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2013

TRAINING REPORT
Bio390


1433-1434


3 ..................................................................................
4 ........................................................
5 ...............................................................:
5 ....................................................................... :
5 ........................................................................ :
)6 ............................................... (Microbiology
: 6 .................................. : Specimens receiving
7 ................................................ :
: 9 ........................................ specimens culture
9 ............................................ :Culture Media
) (15 )Swabs&Bodyfluid specimens
) (16 ...................................... )Urine Specimens
) (17 .......... )Stool & Sputum Specimens
11 ........................................
: 19 .........................................................
Antibiotics
02 .............................................................. susciptbility test
02 .................................................................... :Vitek
04 ................................................................:Phoenix
)07 ............................................. :Manual (AST
01 .............................................. Antibiotics
) )09 ........................................ (SBI

45 ................................................................... :
) (51 ..........................................)Urine Specimen
1

62 ................................ :
) (60 .............. )Stool&Sputum Specimens
64 ............................... :
(67 .................................. )Blood Culture Specimens
71 ...................................................................Flow charts
73 ................................................................................
74 ..................................................................
79 ..........................................................................



, ((
)).

.

.

.
.


-1
.
-0 .
-3 Lab Coat .
-4 yellow Gown .
-5 Gloves .
-6 .Mask
-7 Bench .
-1 .
-9 .Safety Cabinet
Specimens
-12
Loops Swabs .

-11
( ) .

:
0011

.
.
, , ,
.

:


..

:
-1 Phlebotomy
-0 Reception
-3 Microbiology
Parasitology Tuberculosis -4 Molecular Virology
-5 Immunology & Serology
-6 Biochemistry
-7 Hematology
-1 Histology
-9 NAT
Blood Bank
-12

)(Microbiology



.
:

Culture Bench
)Swab & Body fluid bench (SB
)Stool & Sputum Bench (SS
Urine Bench
Blood Bench

: : Specimens receiving


.

:
-1 ()Blood Culture Specimens

()1-1

-0 ()Urine Specimens

()1-2

-3 ()Stool Specimens

()1-3

)Swab Specimens( -4
)Wound Swabs(
)Vaginal Swabs(
)Eye Swabs(
)Ear Swabs(
)Throat Swabs(
)Respiratory Swabs(
)Genital Swabs(
)Body Fluids Swabs(

pus -5
sputum -6
Cerebrospinal fluid (CSF) -7
: sterile body fluid -1
Synovial fluid Peritoneal fluid Precarditis and myocarditis fluid Pleural fluid -

)1-4(

: specimens culture
:Culture Media

.
)BAP( Blood Agar

Haemolysis
.Streptococcus

()2-1

()Chocolate Agar
X & hematin
, hymen V Nicotineamide Adenine Dinucleotide
) (NAD ) (RBCs
Haemophilus

()2-2

(MAC) Macconkey Agar


( )Selective Media
,(GNB) Gram Negative bacteria
, (GPB) Gram Positive Bacteria
( )Differential media
( ,)Lactose fermentation
( )positive (.)negative

()2-3

Sabouraud Dextrose Agar


Yeast, fungus

()2-4

12

XLD Agar
Salmonella, Shigella Differential Media

)2-5(

Selenite Broth Media


Salmonella ) Enriched Media(

)2-6(

11

)THIO( Thioglycollate broth


( )Enriched Media
, ( )Anaerobic
( )aerobic, anaerobic, microaerophilic
( )Obligate ()facultative

()2-7

Mannitol Salt Agar


Staphylococcus aureus
Mannitol
MRSA

(Methicillin Resistant Staph.aureus )MRSA

()2-8

10

Moueller hinton Agar



.

()2-9

)TM( Thayer Martin media


Nisseria
.

()2-10

: Bile Esculin Agar (BEA)


Streptococcus Enterococcus
.

()4-14
13

Todd Hewitt Broth media


Streptococci Group B

()2-11

Campy agar
Campylobacter Selective
media ( )2-12 Anaerobic jar Co2
( )2-13 Co2
()2-14

()2-13

()2-12

()2-14

14

) ( Swabs&Bodyfluid
)specimens
:


. ()2-15
.Fluid
Streaking .Loop ()2-16
04 37.

