Bailey & Scott's Diagnostic Microbiology: Microbiology Module 1 Flashcards


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1

eukaryotic species

a group of closely related organisms that breed among themselves

2

prokaryotic species

a population of cells with similar characteristics

3

clone

population of cells derived from a single cell

4

strain

genetically different cells within a clone

5

species

most basic taxonomic unit; collection of strains that share physiologic and genetic features

6

biotype

may include a specific trait that is different but insufficient to recognize as a distinct subspecies or species; may be serologic or genotypic

7

inoculation

specimen is placed into sterile media container designed to meet organism's nutritional needs

8

incubation

bacteria placed in optimal temperatures to promote growth

9

isolation

end result of inoculation and incubation

10

inspection

cultures are observed for phenotypic characteristics

11

identification

determine the identity of organism through evaluation of phenotypic characteristics

12

binary fission

chromosome replicated, cell membrane and wall grow, cytoplasmic components disperse, septum separates cell into chambers, and split into daughter cells

13

replication fork

initiation point where splitting of DNA occurs

14

topoisomerase

binds to the DNA double helix and begins to unwind the two strands

15

helicase

breaks the hydrogen bonds between the bases

16

elongation

process that starts at the replication fork and goes in both directions

17

termination

where the replication fork meets

18

origin of replication, elongation, and termination

3 phases of bidirectional replication

19

mutation

a change in phenotype due to a change in genotype

20

wild type (strain)

a natural, nonmutated characteristic change in the genetic code

21

mutant strain

an organism that has a mutation, showing variance in morphology, nutritional characteristics, genetic control mechanisms, resistance to chemicals

22

genetic recombination

occurs when an organism acquires and expresses genes that originated in another organism through conjugation, transformation, or transduction

23

conjugation

direct transfer of a plasmid or chromosomal fragment from a donor cell to a recipient cell; gram-negative donor - cell plasmid transferred through pilus, recipient related species without plasmid

24

transformation

chromosomal fragments from a lysed cell are accepted by a recipient cell; genetic code of DNA fragment acquired by recipient; donor and recipient can be unrelated

25

transduction

bacteriophage serves as a carrier of DNA from a donor to recipient cell

26

eukaryotes

animals, plants, fungi, and parasites; single or multi-cell, presence of membrane-bound organelles with specific function

27

prokaryotes

bacteria; no membrane bound organelles; peptidoglycan cell wall

28

appendages and glycocalyx

two external structures

29

flagella and axial filaments

appendage used for motility

30

fimbriae

appendage used for attachment

31

pili

appendages used for channels

32

glycocalyx

the surface coating of molecules external to the cell wall containing sugars and proteins

33

slime layer

loosely organized and attached layer of glycocalyx

34

capsule

highly organized and tightly attached layer of glycocalyx

35

flagella

long filamentous appendages composed of flagellin, containing hook-curved sheath and basal body-stack of rings firmly anchored in cell wall; responsible for motility; antigenic-H antigen

36

monotrichous

single polar flagella

37

lophotrichous

two or more flagella from a single point

38

amphitrichous

single flagellum at two different points

39

peritrichous

multiple flagella surrounding cell

40

fimbriae

fine proteinaceous hairlike bristles emerging from cell surface; adhesion to other cells and surfaces

41

pili

rigid tubular structure made of pilin protein found only on gram negative bacteria; joins bacterial cells for partial DNA transfer called conjugation

42

gram positive cell wall

contains lipoteichoic acid, thick peptidoglycan wall, and plasma membrane

43

gram negative cell wall

contains outer lipid membrane, thin peptidoglycan wall, roomy periplasmic space, and plasma membrane; outer layer contains lipopolysaccharides and porin proteins

44

plasma membrane

semipermeable highly selective inner cell membrane, cell wall biosynthesis, energy production, cell motility, and mediation of chromosomal segregation during replication; made up of phospholipid bilayer, fluid mosaic model, no sterols, and inner membrane; teichoic acid and lipoteichoic acid and tight periplasmic space

45

bacterial cell wall

provides strength, protects the internal contents, determines the shape; made up of N-acetyl glucosamine and N-acetylmuramic acid connected by peptide bond

46

acid-fast cell wall

have gram positive cell wall structure with a waxy layer of lipids and fatty acids bound to exterior of cell wall; includes Mycobacterium and Nocardia

