4A. MICROBIOLOGY PRACTICALS Flashcards
1
Q
4 steps of gram stain test
A
add crystal violet stain
add iodine to bind
decolonise with ethanol
counterstain with safranin
2
Q
why can’t mycobacterium be stained by gram stain
A
they have waxy cell walls that do not retain stain
3
Q
two results of gram stain test and explain why
A
pink= gram negative bacteria- thinner peptidoglycan layer so crystal violet is not retained when washed with ethanol
Purple= gram Positive bacteria-thicker peptidoglycan layer= retention
4
Q
what is the first test for gram negative bacteria?
A
macconkey lactose test
5
Q
What does Macconkey agar include (3)
A
salts, lactose and a pH indicator
6
Q
results of macconkey test
A
pink= lactose fermenting
colourless= non-lactose fermenting
7
Q
how does the macconkey test work
A
if bacteria ferments lactose it will produce lactic acid= pH colour change
8
Q
results of macconkeys test
A
pink= lactose fermenting
colourleSS= non-lactose fermenting
9
Q
bacteria examples for lactose fermenting (2)
A
E.Coli and Klebsiella pneuonomiae
10
Q
bacteria examples for non-lactose fermenting (4)
A
eg shigella, salmonella, proteus, pseudomonas
11
Q
how can shigella and salmonella be differentiated and what is a positive result for each
A
XLD test
red colonies only= shigella
red colonies with black centres= salmonella
12
Q
what are the 3 agars that can be used for lactose fermenting testing
A
uses MacConkey, CLED or XLD agar
13
Q
what type of bacteria is the oxidase test for
A
gram negative non-lactose fermenting bacteria
14
Q
what substance does the oxidase test test for
A
detects presence of cytochrome oxidase in bacteria
15
Q
what does a + and - oxidase test result say about the bacteria
A
positive results mean a bacteria is aerobic
negative results mean a bacteria can be aerobic or anaerobic= colliform
16
Q
postive result for oxidase test
A
positive test= disk turns blue
17
Q
example of 4 bacteria that test + in oxidase test
A
V. cholerae, campylobacter, helicobacter, Pseudomonas aeruginsa
18
Q
what is serotyping, what type of bacteria is this for and how can this identify bacteria
A
identifying cell surface antigens of gram negative bacteria
identifiable species due to distinct pathogenic genome
19
Q
what are 4 modern methods of clinical bacterial identification
A
API strip
RNA gene sequencing
mass spectrometry
serotyping
20
Q
what is the first and second test for gram + bacteria (and what do they differentiate between)
A
- catalase test- staph and strep
2a. coagulase test to differentiate between staph
2b. haemolysis test to differentiate between strep
21
Q
what type of bacteria does the coagulase test test
A
differentiates types of staphylococcus
22
Q
what enzyme does the coagulase test test for and what is the function of this enzyme then explain how the test works
A
test for coagulase- an enzyme that causes fibrin clotting
adds plasma containing fibrinogen which is converted to fibrin for clotting if coagulase enzyme is present
23
Q
what is the + and - result of coagulase test and 1 example of bacteria each
A
positive test= clumps formed eg S. aureus
negative test= no clumps formed eg all other staphylococcus eg S.epidermis
24
Q
what is lancefield grouping test? on what group of bacteria is this used? what is a + test?
