Microbio

• Infections

  • UTI: urinary tract infection

  • Upper Respiratory (cold?)

  • Bronchitis

  • Ear infection (otitis media)

  • Strep Throat 

  • Pink eye (conjunctivitis)

  • “Itis”: Meaning inflammation

  • Lots of causes of inflammation

  • Ends in itis and the prefix often has to do with what part of body infection located

• Not infections

  • Arthritis

  • Alzheimers 

  • Diabetes

  • Ulcerative colitis 

  • Crohn’s disease

  • Difference between infection and not infection

    • Infections caused by microorganisms 

      • (not all of which are alive)

• What is an infectious disease?

  • Infectious disease: meaning a harm or an abnormality caused to the body by a microorganism 

  • Infection: harboring microorganisms (living in you or on you)

    • Been infected since the moment you've been born

    • technical definition

  • Going to use infection to mean infectious disease

• What is the difference between infectious and noninfectious disease?

  • Infections are caused by microorganisms growing within of on the body that cause HARM or the development of an ABNORMALITY

  • Not infections can be brought on by infections at times but are NOT CAUSED BY MICROORGANISMS

• What is a microorganism?

  • Most simplistic definition of microorganism: organisms that are too small to be seen without a microscope

1. Bacteria

2. Viruses

3. Some fungi

   • Mushrooms are fungi but not microorganisms

4. Some algae (that are microscopic)

5. protozoa

• Why are they microorganisms? 

  • Most of them are too small to be seen without a microscope

    • There are ONE or TWO bacteria that are macroscopic 

  • Most are unicellular (one cell makes up the whole organism), and they tend to be microscopic 

    • Viruses are not unicellular 

• Are viruses microorganisms?

  • VIRUSES ARE NOT LIVING 

  • VIRUSES ARE NOT CELLS

    • Some people who say we shouldn't put them on a list of microorganism because some people say only can call living things organisms

      • Too difficult so we list them as major group but acknowledge that not alive

• Communicable disease: Passed from person to person

  • Not all infectious diseases are communicable

  • Microorganism that is passed from one person to another in some infectious diseases

    • Not the disease that is passed

  • Just because microorganism is passed does not mean that the person is necessarily going to get the disease or get sick

• Pathogenic: microorganism that has the ability to cause disease

  • Mostly going to be talking about human pathogens (and occasionally pathogens acquired by animals/insects)

• Infectious disease is a harm or abnormality that is caused to the body by a microorganism

• Communicable: microorganism passes person to person

  • Just because the microorganism passes does not necessarily mean the person will get the disease/get sick

• Microorganisms: viruses, bacteria, (some) fungi, protozoa, (some) algae

  • No virus that is living organism

• How do we know that we have an infection?

  • Inclination

    • Symptoms: such as sore throat, body aches, fever, 

  • Rapid test

    • For one organism

    • What's being detected is some molecule of the microorganism

    • Fast; however, there's only small number of rapid tests for microorganisms

  • Culture

    • Take the specimen, put on petri dish where bacteria allowed to grow into colonies

    • If the particular bacteria is present in the culture

    • Cultures mainly used for bacteria

      • The above cultures cannot be done for viruses because they don’t grow that way

      • Culture for fungi take much longer

  • Serologic test (blood specimen)

    • Check to see if antibodies for particular microorganism are present

  • Urinalysis: can only suggest an infection 

  • Molecular test

    • Newer kind of test

    • Specimen is taken and check for genes of the organism looking for

    • Covid PCR test is an example

    • Advantages

      • Detect even small numbers of the organisms

      • Fairly quick

        • Once test is set up, takes at most, two hours to get an answer

• Does every infection need to be proven and diagnosed by a test?

  • NO certain infectious diseases don’t need to be proven

  • Self limiting: infection in which own defences going to get you over it

    • No serious treatment for cold except OTC (over the counter)

  • DON'T ALWAYS NEED A COLD

• How did you get over infectious disease?

