Specimen Collection, Transport and Processing

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1

asymptomatic carrier

an individual harboring a microorganism without any harmful effects who may transmit the infection to others

2

colony count

colony-forming units per mL of urine determined by using a calibrated inoculating loop; counts equal to or greater than 10^5 are diagnostic for urinary tract infection

3

fastidious

organisms that require special cultivation measures, such as enriched media or special atmospheric conditions such as increased carbon dioxide

4

meningitis

infection or inflammation of the membranes covering the brain or spinal cord, usually purulent and involving the subarachnoid space

5

normal flora

a-hemolytic streptococci (viridians streptococci), Staphylococcus epidermidis, diptheroids, nonpathogenic Neisseria species, some anaerobes, Haemophilus species, and a few Candida albicans

6

nasopharynx

Etiologic Agents: Bordetella pertussis

Carrier State: S. aureus, N. meningitides, asymptomatic carrier

Specimen collection: flexible thin wire swab guided into nares to posterior pharynx

7

Streptococcus pneumonia, Haemophilus influenza, and Moraxella catarrhalis

common pathogens in ears and sinuses

8

lower respiratory tract

Etiologic Agents: Viruses, Streptococcus pneumonia, Klebsiella pneumonia, Serratia species, Staph aureus, Pseudomonas aeruginosa, E. coli, anaerobes, and fungi, Mycoplasma pneumonia (atypical)

Specimen collection: expectorated sputum, endotracheal, translaryngeal aspirates, broncheoalveolar lavage

9

sputum

evaluate for gram stain

10

Bartlett's Classification

enumerate neutrophils (PMN) and squamous epithelial cells (SEC) per low power field

11

PMN's

elevated levels in sputum sample indicate infection

12

SEC's

elevated levels in sputum sample indicate contamination from oral flora

13

purulent

more than 25 PMNs and fewer than 10 SEC per LPF

14

gastrointestinal tract

Etiologic Agents: Viruses and parasites, Salmonella, Shigella, Campylobacter, Vibrio, Yersinia enterocolitica, pt history and travel important

Specimens collection: stools, feces, rectal swabs (not preferred), no leaky containers, gram stains for white cells, mucous, parasites, and yeast, enrichment broth, O&P exam ASAP or preserved in polyvinyl alcohol if delayed

15

urine

Etiologic Agents: E. coli (most common) and other enterobacteriacaeae (Proteus, Enterobacter, Klebsiella), Enterococcus faecalis, Pseudomonas aeruginosa, Staphylococcus aureus, S. saprophyticus

Specimen Collection: clean catch midstream preferred, reject nonsterile, straight cath urine, suprapubic aspirate, collection during cystoscopy, avoid random and Foley due to contamination

16

Urine Colony Count

1 microliter (0.001 mL) calibrated inoculating loop, incubate 24 hours and count colonies; convert microliters to mL by multiplying by 1000 to find CFU/mL

17

types of UTI

cystitis, urethritis, pyelonephritis, pyelitis, glomerulonephritis

18

blood

Etiologic Agents: Staphylococcus aureus, Enterococcus, E. coli, and other Enterobacteriacae

Specimen Collection: proper skin antisepsis; collect at least 20 mL of blood from two sites at least one hour apart

19

before fever spikes

the highest concentration of bacteria in the bloodstream occurs

20

transient bacteremia

bacteria is introduced into bloodstream

21

intermittent bacteremia

bacteria is discharged from extravascular abscesses or infections into the blood

22

continuous bacteremia

constant release of bacteria into the blood

23

septicemia

bacteria multiplies faster than phagocytosis can occur

24

1-10 per mL

how much bacteria can lead to bacteremia

25

cerebrospinal fluid

Etiologic agents: Neisseria meningitides, Haemophilus influenza, Streptococcus agalactiae (Group B strep), viruses, and fungi

Specimen Collection: needle aspirate from 3rd or 4th lumbar vertebra, 3 tubes, 3rd used for micro; Gram stain performed immediately

26

6 hours at 37 C

time and temperature to hold CSF for bacteria and fungi

27

4 C

temperature CSF can be held for viruses

28

genital tract

Etiologic Agents: Neisseria gonorrhoeae, Treponema pallidum, Herpes Simplex Virus type 2, Chlamydia trachomatis, Trichomonas vaginalis

Specimen Collection: urethral exudate, uterine cervix, urethra

29

Neisseria gonorrhoeae

requires chocolate agar to grow; Martin Lewis or Modified Thayer Martin media will inhibit normal flora and allow better recovery of organism

30

Trichomonas

may be identified by a standard wet mount procedure

31

wounds and abscesses

Etiologic Agents: Staphylococcus aureus, Enterococcus anaerobes, fungi

Specimen Collection: aspirates (recommended), irrigation fluids, purulent drainage, necrotic tissue, swabs (not recommended) collected from endogenous or exogenous sources

32

endogenous

bacteria within the patient, including cellulitis, dental infections, and septic arthritis

33

exogenous

animal and human bites, burns, ulcers, and traumatic wounds

34

Cary-Blair

medium used for transport of stool specimens

35

gram stain

assess specimen quality (PMN and SEC); provides clues toward work-up and preliminary identification; positive or negative, cocci or bacilli, chains, pairs or cluster, anaerobes, and fungi

36

broth

media in liquid form

37

agar

medium in gel or semisolid form

38

isolated colonies

required for all biochemical and serological testing

39

supportive (general isolation) media

nutrient agar, trypticase soy agar, nutrient broth; no growth advantage to any specific group of bacteria

40

trypticase soy agar

general isolation media with no growth advantage to any group of bacteria

41

nonselective or enriched media

includes blood agar plates, chocolate agar

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blood agar plates (BAP)

trypticase soy agar with 5% defibrinated red blood cells; sheep blood agar preferred; horse or rabbit blood give different results