A
further test for beta haemolytic bacteria by detecting surface antigens
clumping to show antigen-antibody complexes are formed
25
name bacteria that are lancefield group A, B, D and G positive
A= S.pyogenes
B= S.agalactiae
D= S.bovis
G= S.dysgalactia
26
What do the surface antigens on bacteria group A, B, C, D and G mean the infection is
Group A, C, G= tonsilitis and skin infection
Group B= neonatal sepsis and meningitis
Group D= UTIs
27
what bacteria does haemolysis differentiate between and what is it done on
types of stretococci, blood agar
28
alpha haemolysis colour, how much lysis and example
partial lysis, green colour eg S. pneumoniae
29
beta haemolysis colour, how much lysis and 2 examples
complete lysis, colourless eg S, progenies and S. agalactiae
30
gamme haemolysis colour, how much lysis and example
no lysis eg S. bovis, no colour change
31
what are the follow up identification tests for haemolytic bacteria (2)
alpha- optochin test
beta- lancefield grouping test
32
what does the optochin test differentiate between
differentiates between alpha haemolytic streptococcus
33
how is the optochin test donw
optochin soaked disc placed in agar of bacteria
34
two results of optochin test and an example for each
resistance= bacteria grows around it eg S. viridans
non-resistance= bacteria doesn’t grow around it eg S. pneumonaeie
35
what does the optochin test differentiate between
differentiates between alpha haemolytic streptococcus
36
what is the most common cause of community acquired pneumonia
Streptococcus pneumoniae
37
what are the most common cause of healthcare acquired pneumonia (3)
Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae
38
what are the 2 methods of diagnosing viral infections and what do each of them detect
viral detection- presence of virus in body
serology- presence of immunoglobulins against virus
39
two methods of viral detection and mention adv/disadv
electron microscopy- too expensive and long
PCR- cheap, quick, sensitive, can detect several viruses, but risk of false negatives
40
give 3 examples of serology test
ELISA
immunofluoroscence
complement fixation test
41
what are the two diagnotic swabs and what is their purpose
green viral swab
charcoal swab for bacteria
allows for suitable transport and storage of the pathogen in a favorable environmetn
42
what is infective endocarditis
infection of the endocardium of the heart
43
what are the two complications of infective endocarditis and what can both of these lead to
embolism
aortic regurgitation murmur
heart failure
44
what is the main cause of infective endocarditis and what are some other causes (2)
bacteria that enters the blood and travels to the heart
fungal and viral infections
45
what are the most common bacteria to cause infective endocarditis and how do they enter the blood (3)
staph epidermis via contaminated Hickman lines
coliforms from UTI/
staph aureus from skin/ pneumonia
46
what are the three risk factors of infective endocarditis
immunosuppression
history of rheumatic fever
lines eg cathetors, Hickman
47
what are the general symptoms of infective endocarditis (3)
fever, sweats, weight loss
48
what are the cardiac symptoms of infective endocarditis (3)
murmur, breathlessness, chest pain
49
what are the pathagnomonic signs of infective endocarditis (4)
Roth’s spots, Janesway lesions, Osler’s nodes, Splinter haemorrhages
50
what are the two main investigations for suspected infective endocarditis
blood cultures and echocardiogram
51
how to do blood cultures for infective endocarditis
3 samples from different sites over 24 hours and before antibiotics
52
what two main things can diagnose infective endocarditis
positive blood culture with a microorganisms that typically causes infective endocarditis
new valvular regurgitation
53
what is the typical treatment for infective endocarditis
antibiotics
54
what are examples of broad spectrum antibiotics
ceftriaxone, penicillins and vancomycin
55
give an example of a narrow spectrum antibiotic
gentamicin
56
what is Roth's spots
retinal haemorrhages
57
what are Janesway lesions and what are they caused by
non-painful lesions on palms and soles
caused by septic micro emboli from valve
58
what are Osler's nodes and what is caused by
painful lesions on tips of fingers or toes cause by localised immune response
59
what are splinter haemorrhages and what is it caused by
thin red line of blood under nails, running in the direction of nail growth
caused by haemorrhages from small capillaries under the nails
60
what agar is used to culture stool samples
macconkey
61
what is dysentery and a common cause
bloody diarrhoea
shigella
62
what two drugs can be first line for C diff infections
oral metronidazole/ oral vancomycin
63
what drugs is given for severe diarrhoea
oral vancomycin
64
what drugs is effective against anaerobes
metronidazole
65
what do worm infections not usually have
diarrhoea like symptoms
66
how is the salmonella species further classified
Kauffman white scheme
67
what does API stand for and what is it
Analytical profile index. Bacterial cultures r placed in individual tubes with biochemical tests and seen if there r positive or negative reactions (tests their metabolic and enzymatic properties)
68
what causes the black appearance on XLD and for which bacteria
hydrogen sulphide
salmonella
69
how r campylobacter bacterium cultured and what does it stand for
CCDA plates
charcoal cefazolin sodium deoxycholate agar
70
what is immunoflurescence
staining with fluorescent antibodies
71
why can bacteria and viruses not be detected with stool microscopy
bacteria- requires culture for isolation
viruses- to small to see with light microscopy
72
what is the treatment for many viral infections
supportive treatment
73
under what condition do norovirus infections require isolation of the patient
if they show signs of norovirus gastroenteritis
74
what r risk factors for C diff infection (5)
nursing home
hospital
recent antibiotics
PPI use
elderly
75
what is fecal microbiotica transplant used for
for patients with recurrent C diff infections
76
what needs to happen to a patient suspected of a c diff infection and when does this need to happen until
isolation until 48 hours free of diarrhoea
77
what antibiotics should be started for a suspected appendicitis whilst awaiting results from the labs (2)
Cefuroxime & Metronidazole
78
what does cefuroxime act against (1)
coliforms
79
what type of bacteria is flucloxacillin active against
gram + bacteria
80
why is a Mz disc used on blood agar plates and what is Mz
metronidazole
if the bacteria is not resistant= confirms presence of anaerobic bacteria
81
what is prescribed for upper GI infections
co-amoxiclav
82
how can viral gastroenteritis be diagnosed
PCR
83
what r the 5 causes of diarrhoea in enteric (GI) infections
bacteria, viral, protozoa, food poisoning, antibiotic associated
84
what type of E coli can cause diarrhoea
escherichia e coli
85
what is a red weeping lesion that crusts on face of young children, what does it start off as and what is causing it?