47

absence of cell wall

contain sterols in membrane lacking rigidity; includes Mycoplasma and Ureaplasma

48

ribosomes

combine with mRNA for protein synthesis

49

resident

colonizes site for prolonged period

50

transient

colonizes area for a short time

51

carrier

host carries potential pathogen with no symptoms

52

etiology

cause of infection or disease

53

incidence

fraction of population with disease during a specified period of time

54

prevalence

fraction of population at a given time point

55

sporadic

occasional occurence

56

endemic

constantly present

57

epidemic

many infected in a given area, in a short time period

58

pandemic

worldwide epidemic

59

herd immunity

immunity in most of a specific population

60

pathogen

will cause disease in most cases, regardless of immune status; primary infection, generally acute

61

opportunistic pathogens

can cause disease if there is a change in the environment due to host immune status or other physiological conditions; secondary infections

62

nosocomial

healthcare acquired infections that occur in 5-15% of hospitalized patients

63

iatrogenic

infection resulting from medical treatment or procedure

64

primary defense

includes squamous epithelium, normal microbiota, mucous membranes, environmental conditions, physical processes

65

secondary defense

includes innate and adaptive mechanisms

66

innate mechanisms

secondary defense including phagocytosis and inflammation

67

adaptive mechanisms

secondary defense including antibodies and T cells

68

endotoxins

released by gram negative bacteria

69

exotoxins

produced by gram positive bacteria

70

nucleic acid hybridization

based on the ability of two nucleic acid strands with complementary base sequences to bond with each other to form a hybrid or duplex

71

amplification (non-PCR)

amplification of target nucleic acid; signal amplification

72

sequencing and enzymatic digestion of nucleic acids

methods that elucidate some part of the pathogen's genomic sequence

73

non-amplified hybridization assays

includes purification of nucleic acid, hybridization with a labeled probe, and signal detection

74

amplified hybridization assays

includes purification of nucleic acid, hybridization with a labeled probe, and signal detection with an additional target amplification prior to hybridization and signal detection

75

Southern hybridization

utilizes a membrane as solid support and includes DNA probe to DNA complementation

76

Northern hybridization

utilizes a membrane as solid support and includes DNA probe to RNA complementation

77

Sandwich hybridization

utilizes an unlabeled capture probe and a labeled detection probe

78

in situ

utilizes the patient's cells or tissues as the solid support matrix

79

peptide nucleic acid fluorescent in situ hybridization

technique that uses peptic nucleic acid (PNA) probes that target ribosomal ribonucleic acid (rRNA) sequences; allows rapid identification of certain organisms from positive blood cultures: S. aureus, P. aeruginosa, K. pneumoniae, C. albicans, and E. faecalis

80

PCR

combines complementary nucleic acid hybridization with those of nucleic acid amplification

81

denaturation, annealing, and extension

the three steps to the PCR

82

reverse transcriptase PCR

amplifies RNA target rather than DNA, facilitating diagnostic testing for clinically important viruses; routine PCR performed after DNA is produced by the enzyme

83

real-time PCR

combines target nucleic acid amplification with qualitative or quantitative measurement of amplified product; combines thermocycling to produce amplicons; measures and quantifies

84

multiplex PCR

uses more than one set of primer pairs for amplification of multiple targets

85

restriction endonucleases

includes enzymes that digest DNA; each one recognizes a specific nucleotide sequence kown as restriction site-palindromic sequence; once located the enzyme catalyzes the digestion of the nucleic acid strand, electrophoresis separates fragments

86

capnophilic

fastidious organisms that require CO2 incubator; N. gonnorrhoeae, Haemophilus

87

microaerophiles

require reduced O2 and increased CO2

88

facultative anaerobes

most medically important bacteria

89

agar

gelatinous seaweed extract

90

nutrients

includes proteins and carbohydrates/sugars

91

enrichments

includes yeast extracts and blood

92

buffers

stabilize pH for growth

93

pH indicators

compounds that produce a visible change in color correlating with the pH of the media; general indicator of metabolic processes which produce acidic or alkaline end products

