Monday, June 6, 2011

E. coli Outbreak in the Europe


Europe is currently besieged by a serious outbreak of a rare strain of E. coli foodborne bacteria. One of the largest outbreaks of E. coli ever recorded strikes Germany and several other European countries. An ongoing Escherichia coli O104:H4 bacterial outbreak began in Germany in May 2011. Certain strains of E. coli are a major cause of foodborne illness. The outbreak started after several people were infected with bacteria leading to hemolytic-uremic syndrome in Germany. Hemolytic-uremic syndrome (HUS) is a medical emergency and requires urgent treatment. 19 people have died by 3 June and around 500 had been hospitalised with HUS due to the intensifying outbreak.
Scientists probing the deadly E. coli strain in Europe are finding the bacteria combines a highly poisonous, but common, toxin with a rarely seen "glue" that binds it to a patient's intestines.

It may take months for the global team of researchers to fully understand the characteristics of the bacteria that has killed at least 17 people in Europe and sickened 1,500. But they fear this E. coli strain is the most toxic yet to hit a human population.
Most Escherichia coli or E. coli bacteria are harmless. The strain that is sickening people in Germany and other parts of Europe, known as 0104:H4, is part of a class of bacteria known as Shiga toxin-producing Escherichia coli, or STEC.
This class has the ability to stick to intestinal walls where it pumps out toxins, causing diarrhea and vomiting. In severe cases, it causes hemolytic uremic syndrome or HUS, attacking the kidneys and causing coma, seizure and stroke.
Germany is now reporting 470 cases of HUS. That is absolutely extraordinary, Dr. Robert Tauxe, a foodborne diseases expert at the U.S. Centers for Disease Control and Prevention, told Reuters. The CDC has been working with German health authorities on the case since late last week.

The main source of E. coli is animal, especially cattle, manure. Ground beef is the main culprit. But because we use manure to fertilize crops, E. coli can also make an appearance in leafy greens, watery vegetables like tomatoes or cucumbers, and sprouts. Finally, E. coli can show up in unpasteurized milk, apple juice, orange juice, or even water. Essentially, everything. The best course of action is to buy quality products from quality vendors who know the source of their meat and produce. Avoid bargain meats, especially those that come from multiple unknown sources. As for vegetables, it's also a good idea to try and buy single source varieties, such as buying heads of lettuce as opposed to the pre-packaged stuff.