impetigo
an itchy growing spot
bacterial cause
86
what bacteria have gold colonies on a CBA plate
S aureus
87
what is the 1st line antibiotic treatment for S aureus and what is the alternative for penicillin allergies
flucloxacillin
clarithromycin
88
what antibiotic is given for MRSA and is this okay for penicillin allergies
vancomycin
yes
89
what is cellulitis and symptoms 3
bacterial skin infection
redness, swelling and pain
90
what is the cause of cellulitis 2 and how do they cause infection
staph/ strep bacteria that were commensals but caused infection by going through a break in the skin
91
what test involves suspending colonies in water and mixing them with antibody coated latex beads
lancefield
92
first line for treating S pyogenes and alternative for penicillin allergy
penecillin
clarithromycin
93
if a cannula is infected, what r the 3 microbiological samples that should be sent to the lab
cannula tup, blood cultures, black charcoal swab of skin at site
94
what does MRSA stand for
methicillin (meaning penicillin) resistant staphylococcus aureus
95
alternative to vancomycin for MRSA treatment
teicoplanin
96
what r the follow up investigations that need to be done with S aureus bacteria infections 3
1. take blood cultures daily until negative
2. echocardiogram to rule out infective endocarditis
3. if back pain/ spinal tenderness than MRI of spine needed to look for osteomyelitis
97
one contraindication of vancomycin and why, can this still be given?
acute kidney failure
nephrotoxic
yes to patients with kidney issues but requires closer monitoring to ensure blood vancomycin levels r stable
98
what is the 1st line to treat UTI (2) and why might one be chosen over the other
nitrofurantoin or trimethoprime
nitro chosen as it can be taken during most of the pregnancy and there r fewer resistant bacteria to this compared to trimethoprim
99
what does yellow and blue/ green on a CLED plate mean
yellow= lactose fermenting
blue= non lactose fermenting
100
why r blood cultures done for cellulitis 1
to see if sepsis has occurred
101
what does mixed growth of multiple bacteria on a plate mean and is this diagnostic
suggests contamination of sample
no
102
what is microscopy not performed on urine inside a catheter bag 2
bacteria can grow in bag but this may not necessarily be from the patient and a catheter will produce a urethral mucosal inflammatory response producing leukocytes
103
why is urine collected from asymptomatic pregnant women 2 and how is this screeened for in women 1
common to have asymptomatic bacteria in pregnant women which can cause infection and pylonephritis
mid stream urine samples
104
what is meningitis and what layers are typically affected
inflammation of meninges (typically) pia and arachnoid mater
105
what is the triad of symptoms of patients with meningism what r the general symptoms 3
triad: neck stiffnes, photophobua, severe headache
general symptoms: fever, malaise, rash
106
what is the rash characteristic in meningococcal meningitis
non blanching pruritic rash
107
what is the main cause of meningitis and give 2 examples
viruses eg enteroviruses and herpesviruses
108
what is usually the bacterial cause of meningitis 3 and who does this typically affect 3
strep. pneumonia and neisseria meningitidis and listeria monocytogenes in neonates/ elderly/ immunocompromised
109
what is encephalitis
inflammation of cerebral cortex
110
what r the 3 symptoms of encephalitis
fatigue, fever, reduced consciousness
111
what is the main cause of encephalitis
viruses- same an meningitis
112
what is meningo-encephalitis
combination of encephalitis and meningitis
113
how is a CSF sample obtained and what is its usual appearance and when r results received
CSF sample obtained via lumbar punture- usually gin clear and pressure of <15cm of H20, results within a few hours
114
what further tests should be done for meningo-encephalitis and for what types of pathogens
(2->2, 2-> 1)
do blood cultures/ PCR for strep. pneumonia and neisseria meningitidis
do stool and nose/ throat swab PCR for enteroviruses
115
what antibiotics be prescribed for bacteria 2 causing meningitis and 2 reasons why they r preferred over penecillins
IV cefotaxime/ ceftriaxone
good CNS penetration and broad spectrum activity against all common gram + and - bacteria
116
