How I Spent My Spring Break

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How I Spent My Spring Break
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Ireland Are Grand Slam Champions! Finally, after
61 years of pain, let the party start A late drop
goal from Ronan O'Gara steered Ireland to a
tension-filled 17-15 win over Wales and the
nation's first Grand Slam since 1948.
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The Bacteria
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PHYLUM 1 PROTEOBACTERIA
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Purple Phototrophic Bacteria
Liquid cultures showing colors due to various
carotenoid pigments
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Internal membranes of purple phototrophic
bacteria. (flat sheets-top picture and spherical
vesicles-bottom picture)
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Purple Phototrophic Bacteria

• Anoxygenic photosynthesis
• Bacteriochlorophyll
• Habitat bottom waters of some lakes
• Examples
• Rhodospirillum
• Purple Sulfur Bacteria

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The Nitrifying Bacteria

• Examples
• Nitrosomonas, Nitrobacter
• Chemolithotrophs
• Widespread in soil and water (useful in sewage
  treatment)

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Sulfur-Oxidizing Bacteria

• Example
• Thiobacillus
• Beggiatoa
• Chemolithotroph (obtain Energy from oxidizing
  sulfur compounds)

Thiobacillus
Beggiatoa (note sulfur granules)
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Pseudomonas and the Pseudomonads
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Pseudomonas

• Gram negative rods with polar flagella
• Metabolically versatile as a group, nutritionally
  adept.
• Opportunistic pathogens
• Burns, wounds, UTI, abscesses, septicemia
• Often carry plasmids with genes for antibiotic
  resistance

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Nitrogen-Fixing Bacteria

• Free living
• Azotobacter, Azomonas
• Symbiotic with plant roots
• Rhizobium

Legume roots showing Root Nodules
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Neisseria

• Gram negative cocci
• Neisseria gonorrhoeae
• Neisseria mengitidis

N. gonorrhoeae diplococci in pus smear
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Gonorrhea diagnosis
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http//www.staysafe.co.nz/index.html
STD Web Site
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Enteric Bacteria

• Family Enterobacteriaceae

• Facultative anaerobes
• Gram negative rods
• Extremely well studied, very common pathogens

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Family Enterobacteriaceae

• Escherichia
• Shigella
• Salmonella
• Proteus
• Enterobacter
• Klebsiella
• Yersinia
• Serratia

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Family Enterobacteriaceae

• Escherichia
• Some strains produce enterotoxins (EEC) and cause
  diarrhea
• Fimbriae to aid adherence
• Food-borne disease, UTI, etc, etc, etc.
• Indicator of fecal contamination

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Escherichia coli

• pathogenic strains frequent agents of infantile
  diarrhea greatest cause of mortality among
  babies
• causes 70 of travelers diarrhea
• causes 50-80 UTI
• indicator of fecal contamination in water

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Escherichia coli O157H7
The Ready-To-Eat Spinach outbreak of 06
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E. coli O157H7

• E. coli O157H7 is one of hundreds of strains of
  the bacterium Escherichia coli. Although most
  strains are harmless, this strain produces a
  powerful toxin that can cause severe illness. E.
  coli O157H7 has been found in the intestines of
  healthy cattle, deer, goats, and sheep.

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Escherichia coli O157H7

• Escherichia coli O157H7 is a leading cause of
  foodborne illness. Based on a 1999 estimate,
  73,000 cases of infection and 61 deaths occur in
  the United States each year.
• Infection with E. coli often leads to bloody
  diarrhea, and occasionally to kidney failure.
• People can become infected with E.coli O157H7 in
  a variety of ways.
• Though most illness has been associated with
  eating undercooked, contaminated ground beef,
  people have also become ill from eating
  contaminated bean sprouts or fresh leafy
  vegetables such as lettuce and spinach.

