Clinical Microbiology Test 1 Study Guide – Flashcards
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unicellular organisms that lack a nuclear membrane and true nucleus
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bacteria
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no mitochondria, ER, or Golgi bodies
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prokaryotes
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can be unicellular or multicellular organisms
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eukaryotes
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possess a nuclear membrane, true nucleus, and mitochondria
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eukaryotes
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classified as either yeasts or moulds
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Fungi
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some fungi can be _____which means they exist as either a yeast or a mould
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dimorphic
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smallest infectious particles, cannot be seen with light microscopes
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viruses
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possess DNA or RNA but not both
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viruses
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require host cells for reproduction and metabolism
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obligate parasites
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genetic differences
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genotype
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observable similarities and differences
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phenotype
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closely related to prokaryotes, grow under extreme environmental conditions, not encountered in clinical microbiology
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archaeobacteria
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prokaryotic cells that infect eukaryotic hosts
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pathogenic bacteria
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what do antibiotics target?
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unique prokaryotic structures
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contains DNA as chromosomes (cell structure)
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nucleus
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main sites of energy production; own DNA (cell structure)
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mitochondria
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most eukaryotes do or do not have cell walls?
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do not
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this layer is present in both types (gram neg and gram pos) of prokaryotic cell walls
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peptidoglycan
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acid fast cell wall is seen on what type of cell walls
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gram positive
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what does the acid fast wall contain?
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lycolipids, fatty acid (mycolic acid) bound to the cell wall exterior
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what are some examples of bacteria with an acid fast wall
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mycobacterium, Nocardia
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bacteria without a cell wall and have sterols in their cell membranes
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mycoplasma, ureaplasma
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gram positive and gram negative cells that lose their cell walls
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L forms
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usually made of polysaccharide polymers; act as virulence factors
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capsules
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protein filaments that aid motility
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flagella
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short protein tubes that connect two bacterial cells and mediate DNA exchange
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pilli
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proteinaceous hairlike appendages that adhere bacterial cells to one another and to environmental surfaces
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fibriae
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what are the 3 basic microscopic shapes
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cocci (spherical), bacilli (rod), spirochetes(helical)
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what is the most commonly used stain in the clinical microbiology lab
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gram stain
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gram positive stains
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purple
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gram negative stains
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pink red
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what are the four components of the gram stain
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crystal violet (primary stain) iodine (mordant/fixative) alcohol/acetone (decolorizer) safranin (counterstain)
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used to stain bacteria with high lipid and wax content in their cell walls and mycobacteria
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acid fast stain
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primary stain of acid fast stains
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Carbolfuchsin (red dye)
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the acid fast stain penetrates the cell wall by which methods? (2)
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heat Ziehl Neelsen method detergent Kinyoun method
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acid fast what is the decolorizer and counterstain
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acidified alcohol, methylene blue
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what color do acid fast positive bacteria stain?
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pink red
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what color do acid fast negative bacteria stain?
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blue
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stain that is selective for the cell wall of acid fast bacteria where the AFB appear bright yellow or orange against a dark background
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Auramine Rhodamine Fluorescent
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fluorescent stain that stains gram positive and negative bacteria, binds to nucleic acid of the cell, used to locate bacteria in blood cultures
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Acridine Orange
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simple stain, only one step, used to stain corynebacterium diptheriae for observation of metachromatic granules, used as a counterstain for AFB
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methylene blue
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stain for cell walls of medically important fungi in wet mounts
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Lactophenol cotton blue
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negative stain, stains background and not subject, used for finding yeast Crytococcus neoformans in CSF
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india ink
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what are the thee major nutritional needs for growth in bacteria?
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carbon source for making cellular constituents nitrogen source for making proteins energy (ATP)
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bacteria group that is able to grow simply using Co2 as sole carbon sourc, only require water and inorganic salts in addition
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autotrophs
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bacteria group that require an organic carbon source, obtain energy by oxidation or fermentation, all bacteria that inhabit the human body is of this group
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heterotrophs
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what are the types of growth media?
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minimal, nutrient, enriched, selective, differential, transport
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what are the three environmental factors that influence the growth rate of bacteria?