  • Antibiotics: drugs which either kill or inhibit the multiplication of bacteria

    • Antibiotics only can be used to treat bacterial infections

    • Some anti fungal, viral, and protozoal drugs do exist but less common

  • Immune system

    • Only ONE of your defenses, actually have lot that will work against microorganisms

      • White blood cells 

  • Antibiotics ALONE cannot cure you; have to have own defenses working at least partially

• Why are nurses required to take microbiology

  • Knowing what’s communicable, how the organisms are transmitted, and MOST IMPORTANTLY, how to prevent said transmission

  • Understand the diseases and processes going on for those of your patients with infectious diseases

    • Will understand their physiology

• How many of your patients do you think will have infectious disease

  • How many admitted to hospital because they have infectious disease

  • On the lower side

    • You don’t go into the hospital for infectious disease unless it has gotten very serious

    • Most infectious diseases treated outside the hospital 

• What are nosocomial infections (healthcare associated infection)?

  • Nosocomial infection: infection that the patient did NOT have when they entered the hospital, not even in the incubation period

  • The infection CANNOT even be in the incubation period when one arrives at the hospital (if it is, it is not nosocomial)

    • EXAMPLE: chicken pox takes 21 days to develop symptoms. if an individual gets symptoms 4 days after being admitted, this means it is not a nosocomial infection

  • Might have microorganism in them when entered hospital, but it was NOT harming them at the time

    • Part of their normal or resident flora: living in a balance with you so not harming you

• What are endogenous and exogenous infections?

  • Describe ALL infections, not just nosocomial infections

  • Endogenous: “endo” meaning in

    • infection caused by a microorganism that was already residing in body not harming you at first but then something occurred and now gets to cause harm or abnormality

  • Exogenous: “exo” meaning out

    • Infection caused by microorganism that you newly acquired and its now causing harm or abnormality

  • Example: 

    • E.coli: most common cause of UTIs

      • Endogenous: her own E.coli from intestinal tract that made its way on the outside of the body from the rectal skin area and goes up the urinary tract

    • Covid

      • Exogenous: acquire the virus and now sick

    • MRSA: Methicillin resistant staphylococcus aureus

      • Not just resistant to methicillin but resistant to a lot of things

      • As compared to staph aureus organism that are not MRSA, MRSA causes more serious infections

      • Used to be that only found in hospitals and nursing homes but no organism is gonna stay confined in those kinds of settings so now everywhere

      • Can spread MRSA without knowing it

      • Transmitted by someone getting it on hands from nose and touching something

Why are nosocomial (healthcare associated) infections SO important? 

• Biggest problem hospitals and nursing homes face are nosocomial infections

• Death rate for patients who get nosocomial infections is 5x higher than those who don’t

  • Doesn’t necessarily mean it was the infection that killed them, although it is possible. 

• Prolongs the number of days the patient spends in the hospital, which is an economical issue

• Patient must be treated with antibiotics

  • an additional cost 

  • exposes them to potentially harmful side-effects

So what does one do about nosocomial infections? 

• THE AMOUNT OF NOSOCOMIAL INFECTIONS WERE UNACCEPTABLE: 

  • Hospitals must be observing all measures implemented to prevent nosocomial infections

  • Accrediting agents and insurances required that hospitals do more to lower the rate of nosocomial infections

  • Insurers refuse to pay hospitals if a patient acquires a nosocomial infection that was preventable 

• The hospital is responsible for preventing all nosocomial infections, but they’re mainly responsible for preventing exogenous infections because they’re newly acquired 

• IT IS IMPOSSIBLE FOR A HOSPITAL TO LOWER THE PERCENTAGE OF NOSOCOMIAL INFECTIONS TO 0%

  • Not all nosocomial infections are preventable

  • Not all of them are due to someone’s negligence or ability to observe proper technique

  • Some are simply due to a patient’s underlying state of health

• Refuse to pay the hospital for anything related to the treatment and extended care of patients who get certain types of nosocomial infections

  • Certain types of these infections are preventable

  • So government not going to help pay 

  • Ensures that hospitals are doing everything possible to manage and minimize nosocomial infections

AWARENESS

• How important microbiology and pathogens are to anyone who works in healthcare profession

• The best nurses are the ones who understand the practical things

  • Know what the early signs and symptoms are of infection

What is a pathogen?