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E. Coli 0157H7 outbreak
2006 Spinach-associated outbreak
1-4 5-9 10-14 15

• September 28, 2006 187 people infected in 26
  states (97 hospitalized29 developed HUS)

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Forensic use of DNA patternsDNA Fingerprints
The E. coli outbreak in spinach was investigated
using DNA fingerprinting techniques to trace the
strain of bacteria.
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Newer Outbreaks

• Nestle Toll House cookie dough (E. coli) June
  2009) http//www.cdc.gov/ecoli/2009/0630.html
  (72 cases in 30 states)
• Ground beef (E. coli) ( July 2008)
  http//www.cdc.gov/ecoli/june2008outbreak/ (49
  cases in 7 states)
• Pepperoni pizza (E.coli) (Oct-Nov 2007)
  http//www.cdc.gov/ecoli/2007/october/103107.html
  (21 cases in 10 states)

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Family Enterobacteriaceae

• Shigella
• closely related to E.coli
• causes bacillary dystentery
• Salmonella
• causes diarrhea
• food-borne illnesses

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Salmonella outbreak (Aug 2006 thru May 2007)

• CDC confirms Salmonella in peanut butter
• Over 600 people confirmed infected in 47 states

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Salmonella outbreak (Jan-March 2008)

• Between January 18 and March 5, 2008, state
  health departments identified 50 ill persons in
  16 states infected with Salmonella (Litchfield
  strain ) with the same genetic fingerprint

Cantaloupe from Honduras is the likely source of
the illness.
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Salmonella contamination of drinking water March
2008

• Salmonella Cases Top 200 in Colorado MONDAY, MAR.
  24, 2008 By AP
• Contaminated Colo. water system flushed Tue Mar
  25, 720 PM ET
• ALAMOSA, Colo. - Crews started pumping chlorine
  through this city's water system Tuesday to rid
  it of salmonella bacteria that has sickened
  nearly 250 people

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A recent Salmonella in peanut butter
outbreak(Late 2008 through 2009)
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Proteus

• Swarming motility
• Frequent cause of UTI

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Enterobacteriaceae

• Enterobacter
• Widely found in water, soil, and intestinal
  tracts
• E. aerogenes
• Klebsiella
• Klebsiella pneumoniae (pneumonia, septicemia)
  large capsule

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Enterobacteriaceae

• Yersinia
• Y. pestis
• plague

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Serratia

• Serratia marcescens
• Red pigment
• Soil, water, intestinal tract

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Vibrio

• Curved Gram negative rods
• Vibrio cholerae
• Potent enterotoxin? profuse watery diarrhea.
  Sudden loss of fluid and electrolytes may cause
  shock, circulatory collapse, and death

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Vibrio

• Vibrio parahaemolyticus
• halophile
• acute gastroenteritis
• ingestion of bacteria in raw or undercooked
  seafood, usually oysters

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Rickettsias

• Obligate intracellular parasites
• Rickettsia rickettsii
• Rocky Mountain Spotted Fever
• Fever headache ? rash ? vomiting and diarrhea
• Ehrlichia species
• Ehrlichiosis (begins with flu-like symptoms and
  may progress to fatality or long-term
  neurological, resp. or renal complications)

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Spiral shaped bacteria

• Campylobacter
• (diarrhea)
• Helicobacter pylori
• Gastric ulcer (carcinoma)
• Magnetospirillum megnetotactium

Colored scanning electron micrograph (SEM).
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Stalked Bacteria

• Caulobacter

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Gliding Bacteria
Myxobacteria
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Sulfur-Reducing Proteobacteria

• Reduce sulfate or sulfur to hydrogen sulfide
  under anaerobic conditions
• Desulfovibrio

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PHYLUMS 2 AND 3 GRAM-POSITIVE BACTERIA AND
ACTINOBACTERIA
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Gram Positive Cocci
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Staphylococcus
SEM showing grape-like clusters
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Staphylococcus

• Catalase , halotolerant
• S. epidermidis - nonpathogenic normal flora
  (generally)
• S. aureus
• Causes a multitude of diseases
• Exotoxins
• Entertoxin?vomiting, nausea, diarrhea
• Most common cause of food poisoning
• TSS toxic shock syndrome
• Highly resistant to antibiotics

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S. aureus diseases

• Ranges from localized to systemic
• localized -abscess, folliculitis, furuncle,
  carbuncle, impetigo
• systemic osteomyelitis, bacteremia
• toxigenic disease food intoxication, scalded
  skin syndrome, toxic shock syndrome

