Microbiology Lab Final

Ascaris lumbricoides (HELMINTH)

- "large roundworm" up to 35 cm - live in intestine, Ascaris eggs in feces - live in lumen of small intestine > - largest & most widespread of all human intestinal roundworms (Nematode) - causes: ascariasis - Kingdom: Animalia - Phylum: Nematoda - Class: Chromadorea - Order: Ascaridida - Family: Ascarididae - Genus: Ascaris

Mesophiles

- 20 C to 40 C - live in humans

Clonorchis sinensis (Oriental Liver Fluke)

- 20 mm x 5 mm - trematodes - snails are the first intermediate hosts - snail > fish > mammal - East Asia - Adults live in the lumen of the bile duct and thought to feel on bile, have both male and female parts so don't need another to reproduce - eat bile and reduce nutrients, or bile ducts blocked - require a second intermediate host - Kingdom: Animalia - Phylum: Platyhelminthes - Class: Rhabditophora - Order: Plagiorchiida - Family: Opisthorchiidae - Genus: Clonorchis

Pseudomonas aeruginosa

- Gram negative, rod-shaped single, flagella, obligate aerobic - Negative: indole test, urease, H2S, coagulase, gas, MR, non-spore, VP, urease, Lactose, Sucrose - Positive: motility, catalase, oxidase, citrate, Gelatin Hydrolysis, nitrate reduction, blue green pigment, TSIA (A/A), glucose, Mannitol - Beta hemolysis - Domain: Bacteria - Phylum: Proteobacteria - Class: Gammaproteobacteria - Order: Pseudomonadales - Family: Pseudomonadaceae - Genus: Pseudomonas

Mycobacterium smegmatis

- Gram positive, bacillus single, aerobic - Kingdom: Bacteria - Phylum: Actinobacteria - Class: Actinobacteria - Order: Actinomycetales - Family: Mycobacteriaceae - Genus: Mycobacterium - Negative: non-spore, lactose, Gelatinase, Citrate, gamma hemolysis - Positive: glucose, catalase, Acid Fast

Streptococcus pneumoniae

- Gram positive, cocci diplococci, facultative anaerobic - alpha or beta-hemolytic, - Negative: spore, motile, catalase -Positive: encapsulated, bile soluble - Domain: Bacteria - Phylum: Firmicutes - Genus: Streptococcus

Sporosarcina ureae

- Gram positive, cocci in packets or cluster, spore former, motile, aerobic - Domain: Bacteria - Phylum: Firmicutes - Class: Bacilli - Order: Bacillales - Family: Planococcaceae - Genus: Sporosarcina - Positive: urea to ammonia, Catalase, Milk Agar, Starch Agar - Negative: starch, casein, gelatin, Mannitol, Oxidase, Glucose, Lactose, O2, Gelatinase, Urease, Methyl Red, V.P., Indole, Citrate Morphology: yellow. MacConkey Agar: no growth. Sheep's Blood Agar: 24hr gamma (alpha ?),48hr alpha. TSI: K/K Litmus Milk: K

Proteus vulgaris

- Gram-negative bacterium, rod shape, flagella, single or pair or short chains somewhat cluster - areobe or Facultative anaerobic - Positive: nitrate-reducing, indole-positive and catalase-positive, H2S producing, motility, citrate, urease, H2S, - Negative: non-capsule, oxidase, spore, capsule, gamma hemolysis none - Kingdom: Bacteria - Phylum: Proteobacteria - Class: Gammaproteobacteria - Order: Enterobacterales - Family: Morganellaceae - Genus: Proteus

Moraxella catarrhalis

- Gram-negative, aerobic, diplococcus - upper respiratory tract - positive: oxidase, catalase, fastidious, motility, methyl red, VP, - negative: nonmotile, glucose, maltose, fructose, sucrose, indole, urease, lactose, mannitol, - Kingdom: Bacteria - Phylum: Proteobacteria - Class: Gammaproteobacteria - Order: Pseudomonadales - Family: Moraxellaceae - Genus: Moraxella

Alcaligenes viscolactis

- Gram-negative, aerobic, rod-shaped bacteria - Biosafety Level: 1, Oxidase Positive, Aerobic

Vibrio cholerae

- Gram-negative, comma-shaped vibrio, flagellated - Beta hemolysis - Positive: oxidase, nitrate, Citrate, Gelatin Hydrolysis, Indole, motile, Nitrate Reduction, Mannitol, Glucose - Negative: capsule, gas, H2S, MR, Urease - Domain: Bacteria - Phylum: Proteobacteria - Class: Gammaproteobacteria - Order: Vibrionales - Family: Vibrionaceae - Genus: Vibrio

Klebsiella pneumoniae

- Gram-negative, encapsulated, rod-shaped bacterium - on chocolate agar - non-hemolytic - lactose-fermenting, facultative anaerobic, non-motile - Positive: Catalase, Citrate, Gas, Urease, VP, Mannitol - Negative: Flagella, Gelatin Hydrolysis, H2S, Indole, MR (Methyl Red), Oxidase, Spore,