43

alpha hemolysis

incomplete or greening or browning

44

beta hemolysis

complete clearing

45

non hemolytic hemolysis

no change to red blood cells

46

chocolate agar

red cells are hemolyzed by enzyme or heat to release NAD (nicotinamide dinucleotide, coenzyme I) and hematin; enriched with IsoVitaleX and other nutrients; isolates fastidious bacteria, such as Haemophilus and Neisseria

47

differential media (selective differential)

provides a distinct colonial appearance isolating one group of bacteria; includes MacConkey and Eosin Methylene Blue (EMB)

48

MacConkey agar

inhibit gram positive bacteria; isolates gram negative bacteria and differentiates; if ferment lactose, colonies appear pink to red; if unable to ferment lactose, colonies appear clear;

49

Eosin Methylene Blue (EMB) agar

inhibit gram positive bacteria; strong lactose fermenters such as E. coli with a unique green metallic sheen; if able to ferment lactose, colonies appear purple; if unable to ferment lactose, colonies appear clear

50

enrichment broth

inhibits growth of one group of bacteria and enhance growth of another

51

gram negative, selenite, and tetrathionate broth

inhibit normal flora of colon to enhance growth of stool pathogens, Salmonella and Shigella

52

thioglycollate broth

differentiation of aerobes and anaerobes

53

selective media

inhibit growth of all bacteria except those being sought; includes HE, SS, and XLD agars

54

Hektoen Enteric (HE), Salmonella-Shigella (SS), and Xylose Lysine Deoxycholae (XLD) agars

inhibit normal flora of colon, enhance isolation of stool pathogens, and differentiate based on ability to ferment carbohydrates; those that do ferment appear as yellow-orange colonies

55

hydrogen sulfide

organisms produced appear as black colonies

56

antibiotic media

antibiotics inhibit some bacteria and select for another bacteria; includes Colistin Nalidixic Acid (CNA) and Modified Thayer Martin (MTM) and Martin Lewis

57

Colistin Nalidixic Acid (CNA)

blood agar with antibiotics added; selects for Gram positive bacteria and inhibits Gram negative bacteria

58

Modified Thayer Martin and Martin Lewis

chocolate agar base with antibiotics added; selects for Neisseria gonorrhoeae and inhibits Gram positive bacteria, other Gram negative bacteria and yeast

59

incubation

includes optimal conditions for bacteria to grow including temperature, oxygen, and other atmospheric needs; plates stay for 24 hours and are then examined for growth

60

mesophilic

prefers to growth temp of 30-45 C

61

35+/- 2 C

optimal temperature for human pathogens

62

thermophilic

prefers growth temperature greater than 40 C

63

psychrophilic

prefer growth temperature of 4-20 C

64

strict or obligate aerobes

absolute oxygen required

65

strict or obligate anaerobes

require anaerobic environment

66

facultative anaerobes

will grow with or without oxygen

67

capnophilic

5-10% CO2 with small amounts of oxygen; CO2 incubator or candle jar

68

48 hours

reincubation and no growth requirements

69

3-6 days

incubation period for anaerobic cultures

70

hemolysis

type and width of zone size

71

colonial characteristics

hemolysis, color, unique characteristics such as odor, pigment and motility

72

carbohydrate utilization

specific enzymes needed to break down a carbohydrate

73

fermentation

when a carbohydrate is used in the absence of oxygen which may be accompanied by the production of gas

74

oxidation

when a carbohydrate is used only in the presence of oxygen

75

indicators

pH and gas production

76

deepest part

location of the reading of fermentation

77

uppermost part

location of the reading for oxidation

78

catalase

hydrogen peroxide converted to water and oxygen (bubbles); important in differentiating Staphylococcus from Streptococcus, bacillus from Clostridium; performed by placing a colony on a slide and adding a drop of 3% hydrogen peroxide (H2O2); after mixing a positive reaction has immediate bubbling

79

cytochrome oxidase

oxidizes tetramethyl-para-phenylenedimine dihypochloride in presence of oxygen to form indophenol; performed by smearing an isolated colony over filter paper that has been saturated with reagent; positive reaction noted by purple color

80

oxidase positive

Neisseria, Pseudomonas, Campylobacter, Aeromans, and Pasteurella

81

coagulase

fibrinogen converted to fibrin in the presence of the enzyme; differentiates Staphylococcus aureus from negative staphylococcus; performed by mixing an isolated colony with a drop of rabbit plasma (kit test); positive reaction shown by presence of fibrin clots (clumping)

82

spot indole

detects enzyme tryptophanase which breaks down tryptophan when bacteria are grown on blood agar or chocolate agar; smear filter paper that has been saturated with Kovach's reagent across colony; differentiates E. coli from other lactose fermenting enterobacteriaceae (Proteus mirabilis - from Proteus vulgaris +)

83

PYR hydrolysis

L-pyrrolidonyl-B-naphthylamide (PYR) broken down by L-pyrroglutamyl aminopeptidase; important in differentiating Streptococcus and Enterococcus (Group D strep enterococcus + from non-enterococcus - and Beta hemolytic streptococcus Group A (pyogenes) + from Group B (agalactiae) -)

84

quality control

includes monitoring lab equipment, procedure manual, culture media and reagents, and personnel orientation and training

85

1.0 x 10^5 CFU/mL

urine colony count that indicates infection

86

Grade 0

Fewer than 10 PMNs per low power field

87

+1

10-25 PMNs per low power field

88

+2

Greater than 25 PMNs per low power field

89

+1

Mucus viewed per low power field

90

-1

10-25 SECs per low power field

91

-2

greater than 25 SECs per low power field

92

total score of 0 or less

indicates lack of inflammation or presence of saliva