94

inhibitors

includes dyes, bile salts, NaCl, and antibiotics

95

1+

sparse colonies isolated limited to the 1st quadrant

96

2+

moderate colonies isolated that extends to the 2nd quadrant

97

3-4+

heavy colonies isolated that extend past 4th quadrant

98

nutritive

media that supports growth of most non-fastidious organisms

99

enrichment

media that contains complex organic substances such as blood, serum, hemoglobin, or special growth factors required by fastidious microbes

100

selective

media that only allows specific organisms to grow; contains one or more agents that inhibit growth of some microbes and encourage growth of the desired microbes

101

differential

media that allows colonies of one species to be differentiated from other bacteria growing on the plate; allows growth of several types of microbes and displays visible differences among those microbes

102

nutritional media

includes Mueller Hinton, tryptic soy, and sheep blood agars/broths

103

enrichment media

includes chocolate agar

104

selective/differential for gram negative rods

includes MacConkey, xylose lysine desoxycholate, and Hektoen Enteric agars

105

selective/differential for gram positive organisms

includes colistin-nalidixic acid and phenylethyl alcohol agar

106

nutrient broth

liquid medium containing beef extract and peptone

107

nutrient agar

solid media containing beef extract, peptone, and agar

108

sheep blood agar

most common nutritional media, most organisms grow on it; differential allowing determination of hemolysis; contains casein peptones, soybean peptones, 5% sheep blood, 1% agar

109

Beta hemolysis

total lysis of blood cells in media; clear zone around colony

110

alpha hemolysis

partial lysis of blood cells in media; green zone around colony

111

gamma hemolysis

no lysis of blood cells in media; no zone around colony

112

chocolate agar

enrichment media; always incubated in CO2; intracellular nutrients released; good for growth of fastidious organisms: Haemophilus and Neisseria

113

hemin

V factor

114

nicotinamide adenine dinucleotide

X factor

115

MacConkey agar

contains bile salts and crystal violet; inhibit gram positive and non-enteric gram negative organisms; differential lactose sugar fermentation with pH indicator-neutral red

116

lactose fermenter

interpretation of pink on MacConkey agar

117

lactose non-fermenter

interpretation of clear colonies on MacConkey agar

118

xylose lysine desoxycholate

contains yeast extract, sodium deoxycholate to inhibit gram positives, phenol red-pH indicator, sodium thiosulfate, and ferric ammonium citrate; selective for Salmonella and Shigella

119

lactose fermentation

interpretation of yellow on XLD

120

lysine decarboxylase

interpretation of clear color on XLD

121

H2S production

interpretation of black color on XLD

122

Hektoen enteric

contains meat peptones and yeast extract, bile salts to inhibit gram positives, ferric ammonium citrate, and indicators bromophenol blue and acid fuchsin; selective for Salmonella and Shigella

123

lactose non-fermenters

interpretation of clear colonies on HE

124

lactose fermenter

interpretation of yellow color on HE

125

H2S production

interpretation of black color on HE

126

eosin methylene blue agar

selective for gram negative bacteria; inhibits gram positive bacteria; contains eosin y and methylene blue

127

lactose fermentation

interpretation of dark purple to black with a green metallic sheen on EMB

128

non-lactose fermenters

interpretation of colorless and translucent colonies on EMB

129

colistin-naladixic acid

contains casein peptones, digest of animal tissue, yeast and beef extract, corn starch, 5% sheep blood; inhibits most gram-negative organisms; PEA sometimes substituted

130

phenylethyl alcohol agar

contains casein peptones, soybean peptones, 5% sheep blood; inhibits gram negative organisms; CNA sometimes substitutes

131

modified Thayer Martin

contains peptone starch, amino acids, glucose, nucleotides, lysed blood, higher concentration of glucose and agar than non-modified, and trimethoprim to inhibit Proteus; also contains antibiotics colistin, vancomycin, and nystatin; selective for Neisseria

132

colistin

inhibits gram negative bacteria

133

vancomycin

inhibits gram positive bacteria

134

nystatin

inhibits yeast

135

Martin Lewis agar

substitutes ansamycin for nystatin; has a higher concentration of vancomycin than modified thayer martin

136

reducing medium

contains a substance that absorbs oxygen or slows penetration of oxygen into medium; used for growing anaerobic bacteria; includes thio broth

137

bacitracin

differentiates group A strep from other Beta hemolytic strep and resistant staphylococci from sensitive micrococci; taxo A disks placed on inoculated agar and observed for zones of inhibition; >10mm zone-sensitive, <10mm-resistant

