Chapter 101.odt

Chapter 10 How to classify bacteria There are about 1.7 billion organisms To study they must be separated (organisms) into groups. Diversity – because of natural selection (survival) of stronger traits more suited for environmental Similarity – is due to relatedness, this comes from evolution Taxono...

Chapter 10 How to classify bacteria There are about 1.7 billion organisms To study they must be separated (organisms) into groups. Diversity – because of natural selection (survival) of stronger traits more suited for environmental Similarity – is due to relatedness, this comes from evolution Taxonomists They group organisms into categories called taxa. Look for things like: Growth requirements Morphology DNA Systematics or phologeny is the study of evolutionary history of organisms 1735 Carolus Linnaeus Introduces system of kingdoms Animal or plants 1800 kingdom protesta Animal, plants, fungi, algae, bacteria 1950s fungi get their own kingdom 1969 five kingdoms Animals Plants Fungi Protist Monera 1978 Woese things there should be one more level above kingdom, meaning domains. Kingdoms now into three domains. Domain Animalia Plantae Fungi Protista Eukaryea Monera, bacteria and archaea bacteria Domain bacteria Prokaryotes Archaea = also prokaryotes without peptidoglycan in cell walls Strange group Very very old RNA from 3.5 million years old Extreme habitats (Thermophilic, acidophiles) None of these are known to cause disease. Domain Eukereya are about 2.7 million years old Phylogenetic tree Organism grouped into taxa based on relationship from common ancestor Info from fossil record Becoming more popular to use rRNA sequencing Happens with bacteria constantly Taxonomic Hierarchy Shows evolutionary or phylogenetic relationships among organisms A eukaryotic species – group of organisms that interbreed with each other. They do not breed with other species. Least inclusive to most inclusive heiarchy Individual species – sapien Geneus – homo Family – homindae Order – primates Class – mammalia Phylum – chordata Kingdom – animalia Domain – eukarya Most to least is the most common way we see it. Did, Kara, play, cards, or family, games, Saturday Scientific Nomenclature Every organism is given two names (Binomial) Genes Species Used by scientist worldwide, so they known exactly what it is, regardless of what language you speak. Most based in Latin. Suffix for orders = ales For family = aceae In italic or underlined. Whole name then can be abbreviated. Classifying and identifying organisms 1. Bergy's manual of Detemitive Bacteriology 1923 was gold standard for lab ID of organisms Based on biochemical tests Morphology Staining reactions Can microbe ferment (fermentation abilities) Carbon source Enzymes produced Gram stain results Oxygen requirements What we do in class 2. 2nd edition of Bergy’s manual of systemics of archaea and bacteria The standard reference of bacterial identification Based largely on differences in rRNA sequences Closely related strains make-up a bacterial species It is now possible to classify species based on more reliable comparisons of the rRNA subunites of these organisms What bacteria you can have single strain or subset 3. Morphology Aided by staining techniques 4. biochemical testing What enzymes are being produced What is the carbon source Do they ferment 5. Serological test These involve the reaction of antibody Antigen test When a pathogen is introduced the immune system response is to make antibodies Proteins that destroy antigens are highly specific. Antigen – any foriegn substance that illicits an immune response Antisera Is a solution of known antibodies that are commercially available (anti-serum) to help identify unknown bacteria (pathogens) in a patient. To produce antisera, bunnies are injected with a dead bacteria. They respond by producing antibodies If unknown bacterium is isolated from a patient it can be tested against a known antisera and identify quickly Anti-gen – antibody reaction Different antisera/antibody tests Slide agglutination test The unknown bacteria is placed on a slide with a known antisera. If agglutination occurs then the bacteria can be identified due to the antibody Antigen reaction Not only does this type of test differentiate amoung bacterial species but can also differentiate strains within species. Strains with different antigens are called serotypes, serovars or biovars of the species Enzyme Linked Immunosorbent Assay (ELISA) Another serology test Widely used because it is fast and very specific Many wells on a microplate At home covid-19 test uses a small version of the ELISA technique ELISA preliminary HIV Test Any positive HIV test is confirmed using western blot ELISA HIV and western blot test are about 99.9% accurate Western blot test Separates blood proteins and detects specific antibodies to HIV suggest HIV infection Phage Typing Test to determine