The World Health Organization has confirmed that the strain "has never been isolated from patients before," and said the bacteria had likely acquired some extra genes that may make it especially deadly.
Affected countries
  • Germany
  • Spain
  • Sweden
  • Czech Republic
  • Denmark
  • The Netherlands
  • United Kingdom
  • Switzerland
  • Poland
  • United States
  • Austria
  • France
E. coli is Gram-negative, facultative anaerobic and non-sporulating. Cells are typically rod-shaped, and are about 2.0 micrometres (μm) long and 0.5 μm in diameter, with a cell volume of 0.6 – 0.7 (μm)3. It can live on a wide variety of substrates. E. coli uses mixed-acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate and carbon dioxide. Since many pathways in mixed-acid fermentation produce hydrogen gas, these pathways require the levels of hydrogen to be low, as is the case when E. coli lives together with hydrogen-consuming organisms, such as methanogens or sulphate-reducing bacteria.
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms (endotherms). Most E. coli strains are harmless, but some, such as serotype O157:H7, can cause serious food poisoning in humans, and are occasionally responsible for product recalls. The harmless strains are part of the normal flora of the gut, and can benefit their hosts by producing vitamin K2, and by preventing the establishment of pathogenic bacteria within the intestine.
E. coli bacteria are not always confined to the intestine, and their ability to survive for brief periods outside the body makes them ideal indicator organisms to test environmental samples for fecal contamination. The bacterium can also be grown easily, and its genetics are comparatively simple and easily manipulated or duplicated through a process of metagenics, making it one of the best-studied prokaryotic model organisms, and an important species in biotechnology and microbiology.
E. coli was discovered by German pediatrician and bacteriologist Theodor Escherich in 1885, and is now classified as part of the Enterobacteriaceae family of gamma-proteobacteria.
E. coli normally colonizes an infant's gastrointestinal tract within 40 hours of birth, arriving with food or water or with the individuals handling the child. In the bowel, it adheres to the mucus of the large intestine. It is the primary facultative anaerobe of the human gastrointestinal tract. (Facultative anaerobes are organisms that can grow in either the presence or absence of oxygen.) As long as these bacteria do not acquire genetic elements encoding for virulence factors, they remain benign commensals.
Virulent strains of E. coli can cause gastroenteritis, urinary tract infections, and neonatal meningitis. In rarer cases, virulent strains are also responsible for haemolytic-uremic syndrome, peritonitis, mastitis, septicaemia and Gram-negative pneumonia.
The antibiotic sensitivities of different strains of E. coli vary widely. As Gram-negative organisms, E. coli are resistant to many antibiotics that are effective against Gram-positive organisms. Antibiotics which may be used to treat E. coli infection include amoxicillin, as well as other semisynthetic penicillins, many cephalosporins, carbapenems, aztreonam, trimethoprim-sulfamethoxazole, ciprofloxacin, nitrofurantoin and the aminoglycosides.
Antibiotic resistance is a growing problem. Some of this is due to overuse of antibiotics in humans, but some of it is probably due to the use of antibiotics as growth promoters in animal feeds. A study published in the journal Science in August 2007 found the rate of adaptative mutations in E. coli is "on the order of 10−5 per genome per generation, which is 1,000 times as high as previous estimates," a finding which may have significance for the study and management of bacterial antibiotic resistance. Antibiotic-resistant E. coli may also pass on the genes responsible for antibiotic resistance to other species of bacteria, such as Staphylococcus aureus, through a process called horizontal gene transfer. E. coli bacteria often carry multiple drug-resistance plasmids, and under stress, readily transfer those plasmids to other species. Indeed, E. coli is a frequent member of biofilms, where many species of bacteria exist in close proximity to each other. This mixing of species allows E. coli strains that are piliated to accept and transfer plasmids from and to other bacteria. Thus, E. coli and the other enterobacteria are important reservoirs of transferable antibiotic resistance.
Resistance to beta-lactam antibiotics has become a particular problem in recent decades, as strains of bacteria that produce extended-spectrum beta-lactamases have become more common.
Phage therapy—viruses that specifically target pathogenic bacteria—has been developed over the last 80 years, primarily in the former Soviet Union, where it was used to prevent diarrhoea caused by E. coli. Presently, phage therapy for humans is available only at the Phage Therapy Center in the Republic of Georgia and in Poland. However, on January 2, 2007, the United States FDA gave Omnilytics approval to apply its E. coli O157:H7 killing phage in a mist, spray or wash on live animals that will be slaughtered for human consumption. The enterobacteria phage T4, a highly studied phage, targets E. coli for infection.
Researchers have actively been working to develop safe, effective vaccines to lower the worldwide incidence of E. coli infection. In March 2006, a vaccine eliciting an immune response against the E. coli O157:H7 O-specific polysaccharide conjugated to recombinant exotoxin A of Pseudomonas aeruginosa (O157-rEPA) was reported to be safe in children two to five years old. Previous work had already indicated it was safe for adults. A phase III clinical trial to verify the large-scale efficacy of the treatment is planned.
In 2006, Fort Dodge Animal Health (Wyeth) introduced an effective, live, attenuated vaccine to control airsacculitis and peritonitis in chickens. The vaccine is a genetically modified avirulent vaccine that has demonstrated protection against O78 and untypeable strains.
In January 2007, the Canadian biopharmaceutical company Bioniche announced it has developed a cattle vaccine which reduces the number of O157:H7 shed in manure by a factor of 1000, to about 1000 pathogenic bacteria per gram of manure.
In April 2009, a Michigan State University researcher announced he had developed a working vaccine for a strain of E. coli. Mahdi Saeed, professor of epidemiology and infectious disease in MSU's colleges of Veterinary Medicine and Human Medicine, has applied for a patent for his discovery and has made contact with pharmaceutical companies for commercial production.