138

S. pyogenes and Micrococcus luteus

positive bacitracin QC

139

Streptococcus agalactiae and Staph aureus

negative Bacitracin QC

140

bile esculin agar

differentiates enterococci and group D strep from non-group D viridans streptococci; determines organism's ability to hydrolyze esculin to esculetin; positive noted by dark brown to black precipitate

141

Enterococcus faecalis

positive QC for bile esculin agar; growth with black precipitate

142

Escherichia coli

negative QC for bile esculin agar; growth with no precipitate

143

Strep pyogenes

negative QC for bile esculin agar; no growth

144

bile solubility test

differentiates S. pneumoniae from alpha hemolytic streptococci; bile or bile salts rapidly lyse pneumococcal colonies on blood agar; positive colonies disappear in drop of bile solution

145

Streptococcus pneumoniae

positive QC for bile solubility test

146

Enterococcus faecalis

negative QC for bile solubility test

147

CAMP test

differentiates group B strep from other streps; a diffusible hemolytic protein acts synergistically with the Beta lysin of Staph aureus causing enhanced lysis-arrowhead or campfire shaped zone

148

Streptococcus agalactiae

positive QC for CAMP test

149

Streptococcus pyogenes

negative QC for CAMP test

150

Listeria monocytogenes

not intended test but also produces positive CAMP reaction

151

catalase

differentiates Staph species from Strep; enzyme will convert hydrogen peroxide to water and oxygen, producing bubbles

152

Staphylococcus aureus

positive QC for catalase

153

S. pyogenes

negative QC for catalase

154

citrate utilization

identifies an organism's ability to use sodium citrate as the sole source of carbon; bacteria use citrate and convert ammonium phosphate into ammonia and ammonium hydroxide

155

Klebsiella aerogenes

positive QC for citrate utilization-blue color on slant

156

E. coli

negative QC for citrate utilization-growth on slant but no color change or no growth on slant

157

coagulase test

differentiates S. aureus from CNS; bound or free enzyme or clumping factor on the bacterial cell wall reacts directly with fibrinogen, resulting in macroscopic clumping; tube or slide method

158

Staphylococcus aureus

positive QC coagulase

159

Staphylococcus epidermidis

negative QC coagulase

160

flagella stain

used to visualize the presence and arrangement of flagella for presumptive identification of motile bacterial species; contains a mordant to better visualize flagella

161

E. coli

positive QC peritrichous flagella stain

162

P. aeruginosa

positive QC for polar flagella stain

163

K. pneumoniae

nonmotile, negative QC for flagella stain

164

indole production

identifies organisms that produce tryptophanase-hydrolyzes tryptophan to pyruvate, ammonia, and indole; Kovak's reagent will react with it and produce a red color; spot indole-cinnamaldehyde reacts to produce blue color

165

E. coli

positive QC for Kovac's method indole-red color on top of broth

166

K. pneumoniae

negative QC for Kovac's indole

167

lysine iron agar

differentiates gram negative bacili based on lysine decarboxylation and deamination, H2S production, and fermentation of glucose; aerobic slant, anaerobic butt; glucose fermentation-acid yellow; lysine deamination-red color

168

K/K

lysine iron agar-lysine decarboxylation and glucose nonfermenter

169

K/A

lysine iron agar-glucose fermentation

170

R/A

lysine iron agar-lysine deamination and glucose fermentation

171

Citrobacter freundii

K/K, H2S positive QC on lysine iron agar

172

Proteus mirabilis

R/A QC on lysine iron agar

173

Methyl red

differentiates members of Enterobacteriales family; detects mixed acid ferementation-turning red; yellow-negative

174

Voges-Proskauer

differentiates members of Enterobacteriales family; test detects the ability of the organism to convert the acid products to acetoin and 2,3 butanediol-turning red; yellow-negative

175

Escherichia coli

positive for MR, negative for VP

176

Klebsiella pneumoniae

negative for MR, positive for VP

177

microdase

differentiate gram positive, catalase positive micrococci from staphylococci; micrococci produce enzyme that reacts with reagent and cytochrome C producing indophenol resulting in bluish-purple color; negative-no color

