum/colon
124
where do the adult female threadworms lay eggs
perianal skin at night
125
how are the thread worm eggs ingested
perianal itch - fingers infected - mouth
126
what is the treatment of threadworms
oral mebendazole
often treat all members of family
sounds like Me - bend - over (perianal area)
127
thread worms are a human only infection
| true/false
true
128
what are the s/s of thread worms
worms in stool
| perianal itch
129
length of presenting complaint of helminths tends to be much longer
true/false
true
130
what immune cells are involved in helminth infection
eosinophils
131
how are helminth infections diagnosed
worms/eggs in stool
132
what are nematodes
round worms
133
what kind of nematodes infect the intestine
ascariasis
134
what kind of nematodes infect the tissues/lymph
filariasis
135
what are trematodes
flukes
136
how does one catch schistosomiasis (type of fluke)
fresh water exposure
137
what are some s/s chronic schistosomiasis infection
hepatomegaly
liver fibrosis
portal hypertension
138
give an example of a liver fluke and where are they seen
clonorchis
Fasciola
SE asia
139
what are cestodes
tape worms
140
what food is taenia solium associated with (cestode)
| what is another way of infection
undercooked pork
autoinnoculation
human faeces
141
what food is saginatum associated with (cestode)
undercooked beef
142
how do cestodes cause infection
larval cysts in undercooked meat
143
what do the eggs of taenia solium cause
cysticercosis - tissue cysts in muscle/brain
144
what virus is the cause of the winter vomiting disease
norovirus
145
what are some s/s of norovirus
explosive diarrhoea and vomiting
146
who does norovirus affect
all ages
147
can norovirus cause outbreaks
yes - family/community outbreaks
| CRUISE SHIPS
148
how is norovirus diagnosed
PCR on vomit swab or faeces specimen
149
how long does PCR usually take
6 hours
150
what is the treatment of norovirus
rehydration
151
what is the route of spread of norovirus
faecal-oral
waterborne (droplet)
shellfish
152
what is the incubation period of norovirus
short, often < 24 hours
153
how long should you stay off work after symptoms of norovirus stop
2 days
154
norovirus survives on fomites for days-weeks
| true/false
true
155
what is the most common cause of D and V in children under 3 years
rotavirus
156
what is the route of spread of rotavirus
person-person
| faecal oral
157
what are some s/s of rotavirus
diarrhoea NO BLOOD
158
how is rotavirus diagnosed
PCR of faeces
159
what is the treatment of rotavirus
rehydration (orally where possible)