Escherichia coli

- Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium, sinlge or pair (Biosafety 1) - motile - Domain: Bacteria - Phylum:Proteobacteria - Class: Gammaproteobacteria - Order: Enterobacterales - Family: Enterobacteriaceae - Genus:Escherichia - beta hemolysis: strong fermenter - Negative: urea, H2S, - Positive: Glucose fermentation, gas, lactose, mannitol - Indole production: positive - Methyl red: positive - Voges-Proskauer: negative - Citrate (Simmons): negative - Hydrogen sulfide (TSI): negative - Urea hydrol: negative - Lysine decarb: positive

Alcaligenes faecalis

- Gram-negative, rod-shaped bacteria Phylum: Proteobacteria Class: Beta Proteobacteria Order: Burkholderiales Family: Alcaligenaceae Genus: Alcaligenes Species: faecalis - flagella, motile, aerobic microbe - urinary tract, bacterial keratitis and postoperative endophthalmitis - soil and water environments - ferment galactose, catalase positive, H2S neg

Shigella sonnei

- Gram-negative, rod-shaped pairs or single, nonmotile, non-spore-forming - lactose-fermenting - Negative: Indole, Voges-proskauer, citrate, Urease, H2S, oxidase, motility, Sucrose, Gelatine, lactose, - Positive: Methyl Red, D-mannitol, Oxidase fermentation, Catalase production - Domain: Bacteria - Phylum: Proteobacteria - Class: Gammaproteobacteria - Order: Enterobacterales - Family: Enterobacteriaceae - Genus: Shigella

Salmonella typhimurium

- Gram-negative, rod-shaped single or pair, facultative aerobic, - typhoid fever - gamma hemolysis, none - Negative: lactose fermenter, capsule, citrate, gas, gelatin, indole, oxidase, spore, urease, VP, Lactose, Sucrose - Positive: catalase, flagella, H2S, motility, MR, nitrate, TSIA (A/A), Glucose, Mannitol, - Domain: Bacteria - Phylum: Proteobacteria - Class: Gammaproteobacteria - Order: Enterobacterales - Family: Enterobacteriaceae - Genus: Salmonella

Pseudomonas fluorescens

- Gram-negative, rod-shaped, single - Positive: catalase, oxidase, motility, methyl red test, gelatin, Simmons Citrate Utilization, starch, - hemolytic activity - Negative: indole, Voges Proskauer, urease, lactose - Domain: Bacteria, EMB - Phylum: Proteobacteria - Class: Gammaproteobacteria - Order: Pseudomonadales - Family: Pseudomonadaceae - Genus: Pseudomonas

Lactococcus lactis

- Gram-positive bacterium, non motile, non-spores, cocci, chains - Kingdom: Bacteria - Division: Firmicutes - Class: Bacilli -Order: Lactobacillales - Family: Streptococcaceae - Genus: Lactococcus - Positive: glucose, lactose, mannose, esculin hydrolisis - Negative: catalase, acid production, oxidase, motility, acid fast

Sarcina aurantiaca

- Gram-positive, cocci bacteria 2 or 4 arrangement - bright yellow colonies on agar - Positive: uric acid, catalase - Negative: indole, citrate, mannitol, urease, non-spore - Kingdom: Bacteria - Phylum: Firmicutes - Class: Clostridia - Order: Clostridiales - Family: Clostridiaceae - Genus: Sarcina

Viridans streptococci

- Gram-positive, cocci chains not as long as streptococcus - alpha hemolysis - Negative: capsule, bile insoluble, Optochin resistant, - Positive: oral infections - Kingdom: Bacteria - Phylum: Firmicutes - Class: Cocci - Order: Lactobacillales - Family: Streptococcaceae

Streptococcus pyogenes (group A)

- Gram-positive, cocci chains, facultative aerotolerant bacterium, capsulated - beta hemoysis - bacitracin susceptible - Negative: non-motile, non-spore, Catalase, oxidase, Urease, VP, Mannitol - Positive: Galactose, glucose, Lactose

Streptococcus dysgalactiae (group C)

- Gram-positive, cocci in chain, non motile - Beta hemolysis or Alpha - Negative: catalase, oxidase, VP, - Positive: glucose, maltose, sucrose,

Staphylococcus saprophyticus

- Gram-positive, cocci, non-hemolytic, facultative anaerobe - infection in urine - Negative: coagulase, hemolysis - Positive: Urease, resistant novobiocin disk, sucrose, maltose

micrococcus luteus

- Gram-positive, nonmotile, coccus, tetrad-arranging (4), obligate aerobe - Colonies are circular, yellow, convex and smooth - Negative: oxidase, non-fermenter, glucose, sucrose, - Positive: gelatinase, vancomycin susceptible, bacitracin susceptible, urease and catalase - Kingdom: Bacteria - Phylum: Actinobacteria - Order: Micrococcales - Family: Micrococcaceae - Genus: Micrococcus

Bacillus cereus

- Gram-positive, rod-shaped, facultatively anaerobic, motile, beta-hemolytic, spore forming bacterium commonly found in soil and food. - Catalase Positive (+ve) - Citrate Positive (+ve) - Gelatin Hydrolysis Negative (-ve) - Gram Staining Positive (+ve) - Growth in KCNPositive (+ve) - Hemolysis Positive (+ve) - Indole Negative (-ve) - Motility Positive (+ve) - MR (Methyl Red)Negative (-ve) - Nitrate Reduction Variable - Oxidase Negative (-ve) - Pigment Negative (-ve) - VP (Voges Proskauer)Positive (+ve)

Clostridium sporogenes

- Gram-positive, strict anaerobic, rod-shaped bacterium that produces oval, subterminal endospores, heat resistant common in soil - Phylum: Firmicutes -Class: Clostridia Order: Clostridiales - Family: Clostridiaceae Genus: Clostridium - biosafety level 1 - bete-hemolysis - Catalase-negative. Obligately anaerobic. Motile - H2, gelatin hydrolysis, lipase, acid production from glucose

Which of the following statements best describes the StaphTEX agglutination assay that you will be using in this lab? (Choose all that apply)

- It uses latex beads that are covered in antibodies that are specific to a particular pathogen. - Agglutination will occur only if a specific pathogen is mixed with the StaphTEX reagent.