()2-16

()2-15

( )Pus swab B.A, MAC, CBA


Fluid THIO Swab
.
Centrifuge .
swab
.Loop

15

) ()Urine Specimens
:Urine

( )B.A/CLED ()2-17
Loop ( )2-18 .
Streaking (.)2-19
37 04

()2-17

()2-18

16

()2-19

) ()Stool & Sputum Specimens


:
XLD Agar , Selenite Broth

Swab XLD
swab Streaking
Loop ()2-20
Swab selenite broth .
37 04.
Sputum
:

B.A , CAB , MAC Slide Pus cells,


epithelial cells.

()2-20

17


Specimen

Bile
Cervical
CSF
Ear
Eye
Fluids:

BA
(O2)
+
+
+
+
+

Ascitic-CAPD-Drain fluid
Peritoneal-pericardial

BA
(AN
O2)
+

CBA

+
+

SDA

+
+
+
+
+

MAC
or
EMB
+
+
+
+
+

MSA

THIO

CLED

XLD

+
+
+
+
+

+
+

+
+

+
+
+
+
+

+
+

+
+

SELENITE BROTH

GS

+
+
+

+
+

Pleural-Synovial-Cyst Fluid
Fungal Culture
Mouth
Nasal-MRSA Screaning
Prostatic discharge
Pus
Semen
Sinus Aspirate
Skin Swab
Throat
Catheter Tip:
A (rolling)
Arterial line CVP- Femoral- IV Line
Jugular- Subclavian- Swans Gang- ventricular
B- Drain Tip:
Haemovac- Nephrostomy- Postoperative
Tissues
Umbilical Swab
Urethral Swab
Vaginal Swab
Wound Swab
Blood
Bone Marrow
Sputum
Brounchoalveolar Lavage (BAL)
Endotracheal Tube Suction Tip (ETT Suction Tip)
Gastric Lavage
Tracheostomy Secretion
Tracheostomy Tube Tip
Rectal Swab
Stool
Urine

+
+
+
+
+
+
+
+
+

+
+
+
+
+

+
+

+
+

+
+

+
+
+
+
+
+
+
+
+
+
+
+
+

+
+

+
+

+
+
+
+
+
+
+
+
+
+
+

+
+
+
+
+
+
+
+
+
+
+
+
+

+
+

+
+
+
+
+
+
+
+
+
+
+
+

+
+

+
+

11

G ve MAC G +ve / B.A


B.A.


( )

THIO Sub ( Fluid

. )culture

: Work Sheet
).Heavy Growth of (GNB) or (GPC
).Moderate Growth of (GNB) or (GPC
.No Growth
3 .Mix Growth.
Catheter tip:
)Significant/ No Sig. Growth of (GNB) or (GPC
12
No Significant Growth.

) (AST
) (ID Genus
.
)AST( .Antimicrobial Susceptibly Testing
)ID( .Bacterial identification

19


Antibiotics susceptibility test
:Vitek
Biochemical tests 64

Gram Positive, Gram Negative, Anaerobic, Yeast
Susceptibility Test .

()3-1

:
Suspension 3. Swab 0-1 . Nephelometer 0.50-0.60 (. )3-2

()3-2

02

rack Vitek (.)3-3 (ID) Card rack (.)3-3


- Card )( (AST) (.)3-3

()3-3

- Rack (.)3-4

()3-5

()3-4

- LAB ID Bench .Tech

01

Card Barcode Rack .

()3-7

()3-6

(.)3-8

()3-8

00

03

:Phoenix

()3-9

:
.Panel ( )ID .Bacterial identification ( )AST .Antimicrobial susceptibly testing :
-1 ( )ID
.Nephelometer

()3-10

-0 ( )AST indicator 52
( )ID ( .)AST ()3-11

04

()3-11

-3 Panel
, Panel .

()3-13

()3-12

panel
panel .

05

06

):Manual (AST
Swab
Mueller Hinton .
Antibiotic disks
04 37.