how can WCC % help determine the type of pathogen in a CSF sample
in CNS lumbar puncture, a WCC of mostly neutrophils indicates bacterial infection and lymphocyte= a viral infection
117
What bacteria grows on chocolate agar not on blood agar, why and what is its appearance on chocolate agar 1 1 2
H influenzae (Hib)
fastidious
small white colonies
118
what two things should be given immediately if there is a bacteria causing meningitis and why
ntibiotics should be started along with IV dexamethosome (reduces the risk of long term neurological complications)
119
how do recently born babies get group B causing meningitis
from mothers genital tract
120
what is a appearance of listeria monocytogenes and what test is this on
small semi transparent colonies
alpha haemolytic blood agar
121
what antibiotic therapy should be commenced for immunocompromised and two things about the way it is given
high dose and frequency IV amoxicillin
122
what is another meningitis causing bacteria that has poor growth on blood agar and better growth on chocoalte and what is significant about this bacteria 2 what is prophylaxis for this
neisseria meningitidis
PHE notifiable disease and close contacts offered antibiotic prophylaxis with a single dose of oral ciprofloxaci
123
when is there no need for lumbar puncture and how is diagnosis done for meningitis instead 2
no need for lumbar puncture if characteristic rash and presentation raises strong clinical suspicious of meningitis- diagnosis done instead by peripheral blood culture/ PCR
124
what does a high lymphocyte count in WCC in lumbar puncture suggest
viral meningitis/ encephalitis
125
when should IV acyclovir be given as a treatment for meningitis
for viral unknown cause yet (no results from lab yet) or herpes simplex
126
what are the characteristic physical signs of pneumonia 3
fever
pleural effusion (stony dullness)
consolidation (bronchial breathing and dullness to percussion)
127
what are the signs of pneumonia on an x ray 3
consolidation
parenchymal shadowing
with or without cavities or pleural effusion
128
what are the 2 most common causes of community acquired pneumonia
streptococcus pneumoniae
Haemophilus influenza
129
what two pathogens that cause community acquired pneumonia cannot be identified through gram culture or stain and what is their treatment 2
mycoplasma pneumoniae
chlamydia pneumoniae
macrolide or fluroquinolones
130
what samples are key to collect for respiratory infections 4
blood cultures
sputum
urine
serum
131
explain how to test S. pneumoniae 1 and all of its results 3
culture on blood agar:
gram + cocci
optochin sensitive
alpha haemolysis
132
treatment for pneumonia
amoxicillin
133
presentation for typical pneumonia 3, what does it invade
1. productive rust coloured sputum
2. fever
3. headaches
invades alveolar cavity
134
presentation for atypical pneumonia 2, what does it invade
1. dry cough
2. little fever and headache
invades alveolar interstitum
135
what causes typical pneumonia 1
S. pneumoniae
136
what causes atypical pneumoniae 4
-> legionella pneumophila
-> chlamydia pneumoniae
-> mycoplasma pneumoniae
-> Coxiella burnetii
137
treatment of atypical pneumoniae 1, 3
macrolides eg clarythromycin, doxycycline, ciprofloxacin
138
when should legionelle pneumophila be suspected 2, its treatment 1 and what has to be done when it is diagnosed 1
suspect in severe community acquired pneumonia and travel history eg spain
1st line: clarythromycin
notifiable to PHE
139
1st line antibiotic treatment for mild, moderate and severe CAP (community acquired pneumonia). What is the alternative for penicillin allergies
mild- amoxicillin
mod- amoxicillin
severe- clarithromycin/ co-amoxiclav
alternative= clarithromycin
140
when should a chest x ray be ordered when CAP is presented
within 4 hours
141
what test can classify pneumonia severity
CURB 65
142
what is s pneumoniae from CAP called when it goes beyond the respiratory tract
invasive pneumococcal disease
143
what container is the urine and the serum collected in for CAP tests
urine- universal container
serum= yellow top vacutainer tube
144
why does H influenza respiratory infections have significant complications
leads to disease if immune defences are compromised eg chronic airway disease like COPD
145
what does H influenza need to grow and what is its presentation on blood agar
factors X and V on agar
