Transcript Spring 2015 Chapter 1

SCOPE AND HISTORY OF
MICROBIOLOGY
CHAPTER 1
Bio 308 General Microbiology
Notes and syllabus are on web site:
http://bio.as.uky.edu/users/shellys
My e-mail: [email protected]
Phone: 859-257-3870
Text Book: Microbiology- Principles and Explorations
Jacquelyn G. Black- 7 or 8th edition
Chapter 1 Scope and History of Microbiology
Microbes have a major impact on human health
In 1962, the U.S. Surgeon General,
William H. Stewart, stated, “ The war
against infectious disease has been won.”
In the subsequent decades, emerging diseases
and increasing antibiotic resistance have made it clear
that in reality not only is the war far from won, its
outcome is not longer certain
The above (1962) is the basic climate that I started my
Ph.D. studies in microbiology
'Golden age' of antibiotics 'set to end‘ Far fewer pharmaceutical companies are
working on new antibiotics than in the past. The growing threat of antibiotic resistant
organisms is once again in the spotlight. Prof Farrar told BBC Radio 4's Today
programme that the golden age of antibiotics could come to an end unless action is
taken. Last year she described the growing resistance to antibiotics as a "ticking time
bomb", and said the danger should be ranked alongside terrorism on a list of threats
to the nation. In 1998 a House of Lords report gave this stark assessment: "Antibiotic
resistance threatens mankind with the prospect of a return to the pre-antibiotic
era.“Two bacterial infections illustrate the problem. Multi-drug resistant (MDR)
tuberculosis is rising steadily worldwide. Another example is the rise in infections from
enterobacteriaceae - bugs that live in the gut like E.coli and Klebsiella. They are now
the commonest cause of hospital acquired infection and some are becoming resistant
to carbapenems, a powerful, last resort group of antibiotics. There has also been an
alarming increase in rates of the sexually transmitted disease gonorrhoea, which is
becoming more difficult to treat. He said there are just four pharmaceutical companies
working on antibiotics now compared to 18 companies 20 years ago.
Antibiotics in Animals Tied to Risk of Human Infection A federal analysis of 30 antibiotics used in
animal feed found that the majority of them were likely to be contributing to the growing
problem of bacterial infections that are resistant to treatment in people, according to
documents released Monday by a health advocacy group. The analysis, conducted by the Food
and Drug Administration and covering the years 2001 to 2010, was detailed in internal records
that the nonprofit group, the Natural Resources Defense Council, obtained through a Freedom
of Information Act request and subsequent litigation. In the documents, some of which were
reviewed by The New York Times, scientists from the F.D.A. studied 30 penicillin and tetracycline
additives in animal feed. They found that 18 of them posed a high risk of exposing humans to
antibiotic-resistant bacteria through food. Resistant bacteria make it difficult and sometimes
impossible to treat infections with ordinary antibiotics. The scientists did not have enough data
to judge the other 12 drugs. At least two million Americans fall sick every year and about
23,000 die from antibiotic-resistant infections, the Centers for Disease Control and Prevention
estimates. Representatives of the food industry largely blame hospitals and treatments given
to people for the rise of deadly superbugs. But many scientists believe that indiscriminate use
of antibiotics in animal feed is a major contributor. Farmers and ranchers feed small amounts of
the drugs to animals over their lifetimes to keep them healthy in crowded conditions, causing
bacteria to develop a resistance passed on to people through the environment and eating meat
from the animals.
U.S. Aims to Curb Peril of Antibiotic Resistance WASHINGTON — The Obama administration on
Thursday announced measures to tackle the growing threat of antibiotic resistance, outlining a
national strategy that includes incentives for the development of new drugs, tighter stewardship
of existing ones, and improvements in tracking the use of antibiotics and the microbes that are
resistant to them. The actions are the first major White House effort to confront a public health
crisis that takes at least 23,000 lives a year, and many experts were pleased that a president had
finally focused on the issue. But some said the strategy fell short in not recommending tougher
measures against the overuse of antibiotics in agriculture, which, they argue, is a big part of the
problem. Researchers have been warning for years that antibiotics — miracle drugs that
changed the course of human health in the 20th century — are losing their power because of
overuse. Some warn that if the trend is not halted, we could return to the time before
antibiotics, when it was common for people to die from ordinary infections and for children not
to survive strep throat. Under the order, Mr. Obama created a national task force to be led by
the secretaries of health and human services, defense and agriculture, and he required that
they deliver a five-year action plan by Feb. 15. He also directed the Department of Health and
Human Services to propose regulations requiring hospitals to set up antibiotics stewardship
programs.