()3-14

07

Antibiotics
.
:Gram +ve
Rifampicin (RA),Vancomycin (VA), Gentamicin (GM) : Staph.
Cefoxitin or Oxacillin + Fusidic Acid (FA), Teicoplanin (TEC)
G+ve disk+X2 : Strept
:Gram ve
X1, X2, X3
Urine disk
X3
X2
X1
G+ve Disk
Nalidexic
Colistin
Imipenem
Cephalaxin Pencillin g (PG)
acid (NA)
(CT)
(IMI)
(CF)
Nitrofurantoi Ceftriaxone Ciprofloxaci
Ampicillin Erythromycin
n (NI)
(CRO)
n (CIP)
(AMP)
(E)
Cephalothin Cefotaxime Ceftazidime
Augmentin
Ampicillin
(KF)
(CTX)
(CAZ)
(AUG)
(AMP)
Ampicillin Meropene
Amikacin Cotrimoxazol Cephalothin
(AMP)
m (MEM)
(AK)
e (SXT)
(KF)
(TS)
Tazobacta Azotreonam
Gentamicin
(TS)
Cotrimoxazol
m (TAZ)
(ATM)
(GM) Cotrimoxazol
e
e
Norfloxacin Cefuroxime Piperacillin
Cefoxitin
Augmentin
(NOR)
(CXM)
(PIP)
(FOX)
(AUG)
Vancomycin
(VA)

01

) )(SBI
:
G-ve .G+ve
: : Specimen Slide
-

Crystal violet
.
Iodine .
Alchohol .
.
Safranine .

.

: Blood Agar Macconkey


Mac .

work sheet :
)Heavy growth of (GNB) or (GPC
)Moderate growth of (GNB) or (GPC
No growth
3 Mix growth.
Catheter tip:
)Significant/ NO Sig. growth of (GNB) or (GPC

09

:G +ve
:
Catalase Test -1
Staphylococcus Streptococcus
:
Catalase .
Loop .
:
Staphylococcus

()4-1

)Strept. (-) Staph. (+


Catalase Positive = Staphylococcus :Coagulase test )1
Staph.aureus
:
Staph Latex .
.

32

()4-2

Staph.aureus = (+) Agglutination


)0 Dnase test
Dnase agar 04. - HCL 12.

()4-3
)Staph.aureus = positive (+
)C.N.S = negative (-

Novobiocin sensitivity Disk )3


Staph.epidermidis , Staph.saprophyticus

()4-4

31

Staph.saprophyticus = Resistant
Staph.epidermidis = sensitive
.Phoenix or Vitek (ID), (AST) for Gram positive ) (AST ) )Manual Mueller hinton
.

( )R (.)S

30

Catalase Negative = Streptococcus : B.A :


: -Hemolytic -1
:
Streptococcus pneumonia, Streptococcus viridans
:
)1 (:Taxos p )Optochin Disk Susciptibility

Streptococcus pneumonia ( )4-6
Streptococcus viridans (.)4-5

()4-6

()4-5

)0 Bile Solubility
Streptococcus pneumonia
:
Bile Solubility Streptococcus
( Streptococcus pneumonia = )+ (.)4-7

33

)4-7(

:-Hemolytic -0
.
Group A, Group B, Group C, Group F, Group G :

)4-8(

:
:Taxos a (Bacitracin disk Susciptibility) ) 1
S.pyogenes , S.agalactiae

)4-9(

34

Sensitive = S.pyogenes
Resistant = S.agalactiae
Camp Test )0
Strep.agalactiae Group B
:
-1 Staph.aureus . B.A
-0 Group B
.Staph.aureus
-3 24.
:
Group B

()4-10
)3 Lancefield Grouping Masta strep

()4-11

35

.
Latex card
.
Sticks . Loop
.
Agglutination : . A

()4-12

Gamma-hemolytic -3
Enterococci B.A

()4-13

:
)1 bile esculin, Nacl
36

:
Bile esculine 04 )Positive (+

()4-14

6.5% Nacl 04
.

()4-15

()+
()-
Enterococci
Strep.Group D
grouping
grouping

Bile esculin
+
+
+

37

6.5% Nacl
+
+

Phoenix or Vitek (ID), (AST) for Gram positive ) (AST ) )Manual )X2, GPC disk( B.A
.