Aspergillus spp. (FUNGI)

- Kingdom: Fungi - Division: Ascomycota group - Class: Eurotiomycetes - Order: Eurotiales - Family: Trichocomaceae - Genus: Aspergillus - produce asexual spores= conidia - flower appearance - up to 400 x 50 µm or much shorter - few hundred mold species

Enterobacter aerogenes

- Klebsiella aerogenes - gram-negative, rod-shaped, single arrangement - Facultative anaerobic - nosocomial and pathogenic bacterium - catalase positive, citrate positive, motility, no hemolysis, gas positive, VP positive, nitrate positive, gas flagella capsule positive, lactose fermenter (McConkey) - oxidase negative, indole negative, Gelatin Hydrolysis negative, H2S Negative, MR negative, urease and spore negative - no hemolysis

Citrobacter freundii

- Motility, long rod shape, no spores, gram-negative, single or pair - Capsule Negative (-ve) - Catalase Positive (+ve) - Citrate Positive (+ve) - Flagella Positive (+ve) - Gas from glucose Positive (+ve) - Gelatin Hydrolysis Negative (-ve) - Growth in KCN Positive (+ve) - H2SPositive (+ve) - Indole Negative (-ve) - MR (Methyl Red)Positive (+ve) - Nitrate Reduction Positive (+ve) - OF (Oxidative-Fermentative) Facultative Anaerobes Oxidase Negative (-ve) - Urease Variable VP (Voges Proskauer) Negative (-ve) - Phylum: Proteobacteria Class: Gammaproteobacteria Order: Enterobacteriales Family: Enterobacteriaceae Genus: Citrobacter

Micropipette

- P20 read ex. 20__=20.0 or 03_4_= 3.4 - P200 reads 20-200 ex. 124=124 or 026=26 - P1000 (can be used between 100-1000, but P200 is more accurate) reading ex __23= 230 _1_00=1000

TSA and SDA are inoculated separately

- Sabouraud Dextrose Agar - Tryptic Soy Agar (in inoculator)

Eosin Methylene Blue (EMB) Agar

- Selects for Gram-negatives - Differential for lactose fermenters POSITIVE= dark purple to black (sometimes with a green metallic sheen) - Escherichia coli = green metallic sheen (vigorous fermenter E. coli and sometimes C. freundii) - Enterobacter or Klebsiella = colonies from pink (weak, K. aerogenes) to dark purple on the medium with dark center (weak, Citrobacter freundii) - Nonfermenters and sucrose fermenters = color of media, no change (Alcaligenes viscolactis) - isolates fecal coliforms - contain: peptone, lactose, sucrose, and the dyes eosin Y and methylene blue

SIM (Sulfide, Indole, Motility) (IMViC)

- Tests for enteric bacteria for presence of sulfur & motility the indole - (+) black color due to H2S production from sulfide - (+) Red color, Indole present, change occurs by Kovac's reagent - (+)diffusion, meaning bacteria moved around the inoculated stab

Amoeba proteus (PROTOZOAN)

- aerobic respiration, non pathogenic - carbon dioxide and nitrogenous waste excreted through diffusion - Domain: Eukaryota - (unranked): Amoebozoa - Class: Tubulinea - Order: Tubulinida - Family: Amoebidae - Genus: Amoeba - phospholipid bilayer, single celled, organelles, nucleus, cell membrane, pseudopodia - average: 0.2 to 0.3 mm

Entamoeba histolytica (PROTOZOAN)

- amoebic dysentery in humans, does not have the golgi apparatus, the organelle responsible for modifying and transporting proteins - Cysts (stool, produced in large intestine) and trophozoites (diarrhea stool)(small intestine) - Domain: Eukaryota - Phylum: Protozoa - Subphylum: Sarcomastigophora - Class: Archamoebae - Family: Entamoebidae - Genus: Entamoeba

Trichomonas vaginalis (PROTOZOAN)

- anaerobic, flagellated protozoan parasite - Trichomoniasis infect the vagina, the urethra, under the foreskin of the penis - most common pathogenic protozoan industrial countries - women: foul-smelling vaginal discharge, genital itching, and painful urination - men: often no symptoms - Phylum: Metamonada - Order: Trichomonadida - Family: Trichomonadidae - Genus: Trichomonas

Rhizopus stolonifer (FUNGI)

- black bread mold - Zygomycota considered the most important species in the genus Rhizopus - common in tropical and subtropical regions - Kingdom: Fungi - Order: Mucorales - Family: Mucoraceae - Genus: Rhizopus - grow on ammonium salts or amino compounds - up to 2.5 mm long and about 20 μm in diameter - UV can delay spore germination - zygospores: compatible mating strains of sexual reproduction