E. coli Statistics

General Statistics  
 1 
 Cell length  2 um or 2x10-6 m
 2 
 Cell diameter  0.8 um or 0.8x10-6 m
 3 
 Cell total volume  1x10-15 L or 1x10-18 m3

(other est. at 0.88x10-15 L)
 4 
 Cell aqueous volume  7 x 10-16 L
 5 
 Cell surface area  6x10-12 m2
 6 
 Cell wet weight  1x10-15 kg or 1x10-12 g
 7 
 Cell dry weight  3.0x10-16 kg or 3.0x10-13 g
 8 
 Periplasm volume  6.5x10-17 L
 9 
 Cytoplasm volume  6.7x10-16 L
 10 
 Envelope volume  1.6x10-16 L
 11 
 Nuclear (DNA+protein) volume  1.6x10-16 L
 12 
 Inner Membrane thickness  8x10-9 m
 13 
 Outer Membrane thickness  8x10-9 - 15x10-9 m
 14 
 Periplasm thickness  1x10-8 m
 15 
 Average size of protein  360 residues
 16 
 Average diameter of ave. protein  5 nm
 17 
 Average MW of protein  40 kD
 18 
 Average prot. oligomerization state  4 proteins/complex
 19 
 Average MW of protein entity  160 kD
 20 
 Average size of mRNA  1100 bases
 21 
 Average length of mRNA  370 nm
 22 
 Average MW of all RNAs  400 kD
 23 
 Average MW of single DNA  3.0x109 D or 3.0x106 kD
 24 
 Average MW of all DNA  7 x 106 kD
 25 
 Average length of DNA (chrom.)  1.55 mm
 26 
 Diameter of chromosome  490 um
 27 
 Diameter of condensed chromosome  17 um
 28 
 Spacing between small organics  3.6 nm/molecule
 29 
 Spacing between ions  2.1 nm/molecule
 30 
 Ave. spacing between proteins  7 nm/molecule
 31 
 Spacing between protein entities  9 nm/molecule
 32 
 Mean Velocity of 70 kD protein (cytoplasm)  3 nm/ms = 3x10-6 m/s
 33 
 Mean Velocity of 40 kD protein (cytoplasm)  5 nm/ms = 5x10-6 m/s
 34 
 Mean Velocity of 30 kD protein (cytoplasm)  7 nm/ms = 7x10-6 m/s
 35 
 Mean Velocity of 14 kD protein (cytoplasm)  10 nm/ms = 10x10-6 m/s
 36 
 Mean Velocity of small molecules (cytoplasm)  50 nm/ms = 5x10-5 m/s
 37 
 Mean Velocity of protein in H2O  27 nm/ms = 2.7x10-5 m/s
 38 
 Mean Velocity of small molecules in H2O  87 nm/ms = 8.7x10-5 m/s
 39 
 Concentration of protein in cell  200-320 mg/mL (5-8 mM)
 40 
 Concentration of RNA in cell  75-120 mg/mL (0.5-0.8 mM)
 41 
 Concentration of DNA in cell  11-18 mg/mL (5 nM)
 42 
 Volume occupied by water  70%
 43 
 Volume occupied by protein  17%
 44 
 Volume occupied by all RNA  6%
 45 
 Volume occupied by rRNA  5%
 46 
 Volume occupied by tRNA  0.8%
 47 
 Volume occupied by mRNA  0.2%
 48 
 Volume occupied by DNA  1%
 49 
 Volume occupied by ribosomes  8%
 50 
 Volume occupied by lipid  3%
 51 
 Volume occupied by LPS  1%
 52 
 Volume occupied by murein  1%
 53 
 Volume occupied by glycogen  1%
 54 
 Volume occupied by ions  0.3%
 55 
 Volume occupied by small organics  1%
 56 
 Translation rate  40 aa/sec
 57 
 RNA polymerase transcription rate  70 nt/sec
 Large Molecule Copy Numbers  
 1 
 Number of cell walls/cell  1
 2 