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1. pH 7-7.5 2. Temperature 3. gaseous composition of the atmosphere
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Bacteria category that grows best at cold temp (10-20 C optimal)
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psychophiles
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Bacteria category that grows best at moderate temp (20-40 C optimal)
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mesophiles
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Bacteria category that grows best at high temp (50-60 C optimal)
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thermophiles
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atmospheric requirement for obligate aerobes
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presence of oxygen
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atmospheric requirement for obligate anaerobe
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no oxygen
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atmospheric requirement for facultative anaerobe
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grows either with or without oxygen
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atmospheric requirement for capnophilic
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increased CO2
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atmospheric requirement for microaerophilic
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requires reduced oxygen concentration for optimal growth
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what are the 4 phases of the bacterial growth curve
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1. lag 2. log 3. stationary 4. death
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efficient (aerobic) energy generating process, molecular oxygen is the final electron acceptor
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oxidation (respiration)
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anaerobic process, the electron acceptor is an organic compound, less efficient process than oxidation
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fermentation
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mechanism of gene transfer with uptake and incorporation of naked DNA into a bacterial cell
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transformation
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mechanism of gene transfer with transfer of bacterial genes by a bacteriophage from one cell to another
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transduction
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mechanism of gene transfer with transfer of genetic material from a donor bacterial strain to a recipient strain
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conjugation
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End of Chapter 1 ppts
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End of Chapter 1 ppts
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association of two organisms living together
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symbiosis
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living at the expense of the host
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parasitism
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having a neutral effect on the host
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commensalism
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bacteria that is found on or in body sites of healthy persons
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indigenous flora
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bacteria that colonize an area for months or years
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resident flora
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bacteria that are present at a body site for only a short period of time
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transient flora
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pathogenic organisms established in a host without manifesting symptoms
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carriers
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the most common carrier state is located where?
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hands
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most organisms are found on which layers of the skin?
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superficial
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skin mechanisms that help prevent infection
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skin separates bacteria from tissues fatty acids inhibit many bacteria lysozyme excreted in tears desquamation of the epithelium
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what is the predominant genus of mouth bacteria?
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Streptococcus
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what is the most common flora in the nose?
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S aureus, S epidermidis
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most of the flora in the large intestine is aerobic or anaerobic?
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anaerobic
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the ability of a microbe to produce disease in a susceptible individual
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pathogenicity
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organisms recognized to cause disease in healthy immunocompetent individuals
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true pathogens
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cause disease only if a change occurs in host resistance of the organism itself
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opportunistic pathogens
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an infection that occurs as a result of a medical treatment or procedure
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iatrogenic infection
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the degree of pathogenicity
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virulence
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how is virulence measured?
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the numbers of organisms necessary to cause infection in the host
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produced by both gram positive and negative bacteria, producing a heat labile toxin
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exotoxin
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produced by gram negative bacteria, producing a heat stable toxin composed of the LPS portion of the outer membrane of the cell wall
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endotoxins
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essential component in the resistance of the host to infectious agents
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phagocytosis
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the bodies first lines of defense
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segs, macrophages
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membrane bound vesicles that contain enzymes and other substances that kill and digest invading particles
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lysosomes
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what are the 4 phases of phagocytosis
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1. chemotaxis (segs travel to site and move into tissues via diapedesis, triggered by chemotactic agents) 2. attachment (facilitated by antibodies to the microorganism, opsonization to enhance phagocytosis by segs) 3. Ingestion (occurs rapidly after attachment, bacteria enclosed in a vacuole called a phagosome, the phagosome then fuses with lysosomes, releasing its contens into the phagosome (degranulation) ) 4. killing (increase in metabolic activity occurs in the segs or macrophage (respiratory burst), results in death of organism)
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the body's response to injury or foreign body, the hallmark is the accumulation of large numbers of phagocytic cells
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inflammation
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natural and nonspecific immunity
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innate
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immunity with antibodies and antigens, complement, and B& T lymphocytes
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adaptive
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what are the antibody types?
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IgG IgM IgA IgE
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transmission via animals
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zoonoses
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transmission through insects
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arthropods
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the destruction of all forms of life including spores
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sterilization
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the removal of pathogenic organisms (maybe spores)
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disinfection
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disinfectant applied to living tissue
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antiseptic
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controlling of microorganisms heat methods
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autoclave, dry heat, boiling, pasteurization
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controlling of microorganisms chemical methods
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alcohols, aldehydes, halogens, heavy metals, detergents, phenolics, gases
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what is the main role of handwashing
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to remove transient flora
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2 major sources of biologic hazards in the microbiology lab
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processing of patient specimens, handling of the actively growing cultures
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most common agents associated with lab acquired infections
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mycobacterium tuberculosis, brucella species, francisella tularensis, coccidioides immites, bacillis anthracis, Hepatitis B, C, HIV
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Biosafety level: organisms well classified
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1
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Biosafety level: organisms that cause a moderate potential hazard
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2
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biosafety level: organisms have the potential for aerosol transmission; diseases may be lethal
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3
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biosafety level: organisms are dangerous and exotic; have a high risk of aerosol transmitted infections and death
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4
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identifies chemicals for employee personell
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NFPA diamond
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sheet for every hazardous chemical provided by the manufacturer
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MSDS (material safety data sheets)
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fire extinguisher class: ordinary combustible materials; water or dry chemical type to cool
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A
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fire extinguisher class: flammable liquids, gases, and greases; CO2 or dry chemical type to smother
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B
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fire extinguisher class: electrical fires; CO2 or dry chemical type to smother
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C
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Laboratory response network
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sentinel laboratories, reference laboratories, national laboratories
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measures designed to ensure the medical reliability of laboratory data
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Quality Control
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measures taken to assure high quality patient care
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Quality Assurance
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how is quality assurance measured
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patient outcome
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how often are temperature checks required for temperature dependent equipment?