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S. aureus
Skin Lesions
Boil or Furuncle
Carbuncle
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S. aureus
Osteomyelitis
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S. aureus
Staphylococcal scalded skin syndrome (SSSS)
Exfoliative toxin
Epidermal shedding/separation
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Staphylococcus aureus

• Food Poisoning
• Food contaminated by handling with bare hands.
  Bacteria grow and produce toxin.
• Refrigerate food to prevent growth. Heating
  doesnt always destroy toxin.
• Symptoms usually start within 1-6 hours after
  eating contaminated food (usually gone in a day)
• Symptoms include diarrhea, vomiting, nausea,
  cramps

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Staphylococcus aureus

• Toxic Shock Syndrome (TSS)
• First linked to use of ultra-absorbent tampons
  that bound Mg ions and created a favorable
  environment for increased colonization and growth
  of vaginal S. aureus and increased TSS toxin
  production.
• Toxin enters bloodstream and causes fever,
  vomiting organ damage and potential fatality.
• Height of problem 1980-198415,000 affected/yr
  with 15 mortality.

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SuperBug ?

• MRSA Methicillin Resistant Staphylococcus aureus
• A strain of staph that is highly resistant to
  broad-spectrum antibiotics.
• Once found almost exclusively in hospital
  settings the bacteria is now showing up in the
  wider community
• People can be colonized by the bacteria (skin and
  nose primarily) and be healthy but act as
  carriers to spread the microbe.
• It is thought that perhaps 25-30 of people may
  harbor S.aureus.

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MRSA has become a subject for some intensive
public education efforts
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MRSA-2

• A CDC survey completed recently suggests that in
  2005 there were 94,000 cases of MRSA in the US
  and that perhaps 19,000 people died. (A higher
  rate than AIDS in the US)
• 85 of the cases were in hospitals, nursing homes
  etc. But many are concerned about the large
  number of infections acquired in normal community
  environments.
• Spread may be by hands (direct contact) or from
  contaminated surfaces.
• Infections range from an inconsequential skin
  lesion to a fatal septicemia or pneumonia

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Streptococcus
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Streptococcus

• Catalse negative, Many pathogen species
• S. mutans - common cause of dental caries
• S. pneumoniae
• S. pyogenes
• strep throat
• flesh-eating bacteria
• Rheumatic fever

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Pharyngitis and Tonsilitis Strep Throat
Note white pus patches on tonsils
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Toxic sequelae to Strep throat
http//www.cnn.com/video//video/health/2008/10/22
/tessman.strep.throat.kare
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Rheumatic fever is a possible sequelae to S.
pyogenes infection. Antibodies against the
bacteria may cross-react with host tissue leading
to damage of heart valves
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Impetigo lesions
Streptococcal skin infections
Erysipelas
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FLESH-EATING BacteriaNecrotizing fasciitis
Streptococcus pyogenes
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Gram Positive endospore formers
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Bacillus anthracis With central endospores
Clostridium perfringens With subterminal
endospores
Clostridium tetani With terminal endospores
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Bacillus

• gram-positive, endospore-forming, motile rods
• versatile in degrading complex macromolecules
• source of antibiotics
• primary habitat is soil

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Bacillus anthracis

• virulence factors capsule exotoxins
• 3 types of anthrax
• Cutaneous spores enter through skin, black
  sore- eschar least dangerous
• Pulmonary inhalation of spores
• Gastrointestinal ingested spores
• treated with penicillin or tetracycline
• vaccine toxoid 6X over 1.5 years annual
  boosters
• dead livestock burned/chemically decontaminated
  before burial to prevent soil contamination

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Bacillus anthracis

• Biological warfare threat.
• Letter attacks of 2001
• Resulted in only 22 cases of anthrax and five
  deaths
• Great disruption and concern
• More than 32,000 people who may have come into
  contact with the letters were given prophylactic
  antibiotics.