Schistosoma sp. (Blood flukes)

- blood trematodes (flukes) - Schistosoma haematobium, S. japonicum, and S. mansoni - dioecous (separate sexes) not hermaphroditic - eggs released in feces or urine > hatch & release miracidia > swim and penetrate snails > two generations of sporocysts & cercariae productionin snail > penetrate human host > become schistosomula > lungs > heart > liver, leave once mature > Male and female copulate > release egg in urine... - Kingdom: Animalia - Phylum: Platyhelminthes - Class: Trematoda - Order: Diplostomida - Family: Schistosomatidae - Genus: Schistosoma

Capsule stain

- capsule remains unstained and forms a while ring around stained cell and background -red/pink - This stain is used to detect cells capable of producing biofilm. - Streptococcus pneumoniae and Neisseria meningitides - India ink, no heat or blot dry, crystal violet

acid fast stain

- carbolfuchsin primary stain - heat mordant - acid-alcohol mordant - methylene blue counterstain - only gram positive

Dipylidium caninum (Dog tapeworm)

- cyclophyllid cestode infects organisms with flees - flea tapeworm, double-pored tapeworm, or cucumber tapeworm - proglottids disintegrate and release egg packets > oncosphere penetrates the intestinal wall invades body cavity > develops into cysticercoid > remains in flea & becomes larva into an adult > vertebrate host becomes infected by ingesting adult flea > in small intestine develops into adult > Gravid, double-pored proglottids detach from body and shed in feces - Kingdom: Animalia - Phylum: Platyhelminthes - Class: Cestoda - Order: Cyclophyllidea - Family: Dipylidiidae - Genus: Dipylidium

Uses and evaluation of starch agar

- differential for bacteria that produce amylase will areas around test will digest starch (clear zone) - ex. bacillus subtilis, bacillus megaterium - non ex. pseudomonas aeruginosa, Escherichia coli, staphylococcus epidermidis

Phenol Red (PR) Broth

- differential test medium carbohydrate is added. Contains: dextrose, lactose, sucrose - peptone and phenol red (pH), Durham tube (gas indicator) - preparation= red - acid production fermentation of carbohydrate= yellow

Urea hydrolysis (UREASE TEST)

- differentiate organisms based on ability to hydrolyze urea with the enzyme urease. - produce ammonia and carbon dioxide overcome buffer - positive= pink change - Proteeae (urinary tract pathogens) and other other Enterobacteriaceae

Thermophiles

- exceed 50 C - may be in hot springs

Giardia lamblia (PROTOZOAN)

- flagellated unicellular eukaryotic parasitic microorganism, 2 nuclei, 4 flagella - colonizes and reproduces in small intestine, attaches to epithelial by adhesive disc or sucker, reproduces via binary fission - spread by contaminated food or water, or person to person - tolerant to chlorine disinfectants - Giardia trophozoites are anaerobes in small intestine - Cysts are in feces and are dormant until ingested and in small intestine - 10 to 20 micrometers long, 7 to 10 micrometers across - can break down glucose - Kingdom: Protista Subkingdom: Protozoa - Phylum: Sarcomastigophora - Phylum: Metamonada - Class: Zoomastigophora - Order: Diplomonadida - Family: Hexamitidae - Genus: Giardia

IMViC

- four individual tests, used to identify bacterial species, especially coliforms, differentiating the Enterobacteriaceae - Indole production (for which we use SIM medium) - methyl red test - Voges-Proskauer test - citrate production

Serratia marcescens

- gram negative, rod shaped, facultative anaerobic, - gamma hemolysis, except phlA gene - Positive: Catalase, Citrate, Flagella, gas (sometimes), Gelatin Hydrolysis, Motility, Nitrate Reduction, Pigment, Urease, VP (Voges Proskauer), Galactose, Glucose, Mannitol, Sucrose - Negative: Capsule, H2S, Indole, MR (Methyl Red), Oxidase, Spore, Lactose, - Domain: Bacteria - Phylum: Proteobacteria - Class: Gammaproteobacteria - Order: Enterobacterales - Family: Yersiniaceae - Genus: Serratia

Staphylococcus epidermidis

- gram positive, cocci in clusters - Morphology: pale, yellow, ivory, cream. - Positive: Mannitol, Catalase, Nitrogenase - Negative: Oxidase, Milk Agar, Starch Agar, Glucose, Lactose, Gelatinase, Urease, Indole, Methyl Red, V.P., Citrate - MacConkey Agar: no growth. - Sheep's Blood Agar: 24hr gamma (alpha),48hr alpha TSI: A/K

Kocuria rosea

- gram-positive bacteria, coccus staphylococci obligate aerobe, non-spore - no hemolysis - Domain: Bacteria - Phylum: Actinobacteria - Order: Actinomycetales - Family: Micrococcaceae - Genus: Kocuria - catalase-positive and oxidase-negative

Enterococcus faecalis

- gram-positive bacterium, cocci, short chains or pair - Order: Lactobacillales - Rank: Species - Higher classification: Enterococcus - Phylum: Firmicutes - Family: Enterococcaceae - negative: Capsule, Catalase, Citrate, Flagella, H2S, Hemolysis, Indole, Motility, Oxidase, Spore, Urease - positive: VP, Glucose, Lactose, Mannitol - gamma hemolysis, none