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daily
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the reference thermometer is provided by
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NIST (national institute of standards and technology)
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how often is personnel competency tested via "unknowns"
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at least twice annually
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the frequency of positive test results in patients WITH a disease
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true positive results (sensitivity)
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what is the formula for sensitivity expressed (formula)
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(number of true positive results / number of true positive + false negative results) x 100
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the frequency of negative test results in patients WITHOUT a disease
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true negative results (specificity)
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formula for specificity
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(number of true negative results/ number of true negative + false negative results) x 100
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the number of new cases of a disease over a period of time
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incidence of disease
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the frequency of a disease at a designated single point in time in the population being tested
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prevalence
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for chronic diseases, the prevalence must be _____than the incidence, for acute diseases, the prevalence is _______than the incidence
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greater less
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a test can have what types of predicative values
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positive and negative
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what three elements are needed to compute the positive and negative predicative values of a test
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sensitivity of a test specificity of a test prevalence of the disease being tested
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the proportion of patients with positive test results who are correctly diagnosed. It reflects the probability that a positive test reflects the underlying condition being tested for
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positive predictive value
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the proportion of patients with negative test results who are correctly diagnosed
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negative predictive value
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a specimen should be taken during which phase of an infection (and before antibiotics are started)
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acute
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___is an excellent specimen if taken from line of infection
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tissue
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a tissue sample must be protected from____
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drying
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what is the best specimen from a wound or lesion
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aspirate of pus
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an aspirate of an unopened wound is far better, especially for these types of organisms
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anaerobes
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this collection method is considered inferior and should be used as a last resort
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swabs
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what are the 4 basic rules of swab collection:
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1. clean the wound 2. explore the wound (find sinus tracts if present) 3. obtain fresh culture material 4. obtain adequate quantity of specimen
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why are two swabs needed for a collection?
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one for culture, one for gram stain
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if only one swab is submitted, which specimen should be processed?
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culture
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_____urine specimen is most concentrated
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first morning
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this is among the most difficult specimens to collect adequately, first morning is the best time
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sputum
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three vial kits are usually used for _____collection
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stool
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we do not collect a stool specimen if it has been within 4 days of what type of procedure?
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barium
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ideally, specimens should be transported to the lab in what timeframe
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within 2 hours of collection
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preservatives can be used with what types of specimens
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urine and stool
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what is the most common anticoagulant used for microbiology specimens?
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SPS
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aside from SPS, what type of anticoagulant is acceptable
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heparin
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media that contains substances that do not promote multiplication of organisms
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holding or transport media
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_____is an example of bedside inoculation
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JEMBEC system
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how should patient specimens and culture isolates by shipped?
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triple packaged
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what is the Level 1 prioritization for processing?
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critical/invasive such as CSF, body fluids, brain, BAL
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what is the level 2 prioritization for processing?
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unpreserved such as sputum, stool, tissue, pus, bone
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what is the level 3 prioritization for processing?
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require quantitation such as urine, quantitative tissues, catheter tips
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what is the level 4 prioritization for processing?
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protected specimens such as culturettes, specimens, in holding medium
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anaerobes would be inappropriate in what types of specimens?
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throat, stool, sputum
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what would be some examples of unacceptable specimens?
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requisition and specimen info do not match specimen in inappropriate or leaking container stools contaminated with urine or barium anaerobes on inappropriate specimens dried up specimens specimens in formalin formed stools for culture foley catheter tips
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what is the purpose of the microscopic direct exam
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determines specimen quality aids in infectious disease diagnosis guides routing culture interpretation dictates need for nonroutine processing
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when should culture plates be viewed
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after direct smear has been evaluated
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when is the direct smear not useful?