• Many microorganisms in the world and most are pathogens

• Pathogen: microorganism that has the ability to cultivate disease

• A lot more microorganisms in the world than we thought 

Pathogenicity

• A trait of the microorganism itself

  • An organism that is a pathogen has abilities to do things in our body that can bring about the harm or abnormality

• When a pathogen gets into a human body, the person is NOT NECESSARILY going to get the disease

• An organism’s ability to cause disease, which is dependent on the traits of an organism 

• Only a relatively small amount of organisms in the world commonly cause disease 

Range of pathogenicity

• Most organisms have VERY LITTLE ability to cause disease (left)

  • Don't like to say there are organisms with NO ability

  • Not labeled “0” or “no ability” to produce disease because most (if not all) organisms have a small ability to cause disease IF they found themselves in special circumstance

• Intermediate have moderate ability (middle)

  • Refers to opportunistic pathogens 

    • Organisms that have only a moderate ability to cause disease such that they DO NOT do so in a person who has ALL THEIR DEFENSES working properly

  • Compromised hosts (individuals with immunocompromised systems and nonfunctioning defenses) are at risk

    • Don't have all their defenses fully functioning

• Small number have strong ability (right)

  • THERE IS NO ORGANISM IN THE WORLD THAT EVERY TIME IT GETS INTO A HUMAN IT WOULD BE ABLE TO CAUSE DISEASE

    • Even if talking about one that has great abilities to harm us, what happens when microorganism gets into body depends on traits of the host

  • Example: Neisseria meningitidis

What is a carrier?

• Carriers: a person who is harboring a SIGNIFICANT PATHOGEN but is not being harmed by said organism at the time we are calling them a carrier

  • Living in a nice balance with that pathogen

• Anyone can be called a carrier if they have a pathogenic organism that is part of their residential flora

• One cannot say that they “have the disease” because then that would suggest that it is harming them (individual is NOT being harmed)

• If one is not harmed by the disease then they don’t have it, rather they are a carrier

• The individual is NOT “in the incubation stage” because it ultimately means that they are subtly being harmed

• Why does one not want to be a carrier (dangers)?

1. The disease can be given to others (the individual is contagious, but depends on where the organism is in the body) 

2. While the individual may seem okay with the organism one day, a sudden 180 can occur and harm the individual 

• How is one suspected of being a carrier? 

  • One can be suspected as a carrier when those they interact with developed the disease (i.e. typhoid mary) 

• How can one determine they are a carrier? 

  • Can be determined officially through a bacterial culture check

• Can the microorganism be eliminated? 

  • May be given antibiotics to eliminate the organism which may work

  • HOWEVER, some organisms may have the ability to remain despite extensive treatment (might vary with each person)

What is an example of a carrier?

• Carrier example

  • Typhoid Mary

    • Some of the clientele that she served got the disease typhoid

    • Found that Mary was a carrier of typhoid 

      • Had the organism in her intestinal tract

        • Get it on her hands

      • Can transmit it directly with someone you touch

    • She was banned from the restaurant/job because no way to treat at the time

• Can you treat a person with antibiotics and eliminate the pathogen that they were a carrier of

  • Told to carry out number of daily practices to try to keep them off skin surfaces

When does the typical human first come into contact with microorganisms?