()4-16

( )R (.)S

31

G-ve

:

()4-17

= Lactose Fermentation positive MAC


= Lactose Fermentation negative MAC
:
Oxidase Test )1
Oxidase Swab .

()4-18

= )Oxidase positive (+

= )Oxidase negative (-
39

)0 API 20E
Enterococci
G ve bacilli
02 ( )Micro tube
.

5
.
( )3-0

5
.
.
.

:
| |MAN| |CIT| |VP
.

()4-19


ADH, URE

42

()4-20


37 04.

.

()4-21

41

TESTS

SUBSTRATE

REACTION TESTED

- RESULTS
*negative*

+ RESULTS
*positive*

ONPG

ONPG

beta-galactosidase

colorless

Yellow

ADH

arginine

arginine dihydrolase

Yellow

red/orange

LDC

lysine

lysine decarboxylase

Yellow

red/orange

ODC

ornithine

ornithine
decarboxylase

Yellow

red/orange

CIT

citrate

citrate utilization

pale
green/yellow

bluegreen/blue

H2S

Na
thiosulfate

H2S production

colorless/gray

black deposit

URE

urea

urea hydrolysis

Yellow

red/orange

TDA

tryptophan

deaminase

Yellow

brown-red

IND

tryptophan

indole production

Yellow

red (2 min.)

VP

Na pyruvate

acetoin production

colorless

pink/red (10
min.)

GEL

charcoal
gelatin

gelatinase

no diffusion of
black

black diffuse

GLU

glucose

fermentation/oxidation

blue/blue-green

yellow

MAN

mannitol

fermentation/oxidation

blue/blue-green

yellow

INO

inositol

fermentation/oxidation

blue/blue-green

yellow

SOR

sorbitol

fermentation/oxidation

blue/blue-green

yellow

RHA

rhamnose

fermentation/oxidatio

blue/blue-green

yellow

SAC

sucrose

fermentation/oxid
ation

blue/blue-green

yellow

MEL

melibiose

fermentation/oxidation

blue/blue-green

yellow

AMY

amygdalin

fermentation/oxidation

blue/blue-green

Yellow

ARA

arabinose

fermentation/oxidation

blue/blue-green

Yellow

)4-22(
API 20E

Species and subspecies identification of Enterobacteriacae and groups and


species identification of non-fermenting

API 20NE

Identification of gram-negative non-Enterobacteriaceae

API Rapid
20E

Identification of Enterobacteriaceae

API NH

Identification of Branhamella catarrhalis and Neisseria haemophillus

RAPIDEC
Staph

Identification of the commonly occurring staphylococci

API 20 Strep

Identification of streptococci and enterococcs

API Staph

Identification of clinical staphylococci and micrococci

API Coryne

Identification of Corynebacteria and coryne-like organisms

API 20A

Identification of anaerobes

)4-23(

40

Phoenix or Vitek (ID), (AST) for Gram negative ) (AST ) )Manual Mueller Hinton ( )X1, X2, X3
.

()4-24

Purity Plate .CBA - Pseudomonas spp ( )X2, X3 X1

( )R (.)S

43

44


:
Staphylococcus aureus -1
Staphylococcus saprophyticus -0
Enterococcus -3
Clostridium spp. -4
Pseudomonas spp. -5
Proteus spp. -6
Klebsiella -7
E.coli -1
Acinetobacter baumannii -9
Morganella morgannii
-12
Neisseria spp.
-11
Haemophillus spp.
-10
Cnadida spp.
-13
:

Staphylococcus aureus -1
B.A ) Cocci(
(Beta-hemolytic) ( Catalase)

)4-25(

:Diagnosis
" " Catalase test ) 1
45

Positive (+) = Staphylococci


" " Coagulase test ) 0

)4-26(
Positive (+) = Staphylococcus aureus
" " Dnase test ) 3
Staph.aureus = positive (+)

Vitek or Phoenix (ID), (AST) for Gram positive )4


. Genus
.MRSA Oxacillin or cefoxictin, methicillin -

Staphylococcus saprophyticus -0
. , B.A ( Cocci)
:Diagnosis
" " Catalase test ) 1
Positive (+)
" " Coagulase test ) 0
Negative (-)
" " Novobiocin disk sensitivity ) 3
Novobiocin disk = Resistant = Staph.saprophyticus
Vitek or Phoenix (ID), (AST) for Gram positive )4
. Genus
46

Enterococcus -3
) (Cocci ) (Catalase
) (Gamma-hemolytic B.A .
:Diagnosis
)1 Bile esculine " 6.5% Nacl "
Bile esculine (+) 6.5% Nacl (+) = Enterococcus
Vitek or Phoenix (ID), (AST) for Gram positive )0
Genus .