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gram stain on throat or nasopharyngeal swab routing gram stain on urine rectal smear for gonococci routine gram stain on stool
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media that supports the growth of most nonfastidious organisms (BAP)
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nonselective
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media that support the growth of one type of microbe over another (MAC/CNA)
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selective
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media that groups bacteria on the basis of metabolic differences (MAC)
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differential
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media that contains growth enhancers to allow fastidious organisms to grow (CAP)
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enriched
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broth media designed to encourage the growth of small numbers of a particular organism while suppressing other flora present (GN broth; LIM broth)
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enrichment broth
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media used as a supplement to agar plates to detect small numbers of most aerobes, anaerobes, and microaerophiles (Thio, BHI broth)
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broth media
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what are the requirements for routine primary plating media:
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nonselective agar plate, enriched medium, selective and differential medium for enteric GNRs, selective plate for gram positive organisms, broth medium, special need media
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what is the plating protocol for body fluid (CSF)
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BAP, CAP, THIO
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what is the plating protocol for throat?
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BAP, CAP
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what is the plating protocol for wound/tissue
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BAP, CAP, MAC, CNA, THIO
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what is the plating protocol for urine?
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BAP, MAC, CNA
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what is the plating protocol for sputum?
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BAP, CAP, MAC
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CAP
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chocolate agar
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BAP
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blood agar
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MAC
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Macconkey agar
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CNA
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columbian agar
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THIO
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broth media
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this streak method is used when specimen numbers are expected to be low
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inoculum counter streak method
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with the inoculum counter streak method, 1 colony is equal to what?
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1,000 CFU/ml
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most bacterial cultures are incubated at what temperature?
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35-37C
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most cultures are held for what amount of time?
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48-72 (18-24 for some)
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how do you process an implant soak solution?
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filtration
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how do you process a water sterility specimen?
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filtration
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how do you process a medical equipment specimen?
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swabs (difficult to culture)
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how do you process an IUD specimen
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can require a lengthy incubation
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how do you process a catheter tip specimen
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Maki method (>15 colonies significant)
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how do you prepare a smear from a swab
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roll it
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how do you prepare a smear from thick liquids or semisolids?
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immerse swab in specimen, prepare a thin smear on slide
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how do you prepare a swab from thick, granular, or mucoid materials?
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have thick and thin areas on a smear, crush granules between two slides
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how do you prepare a slide from thin fluids?
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drop but do not spread on slide; allow to dry cytocentrifugation preferred for this type of specimen
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a gram positive reaction (color)
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purple
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a gram negative reaction (color)
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pink-red
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acid fast stains are used for the visualization of
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mycobacteria
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what are the three major acid fast stains?
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Kinyoun, Ziehl-Neelsen, Auramine (fluorescent)
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this white fluorescence stain is used to visualize fungal elements (binds to chitin)
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Calcofluor white stain
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this stain is a simple stain used to visualize metachromatic granules of Corynebacterium diptheriae
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methylene blue
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this is a negative stain used to demonstrate yeast of Crytococcus neoformans in CSF
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india ink
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The Bartlett's Method for scoring sputums is based on the numbers of what?
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squamous epithelial cells, and segs
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10-25 segs per 10x field makes specimen acceptable or unacceptable?
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acceptable
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10-25 squamous epithelial cells (SECs) per 10x field makes specimen acceptable or unacceptable?
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unacceptable
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what does staphylococcus look like
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gram positive cocci in clusters
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what does streptococcus look like?
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gram positive cocci in chains
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what does streptococcus pneumoniae look like?
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gram positive lancet shaped diplococci
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what does clostridium perfringens look like?
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anaerobic, square ended gram positive rods
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what does Neisseria gonorrhoeae look like?
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gram negative, kidney bean shaped diplococci
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what does Haemophilus influenzae look like?
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small, plemorphic gram negative rods
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what does Klebsiella pneumonia look like?
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bipolar staining gram negative rods (safety pins)
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what does candida albicans look like?
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budding yeast with pseudohyphae present
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what does Fusobacterium look like?
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long, thin gram negative rods with pointed ends
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partial clearing of blood around colonies, greenish color
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alpha hemolysis
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complete clearing of blood around colonies, clear zone around colonies
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beta hemolysis
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odor of Staphylococcus aureus
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old sock
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odor of Pseudomonas aeruginosa
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fruity, grape like
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odor of Haemophilus
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"mousey"; musty basement
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odor of Nocardia
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freshly plowed earth
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lactose is a disaccharide of what (2 )
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glucose, galactose
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two enzymes necessary for a bacterium to take up lactose
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beta glactoside permease, beta glactosidase
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acts as a transport enzyme
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beta galactoside permease
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acts to hydrolyze lactose into glucose and galactose
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beta galactosidase
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lactose fermenters possess which enzymes?