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Cutaneous anthrax showing the eschar
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Clostridium

• Obligate anaerobes (lack an electron transport
  system)
• Producers of potent extoxins
• C. tetani? tetanus (toxin blocks inhibitory
  neurons leading to spastic paralysis)

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• Clostridium perfringens
• gas gangrene
• food poisoning

C. perfringens wound infection
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Clostridium perfringens

• treatment of gangrene
• debridement of diseased tissue
• large doses of cephalosporin or penicillin
• hyperbaric oxygen

Hyperbaric treatment chamber Exposure to
increased oxygen levels inhibits anaerobes and
speeds healing
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Clostridium botulinum

• Botulism food poisoning (an intoxication)
  spores are in soil, may contaminate vegetables
  improper canning does not kill spores they
  germinate in the can producing botulinum toxin
• toxin causes paralysis by preventing release of
  acetylcholine (flaccid paralysis)

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Clostridium botulinum

• Botox
• In 2005, almost 3.3 million procedures were
  performed with FDA-approved BOTOX Cosmetic.
• BOTOX Cosmetic works by temporarily reducing the
  contractions of the muscles that cause the
  persistent frown lines that have develop over
  time.
• The benefits may last up to 4 months

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Clostridium difficile

• normal resident of colon, in low numbers
• causes antibiotic-associated colitis
• treatment with broad-spectrum antibiotics kills
  the other bacteria, allowing C. difficile to
  overgrow
• produces entertoxins that damage intestine
• major cause of diarrhea in hospitals

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C. difficile infection. Lining of the colon
as seen via a sigmoidoscope
Mild
Severe pseudomembranous colitis
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Gram positive rods (non-endospore forming)

• Lactobacillus
• Ferment carbohydrates to lactic acid. The
  acidity inhibits many competing bacteria and
  creates an ecological niche where they have the
  advantage.
• Major inhabitant of the vaginal tract
• Used in production of many foods
• L. delbrueckii used in yogurt production
• L. acidophilus used in acidophilus milk production

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Corynbacterium diptheriae

• gram-positive irregular bacilli (pleiomorphic)
• Diptheria (prior to 1935 diptheria was the 1
  infectious killer of children in the U.S.)
• Produces a potent exotoxin
• pseudomembrane formation can cause asphyxiation

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Diptheria

• 1990s epidemic in former Soviet Union countries.
• Reduced vaccination programs resulted in greatly
  reduced herd immunity
• Multitude of susceptible persons allowed spread
  in the community.
• Most cases are in children aged 1-10 in crowded
  settings.

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Gram positive filamentous bacteria

• Streptomyces
• Primarily soil organisms
• Produce antibiotics

Arrows point to Streptomyces colonies surrounded
by zones of inhibition
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Cell-Wall-Less Bacteria

• Mycoplasma
• Very small (smallest organisms capable of
  independent growth)
• They dont stain Gm but are clearly related to
  other Gram positives
• Require sterols to strengthen their membranes
• M. pneumoniae causes a form of walking
  pneumonia

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Acid-Fast Bacteria Mycobacterium
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Mycobacteria

• gram-positive irregular bacilli
• acid-fast staining
• strict aerobes
• produce catalase
• possess mycolic acids a unique type of
  peptidoglycan
• do not form capsules, flagella or spores
• grow slowly
• Mycobacterium tuberculosis
• Mycobacterium leprae

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Mycobacterium tuberculosis

• produces no exotoxins or enzymes that contribute
  to infectiousness
• contain complex waxes other substances that
  prevent destruction by lysosomes of macrophages
• transmitted by airborne respiratory droplets
• only 5-10 infected people develop clinical
  disease

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Tuberculosis (statistics-1)

• Tuberculosis (TB) kills about two million people
  each year
• One-third of the world's population is infected
  with TB. Five to 10 percent of people who are
  infected with TB become sick with TB at some time
  during their life
• Each year, more than 8 million people become sick
  with TB

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Tuberculosis (statistics-2)

• Between 2000 and 2020, it is estimated that
• Nearly one billion people will be newly infected
  with TB.
• 200 million people will become sick from TB.
• TB will claim at least 35 million lives.

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Treatment of TB

• 6-24 months of at least 2 drugs from a list of 11
• one pill regimen called Rifater (isoniazid,
  rifampin, pyrazinamide)
• vaccine based on attenuated bacilli Calmet-Guerin
  strain of M. bovis used in other countries (not
  U.S.)
• Success rate of vaccination 80 in children and
  20-50 in adults.