Corynebacterium pseudodiphtheriticum

- gram-positive, bacilli, single or pair, V formation - non-motile and not acid-fast - nonfermentive, urease catalase & nitrate-positive - Obligate aerobic - vancomycin- susceptible - Domain: Bacteria -Phylum: Actinobacteria -Class: Actinobacteria - Order: Corynebacteriales - Family: Corynebacteriaceae - gamma hemolysis, none

Streptococcus agalactiae (group B)

- gram-positive, coccus chains, facultative anaerobe - beta hemolysis - Negative: catalase, Mannitol, Coagulase, non-flagella, Oxidase, non-motile, Urease, non-spore, - Positive: Capsule, Glucose, VP (Voges Proskauer) sometimes - Domain: Bacteria - Phylum: Firmicutes - Class: Bacilli - Order: Lactobacillales - Family: Streptococcaceae - Genus: Streptococcus

Bacillus subtilis

- hay bacillus or grass bacillus, small clumps short chains or single - Gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants and humans - spore forming, facultative aerobe - phylum: Firmicutes, class: Bacilli, order: Bacillales, family: Bacillaceae - Catalase Positive (+ve) CitratePositive (+ve) Flagella Flagellated Gas Negative (-ve) Gelatin Hydrolysis Positive (+ve) Gram Staining Gram Positive (+ve) Indole Negative (-ve) Motility, MR (Methyl Red) Negative (-ve) Nitrate Reduction Positive (+ve) Oxidase Variable Pigment Negative (-ve) Urease Negative (-ve) VP (Voges Proskauer) Positive (+ve)

Penicillium notatum (FUNGI)

- inhibit gram-positive bacteria - temperate and subtropical regions - damp water damaged buildings - Alexander Fleming figured out that penicillin could inhibit bacteria

Which of the following statements regarding blood agar are correct? (Choose all that apply)

- it is an important clinical medium - it supports the growth of fastidious bacteria - it is typically TSA plus 5% sheep's blood

endospore stain

- malachite green, steam, rinse, safranin

Saccharomyces cerevisiae (FUNGI)

- mature cells (vegetative cells) are gram-positive - ascospores are gram-negative - Kingdom: Fungi - Division: Ascomycota - Class: Saccharomycetes - Order: Saccharomycetales - Family: Saccharomycetaceae - Genus: Saccharomyces - diameter: 2-8 μm - length: 3-25 μm - Blastoconidia (cell buds) - Hyphae are absent

aseptic technique

- method used to prevent the environment, the worker, and the patient from being introduced to bacteria or contamination - heat inoculating tool and test tools, never drop cap, sterilize surface, gloves

Biosafety 1

- non pathogenic, lowest safety, no hazard bin needed, supervision of scientist or trainer - Still must: wash hands, wear gloves, wear coat, wear goggles, limit access to people, disinfecting, warning sings - Ex. Non-pathogenic strain of E. coli

Sabouraud Agar (SAB)

- pH inhibits some bacterial growth, primarily for dermatophytes, fungi - Made up of: dextrose, peptone, agar, distilled water - selective for yeast and fungi - determine: microbial contamination in food, cosmetics, and clinical specimens - Yeasts: creamy to white colonies - Molds: filamentous colonies of various colors

Taenia sp. (Tapeworm)

- parasitic infection caused by the tapeworm - Taenia saginata, T. solium or T. asiatica - eating raw or undercooked beef or pork - Eggs or gravid proglottids pass in feces > ingesting contaminates vegetation infects pig or cattle > oncospheres hatch go to striated muscles and become cysticerci > human infected by eating raw meat > intestines cysticercus develop into adult > attach to small intestine by scolex > gravid detach and go to anus - eggs: 30-35 micrometers - Kingdom: Animalia - Phylum: Platyhelminthes - Class: Cestoda - Order: Cyclophyllidea - Family: Taeniidae - Genus: Taenia

Fasciola hepatica (liver flukes)

- parasitic trematode (fluke or flatworm, a type of helminth), common liver fluke - eating contaminated larvae > through abdominal wall > liver tissue > bile duct > mature into adult flukes that produce eggs - eggs: 130-150 μm by 60-90 µm - adult: 30000 µm width of 13000 µm - use mouth suckers - Kingdom: Animalia - Phylum: Platyhelminthes - Class: Rhabditophora - Clade: Trematoda - Clade: Digenea - Order: Plagiorchiida - Suborder:Echinostomata - Superfamily: Echinostomatoidea - Family: Fasciolidae - Genus: Fasciola

Biosaftey 2

- pathogenic, infectious bacteria or viruses, associated with human disease pose moderate hazard - Ex. Staphylococcus aureus, stains - additional from BSL-1: biosafety cabinet, trained professional, eye wash station, vaccination for workers, gloves, - incubated environmental sampling

Ascomycota

- produce asexual spores called conidia that are born naked on a stalk - Penicillium (paintbrush) and Aspergillus (flower)

Zygomycota

- produce sporangiospores inside a sporangium - sporangium is produced at the end of the stalk originating in hyphal filaments - ex. Rhizopus

Paramecium caudatum (PROTOZOAN)

- protist, unicellular organisms, cilia, marine, brackish and freshwater, deeply embedded oral cavity - Clade: SAR - Infrakingdom: Alveolata - Phylum: Protozoa - Subphylum: Ciliophora - Class: Ciliatea - Subclass: Rhabdophorina - Order: Hymenostomatida - Family: Parameciidae - Genus: Paramecium - 200-300 micrometres