• Baby is not in contact with microorganisms until they descend into the birth canal

• Because the mother does have microorganisms there and baby absolutely does acquire them

  • Can culture skin surfaces the moment baby comes out and will find mother’s organisms

    • In MOST cases, those are mother’s normal flora organisms that won't hurt the baby

• Once baby is born, exposed to microorganisms in the air

  • Begins to established normal flora very quickly

• Sometimes, babies acquire pathogens as pass through birth canal

  • This is a bad thing

  • These pathogens can cause pretty serious infections

Examples of viruses that could get to the fetus during gestation

• Chickenpox, measles

• Effect on fetus depends on organism AND the time of development that the fetus gets infected

  • If infected during time when major organ systems (i.e. central nervous system) still have to develop, then there is a potential for very serious effects on fetus

  • If infected later, the effects MIGHT NOT be quite so severe

• In all cases, if fetus gets microorganisms, won’t be a good thing because they don’t have the defenses we have

  • Newborns don’t have same defenses as we have and they don’t develop them for a few months

What is an opportunistic pathogen?

• Opportunistic pathogens: organisms that have only a moderate ability to cause disease such that they DO NOT do so in a person who has ALL THEIR DEFENSES working properly

  • Moderate level of pathogenicity because they can’t produce disease in a person who has all of their defenses fully functioning

• The cause of many nosocomial infections

Who does opportunistic pathogens affect?

• Compromised hosts: individuals with immunocompromised systems and non functioning defenses; are at risk

  • Don't have all their defenses fully functioning

What are compromised hosts?

• Immunodeficiency diseases: a disease that weakens the immune system and makes it less functional

  • Disease that affects those with immunodeficiencies more

    • Example: AIDS (Acquired Immunodeficiency Syndrome) 

      • HIV (Human Immunodeficiency Virus) virus destroys certain cells in the immune system, making the individual immunocompromised 

      • People who die from AIDS, commonly die from opportunistic infection 

  • AIDS is caused by microorganism, so immunodeficiency is a result of the infection

    • Unlike AIDS/HIV, other immunodeficiency diseases are genetic

  • With other immunodeficiency diseases, an individual’s immune system isn’t fully functioning because of their genetics 

  • Cases can be extreme where the individual has NO immune system defense AT ALL. 

    • i.e. “Boy in the Bubble”, children or teenagers with an extreme immunodeficiency that makes them highly susceptible to infection

    • Must have some normal flora since they weren’t born in a sterile environment, but they need to remain in a sterile environment to survive

  • Can an immunodeficiency disease be developed? 

    • Yes (in a way) 

    • You must be born with it, but some of them do not manifest immediately

• Immunosuppressive drugs: immune system being suppressed as a result of drugs or therapy

  • Therapy – radiation treatments

    • Radiation kills off cells of the immune system

    • Suppressing immune system

  • Drugs – chemotherapy

    • Don’t only kill cancer cells

    • Kill some of normal cells as well, including those of the immune system

  • Drugs – Humira, Enbrel

  • Why use immunosuppressive drugs if they weaken the immune system?

    • Given drugs that suppress the immune system because the immune system in bringing about the pathology of the disease

      • Immune system is CAUSING the symptoms

      • Thus, the treatment must suppress the immune system and tone down its ability to cause the disease

        • HOWEVER, makes immune system not fully functioning to defend individual against microorganisms

• Broad spectrum antibiotics

  • INCLUDE DESCRIPTION OF WHAT THESE ARE

Why don’t you ALWAYS know if you have TB?

• “Get checked for TB before take any of these drugs”

• Wouldn’t a person know they have TB? NO!!

  • TB is unique because of this:

    • When a  person first gets the TB bacteria in them, in ALMOST ALL cases, the person does not get the disease

    • In ALMOST ALL cases, the organism will go to their lungs and they may be controlled there by the immune system and other defenses

      • So then person doesn’t get disease

    • But organisms hiding out in lungs can be alive for YEARS AND YEARS AND YEARS

      • Years after person gets TB organisms, if they get run down, debilitated by another disease, if take immunosuppressive drug, then TB bacteria will now multiple and cause the disease tuberculosis

What are broad spectrum antibiotics?