“This represents a major elevation of the issue,” said Dr. Holdren, who talked of the problem as
a national security issue. He said the order also established a $20 million prize for the
development of a diagnostic test that could be used in hospitals to quickly identify highly
resistant bacterial infections.
www.bbc.co.uk/guides/z8kccdm
Human vs superbug: Too late to
turn the tide?
Pharmaceutical research hasn't kept up with the growing resistance
of bacteria to antibiotics. No new types (classes) of antibiotics
have been discovered for 25 years and some strains of bacteria
now are unharmed by nearly all the drugs designed to kill them,
making infections by these bacteria almost untreatable. Experts
have warned we are decades behind in the race against the
superbugs. We've already exploited the most obvious naturally
occurring antibiotics. So creating new ones requires much
more time and ingenuity, but currently there is little financial
incentive to do so. Pharmaceutical companies target chronic
illnesses to maximise potential profits from new drugs.
New Antibiotic Stirs Hope Against Resistant Bacteria JAN. 7, 2015 An unusual method for
producing antibiotics may help solve an urgent global problem: the rise in infections that resist
treatment with commonly used drugs, and the lack of new antibiotics to replace ones that no
longer work. The method, which extracts drugs from bacteria that live in dirt, has yielded a
powerful new antibiotic, researchers reported in the journal Nature on Wednesday. The new
drug, teixobactin, was tested in mice and easily cured severe infections, with no side effects.
Teixobactin has not yet been tested in humans, so its safety and effectiveness are not known.
Regarding teixobactin, he said: “It’s at the test-tube and the mouse level, and mice are not men
or women, and so moving beyond that is a large step, and many compounds have failed.” He
added, “Toxicity is often the Achilles’ heel of drugs.” Drug-resistant bacteria infect at least two
million people a year in the United States and kill 23,000, according to the Centers for Disease
Control and Prevention. “Drug resistant strains of many diseases were emerging faster than new
antibiotics could be made to fight them.” Teixobactin works against bacteria in a group known
as “Gram-positive,” but not against microbes that are “Gram-negative,” Teixobactin attacks
bacteria by blocking fatty molecules needed to build cell walls, which is different from the way
most antibiotics work.
Microbes help maintain the balance of nature- mostly
microorganisms decompose releasing nitrogen or breaking down
industrial wastes or breaking down cellulose in the digestive tract of
grazing animals.
Microorganisms are important in many human endeavors:
Foods (fermentation products (a long list that will be dealt with
later in the course), antibiotics, products of genetic engineering,
removal of toxic wastes and on and on. In future years many industrial
processes carried out by chemical reactions will be done by bacterial
(e.g., plastics).
In addition, very recent studies suggest that the microflora in the gut, in
particular, influences our health and behavior.
Roles of Microbes
• Pathogens
• Antibiotics
• Food chain
• Biotechnology
– Autotrophs
– Decomposers
• Digestive
• Bioremediation
• Foods and
fermentation
• Disease Research
Microbe Types
• Prokaryotes – 2
Domains/Superkingdoms
• Bacteria
– Some pathogens
– Science of Bacteriology
• Archaea
– Environmental
extremophiles
– Novel biochemistry
Viruses (Acellular)
• Simple structure
– Capsid
– Nucleic acid
• Obligate intracellular growth
• Science of Virology
• Smaller relatives
– Viroids
– Prions
Germ Theory
• Theory definition
• Koch
– Culture
– Postulates
• Semmelweiss
• Lister
Fields of Microbiology
• Infection Control
• Chemotherapy
• Industrial Microbiology
• Biotechnology
• Biofilms and health
THE GERM THEORY OF DISEASE-microorganisms
can invade other organisms and cause disease. Because
the prevailing theory of the day was spontaneous
generation, i.e., that life forms arouse from non-living
things, e.g., fruit flies are made from bananas.