Plasmodium vivax (PROTOZOAN)

- protozoal parasite, human pathogen, over 100 species - vivax vectors most frequent and widely distributed recurring malaria, but not as virulent - Symptoms: hiccups, loss of taste, lack of fever, pain while swallowing, cough and urinary discomfor - carried by female Anopheles mosquito, sporogonic development in mosquito at lower temps, - Infra kingdom: Alveolata - Phylum: Apicomplexa - Class: Aconoidasida - Order: Haemospororida - Family: Plasmodiidae - Genus: Plasmodium

Cryptosporidium parvum (PROTOZOAN)

- protozoan, malabsorptive diarrhea (infect microvilli in small intestine), asexual and sexual, cycle occurs in host - causes: cryptosporidiosis - sporulate in gut & become infectious, don't need to sporulate in feces - oocysts (meiotic spores) in feces may also be infectious - phylum Apicomplexa - Class: Conoidasida - Subclass: Coccidia - Order: Eucoccidiorida - Suborder: Eimeriorina - Family: Cryptosporidiidae - Genus: Cryptosporidium ACID FAST STAIN

Psychrophiles

- range of -5 C to 30 C - optimal 10 C and 20 C - even refrigerating won't stop growth

MSA

- salt concentration is selective - mannitol fermenter = yellow - cannot ferment = red/pink - differentiate staph species - staphylococcus aureus= yellow - staphylococcus epidermidis= red - D-Mannitol: 10.0 gm - Agar: 15.0 gm - Phenol Red: 0.025 gm - Sodium Chloride: 75.0 gm

Biosaftey 3

- serious or fatal diseases caused by inhalation of micro, indigenous or exotic agents may cause lethal disease - medical testing for workers, full body garment and respiratory protection, restrictive access, clean air flow, partial covering of front face

Basidiomycota

- some do not reproduce asexually, others produce conidia

Physiological basis of Gram staining

- stains are made up of salts of positive or negative ions - if chromophore is the positively charged ion, the stain is classified as a basic dye - if the negative ion is the chromophore, the stain is considered an acidic dye - Gram positive= stain VIOLET due to the presence of a thick layer of peptidoglycan in their cell walls, retains the crystal violet - Gram negative= stain RED, which is attributed to a thinner peptidoglycan wall, does not retain the crystal violet during the decoloring process. - crystal violet dye, iodine stain, ethyl alcohol or acetone (decolorizer), safranin (counterstain and gram neg retains it)

How is autoclaving done?

- steam heat works to kill any microbes and sterilizing - completely sealed > sterilized > steam to displace air > close exhaust ramp to increase pressure > pressure released and returns to normal - Temp: 121°C for 30-60min, 15 psi

3M Quick Swab

- sterile swab - excess liquid fall - quick, inexpensive, easy

- Trophozoite: - Sporozoite: - Merozoite: - Cysts:

- the active feeding stage - the motile infective stage - the result of schizogony (a trophozoite replicates its organelles and nuclei multiple times, then the cell divides into multiple daughter cells called merozoites) - he dormant stage, usually resistant to harsh or changing conditions, also the stage that is often part of transmission from host to host.

Trypanosoma gambiense (PROTOZOAN)

- vector-borne disease, genera of tsetse fly - Disease: chronic African trypanosomiasis, or West African sleeping sickness, - treatment: Pentamidine, suramin, melarsoprol, eflornithine, and nifurtimox when used in combination with eflornithine - injects metacyclic trypomastigotes > enter the lymphatic system, pass blood stream > inside bloodstream trypomastigotes > replicate through binary fission everywhere (lymph) > fly infected w. bloodstream trypomastigotes while eating > transforms into procyclic trypomastigotes in fly midgut > leave midgut transforms into epimastigotes (cycle in fly takes 3 weeks) - Phylum: Euglenozoa - Class: Kinetoplastea - Order: Trypanosomatida - Family: Trypanosomatidae - Genus: Trypanosoma - Species: T. brucei

Coccidioides immitis (FUNGI)

-Coccidioidomycosis (valley fever) -distribution: Southwestern US (like California) -route of transmission: inhalation of spores in dust -dimorphic fungus; mold in the cold (soil and dirt) and SPHERULES OF ENDOSPORES in the heat (our bodies particularly the lungs) -cocci spherules > RBC size (cocci > blasto = RBC > histo in size) -cocci is associated with erythema nodosum (shows a robust immune response so only seen in healthy people) -diagnosis: KOH prep or culture and urine antigen test TX: -azoles for local lung infections like Ketoconazole TX: disseminated infections Amphotericin B - Kingdom: Fungi - Division: Ascomycota - Class: Eurotiomycetes - Order: Onygenales - Family: Onygenaceae - Genus: Coccidioides

Enterobius vermicularis (Pinworm)

-Fecal-oral transmission > larvae hatch in small intestine > adults establish in colon > larvae in egg develop in 4-6 hrs in optimal condition (cycle) - female's long, pointed tail, female (8 to 13 mm) and male (2 to 5 mm) -Intestinal infection causing anal pruritus -Diagnosed by seeing egg via scotch tape test (see picture) -Treatment: bendazoles (because worms are bendy) - Kingdom: Animalia - Phylum: Nematoda - Class: Chromadorea - Order: Rhabditida - Family: Oxyuridae - Genus: Enterobius