what phages a bacteria is susceptible to Phages are bacterial viruses that can cause lysis of the bacterial cells they infect (explode) Phage typing is used to trace the spread of infections caused by Mycobacterium tuberculosis, Yerisinia pestis, Bacillus anthracis and Staph aureus. A drop of different phages are placed on bacteria. Where the phages infect the bacteria a clearing of growth will appear due to cell lysis. Example: a bacteria is isolated from a surgical wound and has the same pattern as the bacteria isolated from the surgeon or nurse or machine identifying them as source of infection. Flow Cytometry Can be used to identify bacteria in a sample without culturing the bacteria Detects physical properties using a laser scattering light. Body fluids – urine, pleural fluid, paracentesis fluid. A fluid containing the bacteria is put through a flow cytometer which detects differences in electrical charges between cells and fluid. Can measure physical and chemical characteristics of the cells DNA sequencing (Big daddy) The test to identify bacteria Comparisons of DNA sequences of base pairs (the order of A to T, C to G) Led to great strides in reclassification of known species and identifying new species New bacterium identified in Lyme’s disease Chapter 11 Phylogenetic tree Phylum: Proteobacteria These are the largest and most diverse group of bacteria with over 2000 species Presumes to have arisen a common photosynthetic ancestor Not many are photosynthetic Named after the Greek God Proteus who could change into many shapes Which is fitting because proteobacteria can be many shapes (pleiomorphic) Some members of this phylum are: Phototrophic Obtain energy from sunlight to synthesize organic compounds for nutrition. Autotrophs Make their own food from inorganic material (light, water, carbon dioxide, and other chemicals) Chemotrophs Obtain energy by the oxidation of electron donors Heterotroph Depend on others for carbon source Proteobacteria are gram (-), anaerobes, facultative anaerobes and obligate aerobes They are dived into 5 classes Alpha Beta Gamma – biggest Delta Epsilon These are based nucleotide sequences, also on rRNA Alpha proteobacteria – oligotrophs – they live in environments low in nutrients. Found in deep oceans, deep soil, glacier ice. Makes nitrogen for other life forms Beta proteobacteria – Eutrophs – they live in nutrient rich environments. They like nitrogen and phospherous Gamma proteobacteria – most divers – this includes aerobic and anaerobic organisms Human pathogens Delta proteobacteria – mostly aerobic and gram negative. Many are important for sulfur cycle. Epsilon group – large group of gram negative, curved or spiral rods. Very fastidious *drama queen Phylum: Proteobacteria Class: Alpha Includes a variety of aerobes Many have unusual cellular extensions called prosthecea Important soil organisms Azospirillium and Rhizobuim Both important for agricultural. Symbiotic relationships with roots of plants Azospirillium Roots of tropical grass, sugar cane, corn Rhizobium this is nitrogen fixing organism. Will be found in soils. It forms symbiotic relationships legumes. (clover, alfalfa, beans) 79% N in atmosphere Bacteria use nutrients excreted by plants and return fixes nitrogen from atmosphere the plants need. (N2 ----> NH4) absorbed by plant to make amino acids and proteins <---- Plant (Sugars) ----> Rhizobium (ammonium) Symbiotic relationship Nitrifying bacteria Nitrobacter and Nitrosomonas (actually belongs to B proteobacteria but listed here because these two organisms work together) Agriculturally important soil organism Don’t cause human disease Chemotrophs Use inorganic chemicals as their energy source and CO2 as their only carbon source. Nitrobacter 1st step – ammonia (NH3) is oxidized into nitrite (NO2) Nitrosomonas 2nd step – further oxidation of nitrite (NO2) into Nitrate (NO3) Pathogenic: Alpha Proteobacteria Agrobacterium Bacteria inserts a plasmid (gene for plant growth) This gene causes plant to make a ball that provides nutrients for the bacterium. Tree has a tumor Bartonella Cat scratch fever Cat bites, scratches, or licks open wound of a person. Can cause infection, fever, loss of appetite Not usually serious Rickettsia Very small, obligate intercellular parasite. Transmitted by insects and tick bites. They cannot reproduce outside of host Causes rocky mountain spotted fever. Treat with antibiotics. No vaccine Wolbachia Found in insects Does not make people or animals sick Interferes with egg development. Infected male mosquitos are released in Brazil, Florida, California, and SE Asia to prevent the spread of Zika and Dengue fever. Brucella Obligate parasite of mammals Zoonosis – animal reservoir Causes undulate (rise and fall) fever in humans Catch it from livestock (goats, sheep, diary cows) from raw dairy products. Coccobacillus that responds to antibiotics Brucella abortus