Thus, it was difficult for people to believe the germ
theory. The demonstration by a number of individual that
life only come from preexisting life put an end to the idea
of spontaneous generation.
It is worthwhile mentioning that spontaneous generation,
although totally incorrect, follows Occam’s razor ( "All
other things being equal, the simplest solution is the
best.“).
Although Occam’s razor is a good general idea- It only becomes science when it is
testable. In addition to testability science is hypothesis driven.
A hypothesis is a tentative explanation to account for an observed condition or
event.
Hence, a testable hypothesis is one for which evidence can be collected to support or
refute the hypothesis.
In science, a theory is a mathematical or logical explanation, or a testable model of the
manner of interaction of a set of natural phenomena, capable of predicting future
occurrences or observations of the same kind, and capable of being tested through
experiment or otherwise falsified through empirical observation. It follows from this
that for scientists "theory" and "fact" do not necessarily stand in opposition. For
example, it is a fact that an apple dropped on earth has been observed to fall towards the
center of the planet, and the theories commonly used to describe and explain this
behavior are Newton's theory of universal gravitation (see also gravitation), and general
relativity.
An explanation that cannot be tested is not science.
Louis Pasteur, a chemist, is considered as a giant in the history of microbiology. In
addition to his contribution to the spontaneous generation/germ theory debate he
contributed a great deal to the development of the field of microbiology.
A. Pasteurization of wine so that pure seed cultures could be used in wine
production
B. major contribution to the germ theory of disease in demonstrating that
microorganisms caused silk worm disease and Anthrax..
C. He developed a rabies vaccine (and thereby demonstrated the value of
vaccination) and on and on.
It is worthwhile mentioning that Pasteur popularized the correct explanation of many
things he was not the initial author of any of the above ideas.
Robert Koch – developed a method for pure culture. Probably as important as his work
on tuberculosis, for which he was awarded a Nobel Prize (1905), are Koch's postulates,
which say that to establish that an organism is the cause of a disease, it must be:
1) found in all cases of the disease examined, 2) prepared and maintained in a pure
culture capable of producing the original infection, 3) even after several
generations in culture be retrievable from an inoculated animal and cultured again.
We will visit Koch’s postulates again when we discuss disease.
The finding that there are asymptomatic carriers of typhoid and cholera made Koch
modify the third part of his postulates to be less dogmatic.
WORK TOWARD CONTROLLING INFECTIONS
1. Ignaz Semmelwis (Devils, Doctors and Drugs is a very interesting
biography of Semmelweis). He was an obstetrician who pioneered aseptic
technique and died of sepsis.
His trials at trying to popularize the idea that aseptic technique could defeat
childbed fever (streptococcal infection that accompanies childbirth) is a
classic example of the difficulty in trying to establish a new principle in
the medical community.
2. Lister (who was later made a Lord because of his findings) applied carbolic
acid (phenol) to aseptic technique in the operating room
3. Domagk- Sulfa drugs- 1939
4. Fleming, Chain and Florey- Penicillin-1945
New epidemic model says Ebola in Liberia 'could end by June'A new
computer model that takes into account not only features of the virus and
how it transmits, but also what is being done to halt its spread, predicts that
the Ebola epidemic in Liberia could end by June if current high rates of
hospitalization and surveillance continue. That's a realistic possibility but not a
foregone conclusion," says John Drake, an ecology professor at the University
of Georgia (UGA), who led the project to develop the model with other
ecologists at UGA and also at Pennsylvania State University.
The team reports how they developed the model and ran some scenarios
through it, in the open access journal PLOS Biology.