 Number of membranes/cell  2
 3 
 Number of chromosomes/cell  2.3 (at mid log phase)
 4 
 Number of mRNA/cell  4000
 5 
 Number of rRNA/cell  18,000
 6 
 Number of tRNA/cell  200,000
 7 
 Number of all RNA/cell  222,000
 8 
 Number of polysaccharides/cell  39,000
 9 
 Number of murein molecules/cell  240,000-700,000
 10 
 Number of lipopolysaccharide/cell  600,000
 11 
 Number of lipids/cell  25,000,000
 12 
 Number of all lipids/cell  25,000,000
 13 
 Number of phosphatidylethanolamine  18,500,000
 14 
 Number of phosphatidylglycerol  5,000,000
 15 
 Number of cardiolipin  1,200,000
 16 
 Number of phosphatidylserine  500,000
 17 
 Number of LPS (MW = 10kD)  600,000
 18 
 Average SA of lipid molecule  25 Ang2
 19 
 Fraction of lipid bilayer=lipid  40%
 20 
 Fraction of lipid bilayer=protein  60%
 21 
 Number of outer membrane proteins  300,000
 22 
 Number of porins (subset of OM)  60,000
 23 
 Number of lipoproteins (OM)  240,000
 24 
 Number of inner membrane proteins  200,000
 25 
 Number of nuclear proteins  100,000
 26 
 Number of cytoplasmic proteins  1,000,000 (excluding ribo proteins)
 27 
 Number of ribosomal proteins  900,000
 28 
 Number of periplasmic proteins  80,000
 29 
 Number of all proteins in cell  2,600,000
 30 
 Number of external proteins (flag/pili)  1,000,000
 31 
 Number of all proteins  3,600,000
 Statistics on Larger Molecule Complexes  
 1 
 Number of protein types to make flagella  42
 2 
 Length of flagella  10-20 um or ~15,000 nm
 3 
 Diameter of flagella  25 nm
 4 
 Number of protofilaments in flagellum  11
 5 
 Diameter of each fliC monomer  5 nm
 6 
 Number of fliC monomers in filament  3000x11=33,000
 7 
 Number of flagella/cell  10
 8 
 Number of fliC proteins  330,000
 9 
 Speed at which E. coli move  50 um/sec = 18 x10-5 km/h
 10 
 Number of protein types to make pilus  1
 11 
 Length of pili/fimbrae  200-2000 nm
 12 
 Diamter of pili  6.5 nm
 13 
 Number of papA/nm pilus  1.5
 14 
 Number of papA monomers/pilus  3000-30,000
 15 
 Number of pili/cell  100-300
 16 
 Number of papA/cell  300,000-900,000
 17 
 Number of ribosomes/cell  18,000
 18 
 Number of protein types to make ribosome  55
 19 
 Number rRNA types to make ribosome  3
 20 
 Number of proteins in 30S subunit  21
 21 
 Number of proteins in 50S subunit  34
 22 
 Number of rRNA in 30S subunit  1
 23 
 Number of rRNA in 50S subunit  2
 24 
 Length of all rRNA  5520 nt
 25 
 MW of ribosome  2700 kD
 26 
 MW of RNA component  1700 kD
 27 
 MW of protein component  1000 kD
 28 
 Diameter of ribosome  20 nm
 29 
 Volume of ribosome  4.2 x 10-24 m3
 Small Molecule Copy Numbers  
 1 
 Number of water molecules/cell  2.34x1010 (23.4 billion)
 2 
 Number of ions/cell  120,000,000 (300 mM)
 3 
 Number of small organics/cell  18,000,000 (40-50 mM)