Brucellosis – spontaneous abortion in ungulates Deer, elk, cattle and buffalo All states are currently brucellosis free in domestic herds (vaccinations) Free range herds in yellow stone are always monitored BRUCELLA CAN SURVIVE PHAGOCYTOSIS OF WBC Phylum: Proteobacteria Class: Beta Another diverse group. Thrive in habitats with low levels of nutrients Thiobacillus Soil bacterium that recycles sulfur in the environment by oxidizing hydrogen sulfide (H2s) or elemental sulfur to sulfate (SO4) Miners use it to leach metals from low grade ore Zoogloeal and sphaerotilus Important organisms in sewage plants Zoogloeal: compact flocks that sink (good) Sphaerotilus: flocks that float and cause problems (bad) Pathogenetic Phylum: Proteobacteria Class: Beta Genus: Burkholderia Used to be classified with genus Pseudomonas in the gamma proteobacteria Species B. cepacia Best known species Can use more than 100 different organic molecules for energy sources May contribute to its ability to contaminate equipment and drugs in hospitals Genus: Bordetella aerobic – very fastidious Species B Pertussis Causes whooping cough Potentially lethal for babies and young kids. Paralysis of cilia in the respiratory tract Symptoms start like a cold. 1-2 weeks, then violent coughing occurs. Antibiotics only effective in early stages. Adults can be asymptomatic carriers There is a vaccine Genus: Neiserra Fimbriae attach to the mucus membrane of mammals 2 human pathogens Species N. gonorrhea Causes gonorrhea (the clap) 2nd most commonly reported communicable disease. It is a STD or STI It infects the mucosa of urogenital (oral/anal), conjunctiva Not treatable with penicillin it is antibiotic resistant. Can be spread from mom to baby in pregnancy, labor, or nursing. Conjunctivitis mainly infects infants born to untreated mothers. Can also cause Pelvic Inflammatory Disease (PID) no vaccine but can be treated with antibiotics. N. Menigitidis Causes bacterial meningitis (meniges and spinal cord) Can be asymptomatic in oro/naso cavities. 40% of population is asymtomatic. Symptoms include: bacteremia (from toxins produced by bacteria and fever), headaches, stiff neck, coma, death, very fast progression. Affects infants <2 and college dorm students Treat with antibiotics Most recover. Can cause brain damage, hearing loss, learning disabilities Vaccines are available. There are 4 types of bacterial meningitis, not all caused by Neisseria. Phylum: Proteobacteria Class: Gamma Make up the largest and most diverse class of proteobacteria. Almost every shape, arrangement, metabolic type and reproductive are represented. Most human pathogens. This is why its hard to study this group. Ribosomal studies are done, there are five subgroups. Purple sulfur bacteria Obligate anaerobes. They oxidize hydrogen sulfide to produce sulfur granules instead of O2. Don’t need oxygen. Found in hot springs, and stagnant water. Intracellular pathogens – facultative intracellular parasites. They can grow, reproduce inside and outside of hot cell. Genus Legionella difficult to grow. Common to find in water, streams, water systems (air conditioning systems, hot water tanks, and hot tubs) Species L. pneumophilia primarily human pathogen. It causes Legionaries disease. Spreads through water droplets. Named after vets attending a conference. 25 of them died. Was found in the air conditioning units. Genus Coxiella burneti obligate intracellular parasite causes Q fever. Also known as zoonosis – can catch from animals. Humans infected by contaminated aerosols from domestic animals. People at risk are vets, slaughterhouses, farmers, ranchers. Isn’t terrible but feels like milk flu. Can be treated with antibiotics, not necessary though. Methane oxidizers Mathan is a green house gas. These use methane as carbon source. Would be better if we could use these to reduce methane in atmosphere. Facultative anaerobes Three families Enterobacteriacea Vibrionacea Pasteurellacea Enterobacteriaceae (aea = family) (commonly called enteric) IMViC they inhibit intestinal tract of humans and animals. Most of them can ferment glucose. Can produce proteins bacteriocins. Bacteriocins can kill or inhibit other bacteria. Enteric will include: Estcheria, Salmonella, Shigella, Klebsiella, Serratia, proteus, Yersinia, Erwinia, enterobacteria and corynebacteria. 5. Pseudomonadales 1. Enterics 1. Genus: Escherichia species: coli The work horse of microbiology Indicator of food and water contamination. If its there than there is fecal contamination Not usually pathogenic but can be a cause of UTI’s Some strains produce enterotoxins that cause diarrhea. 