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Directly Observed Therapy (DOT)to assure that
medication is actually taken
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MDR (multiple-drug-resistant) TB

• Most TB patients do not complete their full 6-9
  month regimen. The TB bacillus becomes resistant
  due to incomplete, erratic or inadequate
  treatment.
• Often a few months into a cumbersome and lengthy
  treatment process, patients feel better and may
  stop treatment altogether.
• Up to 20 of TB cases are drug-resistant in TB
  hot-spots
• 4 of TB cases globally are resistant to at least
  one drug
• MDR-TB could be growing as rapidly as 400,000
  cases each year

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MDR (multiple-drug-resistant) TB
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Phylum 4 Cyanobacteria
Anabena
Gloeothece
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Cyanobacteria

• Oxygenic photosynthesis, use chlorophyll a
• Great morphological diversity (some unicellular,
  some long filaments)
• Capable of nitrogen fixation

Oscillatoria
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Phylum 5 Chlamydia

• obligate intracellular parasites
• small gram-negative cell wall
• C. pneumoniae causes an atypical pneumonia that
  is serious in asthma patients
• C. psittaci causes ornithosis, a zoonosis
  transmitted to humans from bird vectors highly
  communicable among all birds pneumonia or
  flulike infection with fever, lung congestion
• C. trachomatis - STD

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PHYLUM 10 GREEN SULFUR BACTERIA

• Obligate anaerobes
• Anoxygenic phototrophs, use bacteriochlorophyll
• Can grow in very low light levels
• Oxidize hydrogen sulfide to sulfur and sulfate
• Example Chlorobium

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PHYLUM 11THE SPIROCHETES

• Gram negative, motile, tightly coiled, typically
  slender and flexible.
• Widespread in aquatic environments and in animals
• Contain flagella that are not free, but are
  within the periplasmic space (endoflagellum)

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spirochetes

• Gram negative human pathogens
• Treponema
• Leptospira
• Borrella

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Treponema pallidum

• human is the natural host
• extremely fastidious sensitive, cannot survive
  long outside of the host
• causes syphilis
• treatment
• penicillin G

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Leptospira

• tight, regular individual coils with a bend or
  hook at one or both ends
• L. interrogans causes leptospirosis, a zoonosis
• bacteria shed in urine infection occurs by
  contact targets kidneys, liver, brain, eyes
• sudden high fever, chills, headache, muscle
  aches, conjunctivitis, vomiting
• 50-60 cases a year in US

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B. burgdorferi - Lyme disease

• transmitted by ticks
• complex 2-year cycle involving mice deer
• nonfatal, slowly progressive syndrome that mimics
  neuromuscular rheumatoid conditions
• 70 get bulls eye rash
• fever, headache, stiff neck, dizziness
• if untreated can progress to cardiac
  neurological symptoms, polyarthritis
• tetracycline, amoxicillin

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Lyme disease
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PHYLUM 12 DEINOCOCCI

• Deinococcus radiodurans
• Most radiation resistant of all known organisms
• Highly efficient DNA repair mechanisms

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Archaea
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Features of Archaea

• Prokaryotes (no membrane bound nucleus)
• Lack Peptidoglycan in their cell walls
• Genome is circular DNA
• Histone proteins are present
• Ribosomes are more similar to bacteria than
  eukaryotes
• Many occupy "extreme' environments. Extremophiles

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Extreme Halophiles

• Require very high salt (not just tolerant)
• Most require at least 9 NaCl
• Most require 12-23 NaCl for optimal growth
• Almost all can grow at 32 NaCl
• Example genera Halobacterium Halococcus

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Extreme Halophiles
Seawater evaporation ponds
Great salt lake
African soda lake high alkalinity, high salinity
SEM of halophiles
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Methanogens

• CH4 (methane producers)
• Strict anaerobes
• Example genus Methanococcus

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Methanogens

• Methanogen habitats

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Hyperthermophiles

• Most are obligate anaerobes
• Most require S? as part of their metabolic scheme
• Example Genera Sulfolobus Thermococcus Pyrolobus
  
• Heat stable biomolecules
• Habitats

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Hyperthermophiles