Necator americanus (Hookworm)

-Tissue worm -"Ground Itch" -uses teeth to burrow in skin from soil -Failure to thrive -Blood sucking worm -Lungs---Coughing/Swallow----Intestines - Kingdom: Animalia - Phylum: Nematoda - Class: Secernentea - Order: Strongylida - Family: Ancylostomatidae - Genus: Necator

Acid fast bacteria

-contain mycolic acid (a wax) -resist decolorization by acids during staining -can be a pathogen (tuberculosis, leprosy) - positive acid fast= red ex. Myobacterium - negative acid fact= blue/green from counter stain Kinyoun ex. Escherichia coli

Candida albicans (FUNGI)

-cutaneous and systemic fungal infections -DIMORPHIC -candida forms germ tubes - true hyphae(mold) at 37 degrees C & yeast at 20 degrees C in cold temperature -pseudohyphae with budding yeast -CATALASE POSITIVE, making individuals with chronic granulomatous disease susceptible to infection -KOH is used to prep oral scrapings when attempting to diagnose oral candidiasis -white pseudomembranes -IV drug users are at increased risk of developing candidal endocarditis which commonly affects the tricuspid valve - Kingdom: Fungi - Division: Ascomycota - Class: Saccharomycetes - Order: Saccharomycetales - Genus: Candida Species: C. albicans

endospore

-non active - often in bacillus or clostridium - central endospore (B. cereus, B. anthrax) - subterminal endospore (B. subtilis) - terminal endospore (C. tetani)

nano (n) micro (u) milli (m) centi (c) none kilo (k) giga (g)

0.000000001 (10^-9) 0.000001 (10^-6) 0.001 (10^-3) 0.01 (10^-2) 1.0 (10^0 =1) 1000.0 (10^3) 1,000,000,000.0 (10^9)

5 growth patterns in broth

1. clear 2. turbid 3. pellicle 4. flocculent 5. sediment

terminology to describe colony growth characteristics

1. size and shape 2. margin, how spread 3. elevation 4. surface 5. pigment/color 6. opacity 7. texture

1. Amoebozoa 2. Excavata 3. Chromalveolata 4. Archaeplastida

1. use pseudopodia for feeding and motility -Entamoeba, (and slime molds) 2. most have a flagellum which aids in feeding -Giardia, Trichomonas, Trypanosoma, Leishmania 3. ciliates and apicomplexans (and Dinoflagellates, Diatoms, brown algae, golden algae) -Balantidium, Cryptosporidium, Toxoplasma, Plasmodium -Rhizaria: (radiolarians, forams) 4. (Green algae)

1. Inoculating loop 2. Inoculating needle 3. Beaker 4. Serological pipette 5. Micropipette 6. Broth 7. Slant 8. Deep 9. Petri dish

1. used to pick up or transfer small sample (inoculum) of liquid, fungi, bacteria for streaking, preparing slide, inoculate broth or slant, aseptic technique 2. used to inoculate deeps, live microorganisms, aseptic technique 3. glass, cylindrical container, not very accurate in measuring small amounts 4. often used for transferring milliliter amounts (1-50ml), read from largest to smallest (top), always used with pump (accurate) 5. disposable pipette tip to aspirate liquid, 3 different types with different amounts of measurment 6. contains various nutrients and is used to culture bacteria and other microorganisms in culture, first steril liquid broth then mixed 7. agar cool with the tube laying at an angle, resulting in a large surface area for spreading a culture, storing pure cultures for a moderately long term (1.5% agar) 8. inoculating needle used (0.5%-0.7% agar) concentration aids in determining motility, used for bacteria that require less oxygen like anaerobic , agar allowed to solidify at bottom 9. small shallow dish with loose cover that is often used to grow or culture bacteria, use clam shell technique

1. Field view 2. Depth of field 3. Working distance

1. what observed through microscope, magnification increases > field of view decreases 2. how deep something is in focus, magnification increases > depth of field decreases 3. distance between slide and lens, magnification increase > working distance decreases substantially

Most pathogenic bacteria prefer to grow at _____°C.

37

What is the TE of an experiment in which 10 uL of plasmid with a concentration of 0.1 ug/uL was used and 38 colonies were observed glowing on the LB/Amp/Ara plate?

38

According to the results from this lab, which of the following organisms is dextrose (+) and lactose (-) when grown in KIA?

A. viscolactis

According to the results from this lab, which of the following organisms is oxidase positive?

A. viscolactis

According to the results from this lab, which of the following organisms is positive for casein hydrolysis?

B. cereus

According to the results from this lab, which of the following organisms is positive for gelatin hydrolysis?

B. cereus

How will you select ONLY for transformants (bacterial cells that have been successfully transformed)?

By plating them on LB agar media that contains ampicillin.

According to the results from this lab, which of the following organisms is MR positive? (Choose all that apply)

C. freundii E. coli

What is the "transforming principle"?

DNA

According to the results from this lab, which of the following organisms is citrate negative?

E. coli

According to the results from this lab, which of the following organisms is indole positive?