 4 
 Number of K ions  90,000,000 (200-250 mM)
 5 
 Number of Na ions  2,000,000 (5 mM)
 6 
 Na (in): Na (out)  1:20 (in concentration)
 7 
 Number of Ca ions  2,300,000 (6 mM)
 8 
 Number of free Ca ions  40 (100 nM)
 9 
 Number of Cl ions  2,400,000 (6 mM)
 10 
 Number of Mg ions  4,000,000 (10 mM)
 11 
 Number of Fe ions  7,000,000 (18 mM)
 12 
 Number of Mn ions  1,700,000 (4 mM)
 13 
 Number of Zn ions  1,700,000 (4 mM)
 14 
 Number of Mo ions  1,700,000 (4 mM)
 15 
 Number of Cu ions  1,700,000 (4 mM)
 16 
 Number of PO4 ions  2,000,000 (5 mM)
 17 
 Number of glucose/cell  200,000-400,000 (0.5-1 mM)
 18 
 Number of PEP/cell  1,100,000 (2.8 mM)
 19 
 Number of pyruvate/cell  370,000 (0.9 mM)
 20 
 Number of gluc-6-PO4/cell  20,000 (0.05 mM)
 21 
 Number of ATP/cell  500,000 - 3,000,000 (1.3-7.0 mM)
 22 
 Number of ADP/cell  70,000 (0.17 mM)
 23 
 Number of NADP/cell  240,000 (0.63 mM)
 24 
 Number of NADPH/cell  220,000 (0.56 mM)
 25 
 Number of all amino acids/cell  6,000,000 (1.5 mM)
 26 
 Number of free Alanine/cell  350,000 (0.8 mM)
 27 
 Number of free Cysteine/cell  80,000 (0.2 mM)
 28 
 Number of free Aspartate/cell  530,000 (1.34 mM)
 29 
 Number of free Glutamate/cell  200,000 (0.5 mM)
 30 
 Number of free Phenylalanine/cell  170,000 (0.4 mM)
 31 
 Number of free Glycine/cell  350,000 (0.8 mM)
 32 
 Number of free Histidine/cell  80,000 (0.2 mM)
 33 
 Number of free Isoleucine/cell  200,000 (0.5 mM)
 34 
 Number of free Lysine/cell  190,000 (0.46 mM)
 35 
 Number of free Leucine/cell  300,000 (0.7 mM)
 36 
 Number of free Methionine/cell  40,000 (0.1 mM)
 37 
 Number of free Asparagine/cell  200,000 (0.5 mM)
 38 
 Number of free Proline/cell  200,000 (0.5 mM)
 39 
 Number of free Glutamine/cell  200,000 (0.5 mM)
 40 
 Number of free Arginine/cell  170,000 (0.4 mM)
 41 
 Number of free Serine/cell  300,000 (0.7 mM)
 42 
 Number of free Threonine/cell  1,400,000 (3.49 mM)
 43 
 Number of free Valine/cell  240,000 (0.6 mM)
 44 
 Number of free Tryptophan/cell  80,000 (0.2 mM)
 45 
 Number of free Tyrosine/cell  300,000 (0.7 mM)
 46 
 Osmotic pressure (pushing out)  75 lb/in2
 E. coli Metabolism  
 1 
 1 glucose generates (total)  36-38 ATP
 2 
 glycolysis yields  6-8 ATP
 3 
 oxidation of pyruvate yields  6 ATP
 4 
 Krebs cycle/e- transport yields  24 ATP
 5 
 Number ATP to make 1 DNA  72,289,000
 6 
 Number ATP to make 1 protein (360 aa)  1500
 7 
 Number ATP to make 1 lipid  7
 8 
 Number ATP to make 1 polysaccharide  2000
 9 
 Number ATP to make 1 RNA (1000 nt)  2000
 10 
 Number ATP to make 1 cell  55 billion ATP
 11 
 Number Glucose molecules consumed  1.4 billion molecules
 12 
 Cell division rate  1 division/30 minutes

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