0157:H7 – deadly strain Inhabitant of the gut in cattle. Young kids and adults more at risk of developing Hemolytic Uremic Syndrome (destruction of RBC’s and kidney failure. DONT EAT RAW OR UNWASHED SHIT. 2. Salmonella Almost all in this genus are pathogens Common in the intestinal tracts of animals. Especially cattle and poultry. There are only 2 species but many serovars 1. S. bongori Found in cold blooded animals most reptiles are carries along with birds (chicken and eggs) 2. S. enterica Infected warm blooded animals Includes more than 2500 serovars (Serological varieties) The only way to differentiate them is through serology test (antigen-antibody) Salmonella typhimurium Not a species but a serovar Salmonella enterica serovar typhimurium Cause of thyphoid fever 2-3 weeks incubation period About 20% fatal if untreated Can be spread by contaminated food/water Bacteria multiply and spread into blood stream. Can cause sepsis. Chronic carriers have the bacteria in their gall bladder. Asymptomatic super spreader – typhoid mary mary mallon 3. Shigella Causes infection called shigellos Estimated 450,000 infected in us causes 93 million in medical costs Symptoms: watery diarrhea, vomiting, mild to moderate dehydration Dysentery – bloody mucoid stools Shigella is spread easily and only takes a small amount. Oral/fecal route – touching contaminated object, eating/drinking, swallowing water you swim in. Children <5 likely to get. Common at child care facilities Travelers – drinking food and water in places that aren’t sanitary. 4. Yersinia Two important species Y. enterolitica Typically found in domestic animals. Passed to humans primarily in undercooked pork. Meat contaminated at slaughterhouses. Causes fever, diarrhea and abdominal pain Mistaken for appendicities in adults Y. pestis Causes bubonic plague (black dealth) Rodents are reservoir and fleas are vectors Killed millions in middle ages Infection still occurs in rural western US There are three forms of bubonic plague Bubonic = bubos in lymph nodes size of golf balls Septicemic plague = bleeding into the skin and other organs. Turning them black. Pneumonic plague = most serious and the only form that can be spread from person to person through droplets All are treatable with antibiotics. 5. Cronobacter Cause of recall of infant formula in 21-22 Causes meningitis and necrotizing enterocolitis in infants Health care (nosocomial infections) associated infections enterics 6. E. aerogenes UTI’s respiratory infections soft tissue infections, osteomyelitis and endocarditis 7. Serratia marcescens Infections include contamination of the respiratory equipment and poor catheterization techniques. Also found in saline and other sterile solutions 8. Proteus P. uulgaris and P. mirabilis Most common species found in hospital settings. But not most common cause of nosocomial infections 2. Vibrionales Found mostly in aquatic habitats such as untreated water and brackish water V. cholera Causes cholera Bacteria produce enterotoxins in small intestine causing it to secrete fluids that cause large volumes of watery stool “rice water stool” Up to 1 liter/hr Severe dehydration Hypovolemic shock Huge problem in under developed countries 3. Pasteurellales Pasteurella is a pathogen of domestic animals and cause sepsis in cattles, fowl, cholera in chicksn and other birds and pneumonia in other animals. Haemophiles Responsible for several diseases H. influenza – often the cause of earaches, bronchitis and pneumonia in kids. 5. Pseudomonadales Have the ability to break down more than 80 different organic compounds including oil, rubber and plastic Since they can use so many universal carbon sources they are medically concerning. Able to grow in some antiseptics Becoming more resistant to antibiotics Many cause plant disease but not normally pathogenic to humans But are very opportunistic P. aeruginosa Cause of noscomial infection Cause burn and would infections UTIs and septicemia The leading cause of morbidy and mortality in cystic fibrosis patients. Phylum: Proteobacteria Class: Epsilon Campylobacter Causes campylobacteriosis Transmitted to humans from animals or animal products Microaerophilic and comma shaped Found in the intestines of many wild and domesticated animals Bacteria spread by cross contamination of cutting boards, tools C. jejuni Cause of foodborne intestinal disease (food poisoning) C. fetus Causes spontaneous abortions in domestic animals Helicobacer H. pylori Causes peptic ulcers and stomach cancer (stomach ulcers) The non proteobacteria (Gram - ) Cyanobacteria (blue green algae) Bacteria not algae (eukaryote) Photosynthetic and nitrogen fixing Huge o2 output Heterocysts – enzymes that fix N2 ----> NH4 Common everywhere Pond scum Green sulfur bacteria and green non-sulfur bacteria Both photosynthetic but they do NOT provide o2 Use reduced sulfur compounds such as hydrogen sulfide (H2s) instead of H2o and produce sulfur granules instead of O2 2(H2s) + Co2 ---light---> (CH2o)+ H20 +2S Non proteobacteria (Gram +) There are two groups, they are classified by DNA composition of base pairs. Low G-C ratio = Firmicutes High G-C ratio = Actinobacteria 1. Firmicutes Clostridium