grows in region around paper disc with factors X and V and nowhere else
146
what is the 1st and 2nd line treatment for COPD/ bhronchitis exacerbations and why for each
1st- doxycycline (less resistance to this compared to penecillins/ macrolides)
2nd- co-amoxiclav (2nd because it is broader so it promotes resistance)
147
alternative stain for mycobacterium (not Z-N stain) and what is the advantage of this stain
auramine phenol fluorescent stain
faster and more sensitive detection under microscope
148
what is the culture medium for the auramine phenol fluorescent stain and why is this used instead of normal culture medium
Lowenstein Jensen slope
contains growth factors that promote faster mycobacterial growth
149
what is a rapid culture technique for mycobacteria 1 and what is it 3
mycobacteria growth indicator tube
liquid broth with growth factors and fluorescent indicator
150
what is an better alternative to sputum microscopy and how does it work
GeneXpert
detects DNA sequences specific to Mycobacterium Tuberculosis
151
what are the 6 methods of detecting TB
1. ziehl nelson stain
2 auramine phenol fluorescence microscopy
3. lowenstein jensen culture
4. mycobacteria growth indicator tube
5. GeneXpert PCR
6. histology: granulomas with central caseous necrosis
152
what is pneumocytisis pneumonia and what type of people does it affect
fungal infection caused by P. jirovecci
immunocompromised
153
what two species cause TB
Mycobacterium tuberculosis and Mycobacterium bovis.
154
describe the difference between primary and secondary tuberculosis and compare symptoms for both
primary= organisms inhaled into the lungs and local granuloma formation occurs, mild symptoms
secondary= dormant organisms reactivate due to reduction in the host's immune system, severe symptoms: fever, weight loss, haemoptysis
155
what two test are done to get sputum in a patient that is not spontaneously producing sputum and what is an additional advantage
1. Induced sputum
2. Broncho-alveolar lavage
greater sensitivity than sputum
156
define COPD
production of sputum on most days over at least three months for more than
two years
157
what can cause COPD 2
smoking
previous infections
158
physical presentation of a COPD exacerbation 3
increased GREEN sputum production, cough and shortness of breath
159
what are the 2 main bacteria involved in acute exacerbations of COPD and which is most common and treatment for each
1. H influenzae MC
2. S. pneumoniae
treatment= amoxicillin unless beta lactamase resistant (H influenza is sometimes), then co-amoxiclav
160
what virus can cause COPD 2
influenza, seasonal coronovirus
161
how is sputum cultured for COPD diagnosis 2
chocolate agar incubated aerobically, 37oC.
blood agar incubated anaerobically, 37oC
162
what is the designated microbiology test for atypical pathogens
sputum
163
how is a P. jiroveci infection diagnosed and why
by PCR from induced sputum or Broncho-alveolar lavage
cant be cultured in vitro
164
treatment for pneumocytitis pneumonia 2
co-trimoxazole and prednisolone if there is respiratory failure/ oxygen before 8kPa
165
what is a good test to collect lower respiratory tract organisms if there aren't enough in the upper respiratory tract 1
induced sputum
166
what is bronchiectasis and what is the cause
permanent damage to airways
causes unknown
167
associations of bronchiectasis 4
1/3 of cases have history of severe pneumonia, TB, whooping cough, cystic fibrosis
168
what colour is mucus in bronchiectasis and how can this change
yellow sputum
changes to green if bacterial exacerbation
169
treatment for bronchiectasis and alternative and what is this for 2
1st line: amoxicillin
p. auruguosa give pipercillin-tazabactam
170
what 3 bacteria cause bronchiectasis and cystic fibrosis
p aruguosa
s pneumoniae
h influenzae
171
what class of drug is piperacillin-tazobactam
antipseudomonal beta lactam
172
what two things does sabouraud agar contain and give one example of what it grows
peptones and dextrose
candida albicans
173
what pathogen commonly contaminates RESPIRATORY samples ONLY and therefore is unlikely to be the infectious pathogen
candida albicans
174
how is bronchiectasis and cystic fibrosis diagnosed
sputum culture
175
what can cystic fibrosis lead to
bronchiectasis
176
what does candida albicans cause in immunocompromised
thrush