E. coli

According to the results from this lab, which of the following organisms formed dark purple growth with a green sheen on EMB? (Choose all that apply)

E. coli C. freundii

Staphylococcus aureus

Gram-positive, round-shaped, staphylococci - Mannitol Salts Agar selective media Morphology: pale orange. MacConkey Agar: no growth. Sheep's Blood Agar: 24hr beta,48hr beta. - positive: mannitol, Catalase, COAGULASE + - negative: Oxidase, Milk Agar, Starch, Glucose, Lactose, Gelatinase, Urease, Indole, Methyl Red, V.P., Citrate, non-spore TSI: A/A Litmus MIlk: R - Domain: Bacteria - Phylum: Firmicutes - Class: Bacilli - Order: Bacillales - Family: Staphylococcaceae - Genus: Staphylococcus

How were the cells made competent during the procedure?

Heat shock along with the calcium chloride

According to the results from this lab, which of the following organisms is catalase negative?

L. lactis

On which of the following plates do you expect to have cells that fluoresce after incubation?

LB agar media that contains ampicillin AND arabinose.

ubiquitous

Microbes are found on all surfaces and can be airborne. Viruses and fungi could be in air or on shoes, etc.

What explains the results of Frederick Griffith's famous transformation experiments in 1928?

One or more virulence genes passed from the dead pathogenic bacteria to the live, nonpathogenic bacteria.

Biosafety 4

Rare and fatal, often no vaccine or treatment, high risk of aerosol transmission, fatal disease, no vaccine or treatment - infectivity, severity of disease, transmissibility, and the nature of the work, route of exposure, - clean air flow, Change clothing before entering, Shower upon exiting, Decontaminate all materials before exiting, complete covering of head

which plate forms fungi

SDA

What is the purpose of the ampicillin resistance gene?

Selective marker

What is NOT considered a method of horizontal gene transfer?

Sexual reproduction

The StaphTEX agglutination assay that you will be using in this lab will test for

Staphylococcus aureus antigens.

class- Cestodes

Tapeworms, part of Platyhelminthes (flatworm) Phylum - long, ribbon body - scolex for attachment, reproductive segments called proglottids - often require 2 or more hosts - no digestive system

What are you going to use to transform your E. coli cells?

The pGLO plasmid

Trichinella spiralis

Trichinosis - "pork worm" - requires 2 hosts often pigs and anthropophilic rodents - uncooked meat by encysted larvae > gastric acid and pepsin exposure results in larvae released from cysts > small bowel mucosa & develop into adult > females release larvae - encysted or non-encysted - Kingdom: Animalia - Phylum: Nematoda - Class: Enoplea - Order: Trichocephalida - Family: Trichinellidae - Genus: Trichinella

True or False: Bacterial transformation is an important mechanism for the acquisition of genetic elements encoding virulence factors and antibiotic resistance.

True

What is the purpose of the arabinose in the LB/Amp/Ara agar?

Turn on GFP expression

Sediment

a mass of bacteria usually at bottom

Pellicle

a visible layer of growth at surface of broth

What are bacterial cells that are capable of taking up DNA from the environment called?

competent

What causes different colored colonies to form on chromogenic media?

different enzymes produced by different species of microbes

What is the best description of the HardyCHROM chromogenic media that you will be using?

differential

What is the best description of the blood agar media that you will be using?

enriched & differential (based on hemolysis pattern)

fungi are part of

eukaryote not bacteria or archaea

True or False: In an ELISA, the enzyme is conjugated to antibodies from the patient's serum.

false

class- Trematoda

flukes, part of Platyhelminthes (flatworm) Phylum - leaf shaped, Mollusk often intermediate host - Vertebrate id usually definitive host - has digestive system

condenser lens

focuses focuses light as goes through

ocular lens

further magnifies image and creates virtual image

Which of the following is the gene that codes for the glowing protein in this lab?

gfp

GFP

green fluorescent protein

objective lens

magnify the specimen, capture transmitted and reflected light and create a real image

hermaphroditic

male and female sex organs occur in the same individual worm (cestodes and many trematodes)

Flocculent

medium has small masses visible in suspension

Transformation can be described as

naked DNA is taken up from the environment.

Calculate total magnification

ocular magnification x objective magnification (100x)= 10 * measurment = maginfication (um) (200x)= 5 * measurment = magnification (um) (400x)= 2 * measurment = magnification (um) (1000x)= 1 * measurment = magnification (um)

Voges-Proskauer

organisms that are able to ferment glucose, but quickly convert their acid products to acetoin and 2,3-butanediol - VP result, therefore, is red

Phylum Nematoda (roundworms)

sexual reproduction, major players in decomposition and nutrient recycling. Some parasitic, plant roots and humans (raw pork). - Ascaris, Turbatrix, Trichinella, Ancylostoma, Enterobius - pinworm, hookworm, roundworm - cylindrical, diverse, free living predatory and parasitic types - complete digestive system

antifungal medications

target ergosterol or chitin

Many protozoa are clinically important and may cause serious disease in animals - Malaria one of most important protists - protists are usually single celled eukaryotic organisms

true

Most algae are not clinically important

true

Prepared slides: Examine the prepared slides (use Bright Field only)

true

True or False: Petri dishes should always be inverted (up-side-down) when incubated.

true

oil immersion

working distance reduced, NOT use coarse focus with any objective other than 10x - use at 100x, with oil on slide, doesn't increase magnification but helps with clarity because light passes directly from oil to oil