Produce endospores and toxins Are obligate anaerobes Most are soil organisms C. tetani (tetanus) Neurotoxins cause very painful muscle spasms. Can cause death Vaccine to prevent tetanus otherwise no cure. C. botulinum (botulism) Neurotoxins block nerve functions and can lead to respiratory and muscle paralysis (flaccid paralysis) Loss of muscle tone Associated with home canning Also reason you never feed raw honey to an infant Dermatologist use very small amounts of purified botulinum toxin to temporarily relax targeted muscles of face (botox) Also can be used to be injected for migraines C. perfrigens (gas gangrene) Found nearly everywhere Bacteria growing in body emit gas and cytotoxins that damage body and tissues, cells and blood vessels. Associated with diabetics with uncontrolled sugar levels. Causes nerve damage in extremities Issues with injury from stubbed toes C. difficile (C. Diff – nosocomial infection) Produces enterotoxins Antibiotics wipe out normal flora and C. diff takes over Very difficult to get rid of. Bacillus Gram + rods, endospore forming, facultative anaerobes, non-motile B. anthracix (anthrax) Zoonose infection Animals become infected by breathing in or eating spores from contaminated soil, plants or water. Humans become infected through breathing in spores or getting spores in a cut or scrape, working with infected animals. B. cereus Toxins can cause diarrhea. Associated with cereal grains B. thuringiensis (insecticide) Doesn't affect humans but is deadly to catepillars Good for tomato plants Toxin is a protein that we regularly extract the gene and put it in corn GMO corn resistant to catepillars Lactobacillus No spores, aerotolerant anaerobe, acidophils Sour foods like pickles/yogurt L. acidophilus Probiotic Staphylococcus Grape like clusters of GRAM + COCCI Tolerates high osmotic environments (salt and sugar) Normal flora of skin and nasal passages S. aureus (antibiotic resistant MRSA) Can be a source of food contamination – toxins in food Oppurtunistic in wounds Nosocomial infections Streptococcus 2 groups A+B very Very complex group and probably responsible for more infections and diseases than any other group Group A S. pyogenes Aerotolerant, found on skin surfaec and in throat Produces hemolysins, toxins and extracellular enzymes Diseases: parayngitis, tonsilitis, scarlet fever, necrotizing fascitis, strep, toxic shock syndrome and bacteremia. Group B S. agalactia Facultative anaerobe Found in digestive system and vagina Produce few if any virulent agents Diseases: mastitis in cattle, severe neonatal infections, UTI’s pneumonia and endocarditis Enterococcus Formerly group D strep E. faecalis Nosocomial infections like UTI’s and wounds Found in root canal treated teeth Listeria L. monocytogenes (listeriosis) Food borne illness – very serious for pregnant women Can cause spontaneous miscarriage Bacteria can survive refrigeration and freezing Common food to avoid when pregnant are unpasteurized milk, any raw dairy, soft cheese, hot dogs, deli meats. Unborn babies can contract listeria infection from the mom Mycoplasm No cell wall, DNA related them to Gram + Pleomorphic – no definitive shape Sometimes filaments Really small Look like fried egg colonies M. pneumoniae Walking pneumonia Arthritis in goats M. hominis Urogenital infections and causes complications of pregnancy 2. Actinobacteria Obligate aerobes facultative anaerobes Filamentous soil organisms Fresh dirt smell Capable of nitrogen fixation Common source of antibiotics Streptomyces S. aurofaciens ----> chlortetracycline S. rimosis ----> tetracycline S. griseus ----> streptomycin S. erythraeus ----> erythromycin S. venezulae ----> chloramphenicol Mycobacterium Waxy walls, acid fast, very slow growing M. tuberculosis (TB) Tubercules of connective tissue surrounding bacteria. “White death” or consumption M. leprae (leprosy – hansen’s disease) Prevalent in under developed countries Still in US with 200 cases/yr Found in nine banded armadillos Brazil and india Diseases of skin and nervous system Disfiguring Circulatory problems Nerve damage Treatable Miscellaneous stuff Chlamydia: obligatory intracellular bacteria also an STD. Some species cause chlamydia, trachoma and pneumonia C. trachomatis Cause of chlamydia Also called goncocal urethritis Trachoma of newborn Can have in eyes – causes blindness Infected through birth Phylum Spirochetes Sprial with axial filaments Moves like a drill Most are free living Water environments Have various o2 requirements Borrelia B. burgdorferi (lyme disease) Vector tick ----> deer ----> humans Characteristic bullseye rash at site of infection Fever, joint pain, neurological problems Treponema T. pallidum (syphilis and yaus) Syphilis in the 1st stage presents with sores on genitals, rectum and mouth. Sores heal ----> 2nd stage and damage to nerves eyes and heart Yaws infects skin, bones, joints, hard swelling