Clostridium spp. -4
) (Bacilli ) (Sporulating
) (Motile .Catalase Negative

()4-28

()4-27

:Diagnosis
)1 :
C.tetani
)0 " Catalase test "
Negatve (-) = Clostridium
: Morphology )3
47


" " Camp test )4
Camp test = positive = Clostridium sp.

)4-29(

API 20A )5
Vitek or Phoenix (ID), (AST) for Gram positive )6
. Genus

Pseudomonas spp -5
Beta- Oxidase Positive /Negative
.)) ( P.aeroginosa( hemolytic

)4-30(

:Diagnosis
:Oxidase test ) 1
Pseudomonas = Oxidase Positive
41

:Morphology )0
( ).
API 20NE )3
Vitek or Phoenix (ID), (AST) for Gram Negative )4
Genus .

Proteus spp. -6
( )Bacilli ) (MAC), (B.A
) (Swarming .

()4-31

:Diagnosis
)1 Oxidase test
Negative (-) = Proteus sp.
:Morphology )0
( ) .
)3 Indole test

49

()4-32
)Proteus vulgaris = Positive (+
)Proteus mirabilis = Negative (-
API 20E )4
Vitek or Phoenix (ID), (AST) for Gram Negative )5
Genus .

Klebsiella -7
( )Bacilli
) (Mucoid ) (Capsule .

()4-33

:Diagnosis
:Morphology )1
.
Oxidase test )0
52

Negative (-) = Klebsiella


API 20E )3
Vitek or Phoenix (ID), (AST) for Gram Negative )4
. Genus

E.coli -1
(B.A), ( Bacilli(
.MAC Flat ( MAC)

)4-34(

:Diagnosis
Indole test )1

)4-35(

Positive (+) = E.coli


Oxidase test ) 0
Negative (-) = E.coli
51

:Morphology )3

( Macconkey) 42
API 20E )4
Vitek or Phoenix (ID), (AST) for Gram Negative )5
Genus .

Acinetobacter bumannii -9
Coccobacillus .

()4-36

:Diagnosis
)1
)0 MAC

Indole, Oxidase tests )3


)Negative (-
Catalase test )4
)Positive (+
API 20NE )5
Vitek or Phoenix (ID), (AST) for Gram negative )6
Genus .
50

Morganella morgannii -12



.Swarming

()4-37

:Diagnosis
)1
Oxidase test )0
Negative
Catalase, Indole tests )3
Positive
Vitek or Phoenix (ID), (AST) for Gram negative )4
Genus .

Neisseria spp. -11


Diplococci ,
B.A, CBA, MAC , .

53

)4-38(

:Diagnosis
.) 1

)4-39(

Thayer Martin Agar, New York Agar ) 0


Neisseria spp. Selective

)4-40(
Oxidase Test )3
Positive
Catalase Test )4
Positive
54

Vitek or Phoenix (ID), (AST) for Gram negative )5


Genus .
N.gonorhoeae N.meningitidis Acid production from Glucose, Lactose, Maltose ()

()4-41

Haemophillus spp. -10


Pleomorphic
Coccobacilli ) (X,V factors
, CBA B.A (Staph
) .streak ,
.

()4-42

55

:Diagnosis
) 1

)4-43(

X,V growth factors ) 0


Mueller X, V disks
. 04 , Hinton

)4-44(
Haemophilus species

Growth Around Disk


X
V
XV
+
v/+
+
+
+
+
+
+
+
+

Haemophilus aegyptius
Haemophilus aphrophilus
Haemophilus ducreyi
Haemophilus haemolyticus
Haemophilus influenza
Haemophilus parahaemolyticus
Haemophilus parainfluenzae

)4-45(

56

Oxidase test )3
Positive
Vitek or Phoenix (ID), (AST) for Gram negative )4
Genus .