178

M. luteus

positive QC microdase test-purple color

179

S. aureus

negative QC microdase test-no color

180

motility testing

determines whether an enteric organism is motile; must possess flagella; semisolid agar used to visualize diffuse zone of growth extending from line of onoculation; positive diffusion and turbidity; negative clear and no diffusion

181

E. coli

positive motility-diffusion and turbidity

182

S. aureus

negative motility-no diffusion and clear

183

nitrate reduction

determines whether an organism can produce nitrites

184

Proteus mirabilis

positive QC nitrate reduction-produces colorless gas

185

Acinetobacter baumannii

negative QC nitrate reduction-red, no gas

186

optochin-P disk

differentiates pneumococci-sensitive from other alpha hemolytic strep-resistant

187

Strep pneumoniae

positive optochin-susceptible zone >=14mm

188

Strep pyogenes

negative optochin-resistant zone <14mm

189

oxidase

determines presence of cytochrome oxidase activity for enteric bacteria from other GNR's using tetramethyl-p-phenylenediamine dihydrochloride to indophenol

190

P. aeruginosa

positive QC oxidase-bluish-purple color

191

E. coli

negative QC oxidase-no color

192

phenylalanine deaminase agar

determines if organism deaminates phenylalanine into phenylpyruvic acid which combines with ammonia then ferric chloride reagent is added forming a green color on slant

193

Proteus mirabilis

positive QC PDA-green color

194

Escherichia coli

negative QC PDA

195

L-Pyrrolidonyl arylamidase PYR test

used for the presumptive ID of group A streptococci and enterococci; turns red in presence of N,N-dimethylamino cinnamaldehyde reagent

196

E. faecalis and S. pyogenes

positive QC for PYR test-red color

197

S. agalactiae

negative QC for PYR-no color

198

triple sugar iron agar

determines whether gram negative rod ferments glucose, lactose, or sucrose and forms hydrogen sulfide; contains 10 parts lactose, 10 parts sucrose, 1 part glucose, and ferrous sulfate

199

glucose fermented-acid

TSI interpretation butt of tube turns yellow

200

lactose or sucrose fermented-acid

TSI interpretation slant of tube turns yellow

201

hydrogen sulfide produced

TSI interpretation tubes turn black; happens in acid-yellow

202

gas formation

TSI interpretation bubbles or break in agar

203

K/K alk/alk

TSI glucose, lactose, and sucrose fermenters

204

K/A alk/ac, H2S

TSI ferments glucose only and produces H2S

205

A/A

TSI ferments glucose, lactose, and sucrose

206

K/A, no H2S

TSI ferments glucose only

207

P. aeruginosa

TSI K/K alk/alk

208

P. mirabilis

TSI K/A alk/ac, H2S production

209

Shigella flexneri

TSI K/A

210

E. coli

TSI gas production

211

urease test

determines organism's ability to hydrolyze urea-product of decarboxylation of amino acids, producing ammonia and CO2, changing pH turning agar bright pink; negative yellow

212

Proteus vulgaris

positive urease QC

213

K. pneumoniae

weakly positive urease QC

214

E. coli

negative urease QC

215

X and V factor tests

differentiates Haemophilus species; organisms grow around the disk or strip that provides the appropriate growth factor

216

Haemophilus influenzae

requires XV for growth; grows around XV only

217

Haemophilus parainfluenzae

requires V for growth; grows around XV and V

218

Haemophilus ducreyi

requires X disk for growth; grows around X and XV

219

Ziehl Neelsen stain

carbol fuschin is primary stain; low phenol concentration, cells heated for five minutes, low concentration of primary stain, phenol and heat mordant, primary stain removed by acid-alcohol; highly toxic; used for mycobacteria-acid fast organisms

220

Kinyoun stain

basic fuschin is primary stain, high concentration of phenol, cells not heated, high concentration of primary stain, high concentration of phenol and basic fuschin, primary stain not removed by acid-alcohol; low toxicity

221

modified Z-N/Kinyoun

used for partially acid-fast organisms-Nocardia, carbol-fuschin, 1% H2SO4 instead of 3% HCl, and methylene blue

222

fluorochrome-auramine/rhodamine

used for mycobacteria; 0.5% HCl in 70% EtOH, potassium permanganate

223

endospore stain

malachite green driven into spore using heat, rinsed, and coutnerstained with safranin

224

negative stain

used for capsules; acidic dyes stain background and not cells; includes nigrosin, india ink, and eosin