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beta galactoside permease beta galactosidase
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species that have only beta galactosidase are called what (2)
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delayed lactose fermenters or slow fermenters
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in what two ways can bacteria utilize carbohydrates?
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oxidation, fermentation
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bacteria that do not use any carbohydrates are called
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asacchrolytic
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test with carbohydrates and peptone. 2 tubes, one open and one overlaid with mineral oil.
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Hugh Leifson oxidation fermentation (OF) medium
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in the OF medium, no acid in either tube signifies
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nonoxidizer/nonfermenter
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in the OF medium, acid in the open tube only signifies
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oxidizer
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in the OF medium, acid in both tubes signifies
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oxidizer and fermenter
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what are the sugars and ratios in the TSI agar
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lactose, sucrose, glucose 10:10:1
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ferrous sulfate added to the sugars in the TSI agar are used to detect what?
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presence of H2S
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what is the pH indicator for TSI?
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phenol red
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when should reactions be read for TSI?
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within an 18 to 24 hour incubation period
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TSI agar no fermentation (typical of organisms that are NOT enterobacteriacaea) is written as
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K/K
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TSI agar glucose only fermentation (critical to read at 18-24 incubation) is written as
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K/A
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TSI agar lactose (sucrose) fermentation is read as
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A/A
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TSI agar black butt means
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hydrogen sulfide production H2S
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how is gas production visualized?
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bubbles or splitting of the medium, complete displacement of the medium
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this test determines if the organism is a slow or late lactose fermenter
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ONPG
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In the ONPG test, bta galactosidase acts on the ONPG and cleaves it, forming what color compound (positive result)?
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yellow
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what two pathways do enterics take to degrade pyruvic acid?
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mixed acid fermentation pathway butylene glycol pathway
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what tests detect the end products of glucose metabolism
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Methyl Red, Voges-Proskauer
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methyl red test detects what?
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acidic end products (lowers the pH)
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what is a methyl red test positive result
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red
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what does Voges Proskauer test detect?
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presence of acetoin
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Voges Proskauer test, what is acetoin converted to?
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diacetyl
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Voges Proskauer test, diacetyl in the presence of KOH and a-naphthol forms what complex (positive result)
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red
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what are the three amino acids tested in Decarboxylase tests
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lysine ornithine arginine
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what is the base medium in Decarboxylase tests
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Moeller
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How are Decarboxylase tests read?
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purple negative, yellow positive
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Phenylalanine Deaminase (PAD) has a positive test result if when there is an addition of _______, it produces the color______
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ferric chloride, green
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what does Phenylalanine Deaminase (PAD) help to differentiate
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Proteus, Morganella, Providencia from other Enterobacteriaceae
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what does citrate utilization determine
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whether an organism can utilize citrate as its sole carbon source
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what is the pH indicator in citrate utilization
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bromthymol blue
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what are the possible results of the citrate utilization test
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green to blue if positive
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indole is a byproduct of what?
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the degradation of the amino acid tryptophan
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what is the enzyme in the indole test?
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trayptophanase
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is ecoli positive or negative for the indole test?
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positive
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a positive indole test has what type of color?
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red
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in this test, two tubes are used; one at room temp and one at 35C
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motility test
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what two reagents are added after incubation in a nitrate bath for the nitrate reduction test
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alpha naphthylamine, sulfanilic acid
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in the nitrate reduction test, a positive red test means what?
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reduced nitrate to nitrite
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in the nitrate reduction test, a clear result means what
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to add zinc leading to either a pink for negative or clear for positive result
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what does the oxidase test detect
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the presence of the enzyme cytochrome c oxidase
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in the oxidase test, what color compound is produced when tetramethyl p phenylendiamine reacts with cytochrome c
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blue
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is pseudomonas positive or negative for the oxidase test
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positive
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the urease test determines what?
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whether an organism hydrolyzes urea, releasing ammonia to produce a color change
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in the urease test, a positive result looks like
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bright pink
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what medium can be used for the urease test
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Stuart's Urea Broth, Christensen's Urea Agar
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lyophlized biochemicals and carbohydrates in cupules (test)
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analytical profile index (API)
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lyophilized biochemicals and antibiotics in cred card sized cards for ID and sensitives
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Vitek 2 system