160
what kind of vaccine is available for rotavirus and when is it given
live attenuated
oral
2 doses at 2/3 months old
161
what kind of infection is amoebiasis
protozoan
162
what causes amoebiasis
entamoeba histolytica
163
where is amoebiasis seen
areas of poor sanitation
164
what is the treatment of amoebiasis
metronidazole
| + diloxanide furoate/paromomycin to clear gut
165
what is the route of spread of amoebiasis
faecal oral
| by ill/asymptomatic carrier
166
acute bloody diarrhoea
fever
abdominal pain
may mimic acute colitis
s/s amoebiasis
167
how is amoebiasis diagnosed
hot stool microscopy/culture for ova/cysts
168
what is a complication of amoebiasis
amoebic liver abscess
169
amoebic liver abscess is more common in males
| true/false
true
170
```
fever
cough
aching abdominal pain
hepatomegaly
raised RHD on CXR
large opacity over right lung base
abnormal LFTs
```
s/s amoebic liver abscess
171
what are some investigations done for amoebic liver abscess
serology
| U/S, CT, CXR, LFTs
172
what should be done before drug use in amoebic liver abscess
drainage
173
what are some other complications of amoebiasis
colitis
perforation
peritonitis
174
C. diff is ...
gram positive
anaerobic
bacillus
spore forming (innoculum 10 spores)
175
C. diff spores are resistant to disinfectant
| true/false
true
176
what is the route of spread of C. diff
faecal oral
177
how is C. diff infection caused
part of normal flora
| broad spectrum ABs destroys bowel flora allowing C. diff to predominate
178
who is at risk of getting C. Diff infection
```
>65
previous CDI
hospitalised
immunosuppressed
PPI use / H1RA use
chronic renal disease
chemotherapy
IBD
```
179
what are some complications of C diff
pseudo-membranous colitis
bowel perforation
bowel dilation
peritonitis
180
what toxins does C diff produce
```
toxin A (enterotoxin)
toxin B (cytotoxin)
```
181
how is C. diff diagnosed
stool toxin test
182
what are some s/s of c diff infection
diarrhoea +/- blood
| abdominal pain
183
what are the 3 stages of lab diagnosis of c diff
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
screening test positive
| toxin test positive
positive c diff
185
screening test positive
| toxin test negative
indeterminant
| send repeat specimen
186
screening test negative
| toxin test positive
positive
187
how can c diff infection be prevented
reduce 4 Cs
prompt isolation and treatment
hand washing - not alcohol gel
188
what 3 things are taken into account in a severity test of C diff
suspected pseudomembranous colitis/colonic dilation > 6cm/toxic megacolon/ileus
WCC > 15
high creatinine
189
what are the 4 Cs associated with C diff infection
Clindamycin
Ciprofloxacin (quinolones)
Co-amoxiclav
Cephalosporins e.g. ceftriaxone
190
what is the treatment of C Diff
mild - metronidazole
severe - Vancomycin PO/NG + metronidazole
1st recurrence - fidaxomycin
191
define travellers diarrhoea
3 loose stools in 24 hours
192
how is travellers diarrhoea diagnosed
stool culture
| stool wet prep
193
what is travellers diarrhoea caused by
enterotoxigenic E. Coli (not enterohaemorrhagic)
```
campylobacter
salmonella
shigella
norovirus
rotavirus
```
194
what is the treatment of travellers diarrhoea
early symptomatic - single dose ciprofloxacin
ST antidiarrhoeals
fluid replacement
195
what do all stools automatically get tested for
```
salmonella
shigella
campylobacter
e coli 0157
cryptosporidium
c.diff if > 15
```
196
what kind of medium should be selected if the infective cause is unknown
enrichment medium
197
how can different types of salmonella be detected
agglutination in lab - serogrouping
198
how is malaria transmitted
mosquitos
199
what does malaria cause
haemolytic jaundice
200
what is the most common GI group of E. coli
enterohaemorrhagic
| 0157 is most toxic
201
what kind of typing is used for E. Coli
EHEC
McKonkey agar
antisera serotypes
ELISA test
202
what are 3 types of antidiarrhoeals
anti motility agents
antisecretory agents
absorbents
203
give 2 examples of anti motility agents
opiates
| loperamide
204
when should anti-motility agents be avoided
dysenteric symptoms - fever, abdominal pain, bloody diarrhoea
205
empirical treatment of GE
ciprofloxacin 500mg BD 3-5 days
206
what 4 organisms should you think of if there is blood in the stool
e coli 0157
campylobacter
c. perfringens
salmonella
207
what is dysentery
blood/mucus in stool
| - E. Coli / shigella
208
```
diarrhoea
steatorrhoea
weight loss
nausea
anorexia
anaemia
```
tropical sprue s/s
209
what is the treatment for tropical sprue
tetracycline + folic acid
210
how is tropical sprue diagnosed
biopsy
211
what causes Whipple's disease
tropheryma whipplei
212
how is whipple's disease diagnosed
tissue microscopy
213
what is the treatment of whipple's disease
ceftriaxone
| trimethoprim-sulfamethoxazole
214
what is meant by the 'source/reservoir' of an infection
original source e.g. animal gut
215
what is meant by 'vehicle' of an infection
how it is transmitted e.g. food
216
what is the source of E. Coli
cattle gut
217
what is the vehicle of E. Coli
undercooked burger