Prof. Drake says their epidemic model is probably the first to take into account
factors such as where infections occur, where patients are treated, growth in
hospital bed numbers, and the adoption of safe burial practices.
He and his colleagues hope the tool will help public health authorities fight
the Ebola epidemic, because unlike many other models, it offers realistic
forecasts.
New Ebola model captures what is most important and 'ignores the rest'
Is U.S. ready for a pandemic? Investigation says we're 'ill-prepared‘ Somewhere in a
Department of Homeland Security warehouse, thousands of doses of antiviral medications are
about to expire.
Another warehouse stores thousands of expired respirators.
This is the equipment and medicine that was supposed to help protect government personnel in
the event of a deadly pandemic.
A federal investigation has found that the DHS is totally "ill-prepared" for something like the
2009 H1N1 influenza pandemic -- or something worse, such as a global Ebola outbreak or the
1918 flu pandemic that killed an estimated 21.5 million people, according to a report released
by the Office of the Inspector General on Monday.
In 2006, Congress gave DHS $47 million to prepare for such a national medical crisis. And the
department did go shopping; it spent millions on this equipment that might now be completely
worthless, missing or unnecessary. Overall, DHS failed to keep good records about what it
purchased and what it received, according to the report. That may be why the government had
to report a secondary stockpile containing 25,000 surgical masks and hand sanitizer as "lost."he
report concluded "it is imperative that DHS be prepared to continue mission-essential
operations should a pandemic occur," and yet it found that DHS didn't develop a clear plan on
how to replenish their stockpiles of equipment. Nor did they have a good way to keep a good
control over their inventory to monitor expiration dates on material. DHS agreed with all 11
suggestions the Inspector General's Office made to improve the program. The department will
assign an office to oversee the supplies and develop an adequate strategy for making sure the
material stays current. It has applied for a shelf life extension with the Food and Drug
Administration to extend the expiration dates on the antiviral medicine it has that will expire in
2015.
Immunology-Milestones
1.
Elie Mechnikoff- Cellular Immunology- identified white blood cells as phagocytic
immune agents of the blood.
2.
Edward Jenner- showed that an 8 year old could be protected against small pox by
introduction of cowpox virus obtained from the lesions of milk maids that had contracted
cowpox. Termed the word vaccination (vacca-latin name for cow).
3.
Pasteur use a dried spinal cord of rabbits infected with rabies to develop an anti-rabies
vaccine. Drying of the spinal cord effectively attenuates (weakens) the virus.
4.
Gerald M Edleman and Rodney Porter-for their discoveries concerning the chemical
structure of antibodies- 1972
5.
Cesar Milstein, Georges Kohler and Niels Jerne-for theories concerning the specificity in
development and control of the immune system and the discovery of the principle for
production of monoclonal antibodies- 1984
6.
Tonegawa- for his discovery of the genetic principle for generation of antibody diversityReceived the Nobel prize in 1987.
7.
Doherty and Zinkernagel- Recognition of virus-infected cells by immune defenses. Drs.
Doherty and Zinkernagel discovered that T cells simultaneously recognize MHC self-protein
and a foreign antigen on the surface of virally infected cells. - We will learn about these
findings in the immunology part of the course. Received the Nobel prize in 1996.
Bacterial genetics molecular biology-Nobel Prizes
The Nobel Prize in Physiology or Medicine 1933
Thomas H. Morgan
The Nobel Prize in Physiology or Medicine 1933
Thomas H. Morgan
"for his discoveries concerning the role
played by the chromosome in heredity“First Nobel Prize in what would become
Molecular Biology/Molecular Genetics
Morgan was born in Lexington, Kentucky, to Charlton Hunt
Morgan and Ellen Key Howard Morgan.[2][4] Part of a line of
Southern planter elite on his father's side, Morgan was a nephew
of Confederate General John Hunt Morgan and his greatgrandfather John Wesley Hunt had been the first millionaire west
of the Allegheny Mountains. Through his mother, he was the
great-grandson of Francis Scott Key, the author of the "Star
Spangled Banner", and John Eager Howard, governor and senator
from Maryland.[