Candida albicans. -13

()4-46

:Diagnosis
)1 Germ Tube Test
0.5 0-1 Suspension Yeast 3-0
Pasteur pipette Cover slide .

()4-47

Vitek (ID) for Yeast )0

57

) ()Urine Specimen
( )

,

Report
No Growth
No significant Growth
ID (Identification) & sens if
pure
If 2 or more types, mixed
bacterial flora.
Culture is contamination
ID & sens if pure
If 2 or more types, mixed
bacterial flora.
Culture is contamination
-

Colony count
0 cfu
1-10 cfu

11-100 cuf

>100

Catheter Voided .
.Blood Agar, C.L.E.D
4
Work sheet 103 10
.105
Catheter , Significant growth of .. :
No.sig.g .9
Voided : :
.105 GNB
.Pus cells
:
Vitek or Phoenix (ID), (AST) for Gram negative or positive
Genus .
) (AST ) )Manual
X2, ( )GPC( B.A / )U, X2, X3( )GNB( Mueller hinton
)GPC .
51

( )R (.)S

59

E.coli C.L.E.D

()5-1

Vitek or Phoenix (ID), (AST) for Gram negative Genus .

Klebsiella .

()5-2

Vitek or Phoenix (ID), (AST) for Gram negative Genus .

62

Proteus spp. C.L.E.D Swarming

)5-3(

Vitek or Phoenix (ID), (AST) for Gram negative . Genus

Pseudomonas spp. C.L.E.D

)5-4(

Vitek or Phoenix (ID), (AST) for Gram negative . Genus

Staphylococcus saprophyticus (female)


Acinetobacter bumannii
Enterococci
Staphylococcus aureus
61

) ()Stool & Sputum Specimens


Normal Flora
).(Salmonella & Shigella
Stool XLD .Selenite Broth Salmonella Shigella No : Work sheet Salmonella or Shigella isolated Sub culture
.Selenite broth

Salmonella spp. -1

.

()6-1

:Diagnosis
:Morphology )1
XLD .H2S
)0 API 20E
Vitek or Phoenix (ID), (AST) for Gram negative )3
Genus .
60

Shigella spp. -0
.

()6-2

.
:Diagnosis
: Morphology )1
XLD .
API 20E )0
Vitek or Phoenix (ID), (AST) for Gram negative )3
Genus .

63

:Sputum
. Crystal violet Slides
.Epithelial cells Pus cells
.CBA B.A MAC
Heavy,Moderate,Low Growth of Work sheet
.Normal Flora
Neisseria : )6-3( sputum
catarrhalis, Candida albicans,diphtheroids, alphahemolytic streptococci, and some staphylococci

)6-3(

:
Streptococcus pyogenes -1
Beta-hemolytic streptococci -0
Haemophillus influenzae -3
Staphylococcus aureus -4
Klebsiella -5
Pseudomonas -6
Candida spp -7
Proteus -1
64

Streptococcus pyogenes Beta-hemolytic Strept

)6-4(

: Diagnosis
Catalase test )1
Negative = no bubbles
:Taxos a (Bacitracin disk Susciptibility) ) 0
""
Sensitive = S.pyogenes
Lancefield grouping ) 3
Vitek or Phoenix (ID), (AST) for Gram positive )4
. Genus

) Manual) ( AST) ) X2, GPC disk( B.A


.

65

( )R (.)S

66

()Blood Culture Specimens


blood culture bottles
,
Bactec alert ( )7-1

.Positive
:
Bactec
()7-2
:

()Patient ID
()Patient name
()Accession
(F11 )Collection Date
( )Bar code .

: F10

()7-2

()7-1


Bar code
( )slot ()7-3

67

( )

( )7-5
( )
,
Bottle .bottle barcode

()7-3

,
.
)Macconkey Agar( , )Chocolate Agar( , )Blood Agar( :
Slide ()G +ve( )G ve
:
-

.
,Streaking
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