• Narrow spectrum antibiotics: affect (relatively speaking) a narrow range of types of bacteria

• Broad spectrum antibiotics: affect wide range of bacteria

• The antibiotics CAN'T go into body and ONLY HARM THE PATHOGEN being treated for

• The antibiotic goes through the body, some get broken down, others reach all parts of body

  • BUT when antibiotic encounters normal flora bacteria, that are sensitive to it, then those normal flora bacteria will be killed or inhibited

• Broad spectrum are going to affect more of normal flora than narrow spectrum

  • Good reason for doctors to give narrow spectrum when possible

• Why is normal flora important?

  • Normal flora bacteria is working as PART of your defense against infection

    • Can create a problem when killed

  • If get rid of normal flora, getting rid of part of defenses

• How might broad spectrum antibiotics affect a person?

  • Yeast: Candida albicans

    • Opportunistic pathogen

      • Not going to hurt you if all defenses are intact

  • If take broad spectrum antibiotic that wipes out SOME (not all) of normal flora, also knocked out some of defense against Candida

    • Candida no longer being controlled because killed off some of normal flora

    • Now Candida going to multiply like crazy and cause a yeast infection

  • When yeast infection in mouth, called thrush

• What can you do to combat the effects of broad spectrum antibiotics?

  • If you are going to take broad spectrum antibiotics, you must be immediately told to take probiotics (yoghurt, kombucha, can be bought, etc.)

• Another example

  • Clostridium difficile (“C-diff”): bacterium within our intestinal tract that is controlled

    • Not causing any harm until take broad spectrum antibiotic that kills off some of intestinal normal flora bacteria

    • Toxin: harmful substance caused by this bacteria

    • Causes horrendous diarrheal disease

    • ALSO COMMUNICABLE

      • Cases in which organisms from original infected person get into another person and cause the disease even if that person wasn’t given the antibiotic

    • SOMETIMES, antibiotics and probiotics DON'T WORK

      • Treating with fecal transplants

        • Taking feces from another person and putting it in the infected patient to re-establish the bacterial flora in the intestinal tract

Compromised Hosts

• 1. Immunodeficiency

• 2. Immunosuppressive drugs

• 3. Broad spectrum antibiotics

What are some other examples of compromised hosts?

• 4. Any break in skin

  • Skin is the biggest barrier that you have against microorganisms

    • True bc MOST microorganisms cannot get through UNbroken skin

    • Thus, skin serves as huge defense

  • Anything that keeps skin from being intact, means that site is compromised

    • Skin barrier is broken and organisms can get in

  • Examples

    • Cut, splinter, etc. 

    • Also includes chapped skin (not a cut) or even dry skin

    • Contact dermatitis

    • Eczema 

  • Microbiologists believe we should never trust our skin to be fully healthy and fully intact

    • All areas of skin have microscopic cuts/breaks (things cant see) 

      • Places where skin isn't actually intact and microorganisms cna get in

  • Why wear gloves for everything done in the hospital now

• 5. Debilitation

  • big , broad term that refers to anything that causes a person to not be fully healthy

  • Could be an underlying disease (like cancer)

    • But does not have to be as extreme as cancer

    • Can be milder form of debilitation

      • Stress 

      • Malnutrition or poor nutrition

  • More susceptible to infection

What are the possible outcomes of acquiring a pathogen? 

All the things that can happen AFTER acquire a pathogen/encounter with a pathogen

1. Immediate elimination of pathogen: washing one’s hands so well that it gets rid of the organism

   • Maybe know just touched pathogen, maybe you aren’t aware

     • But know as we go about day and touch things, likely to get pathogens on hands

   • Go wash hands

     • Whether knew you touched it or not

   • Nothing can happen after this because got rid of organism immediately

2. Colonization: microorganism acquired has attached at some bodysite and started to grow

   • Organism at some point in or on body attaches and begins to grow (colonizing)

     • Might occur at portal of entry

       • Place where microorganism got into or onto body

       • Sometimes portal of entry  is not good location or certain organisms and they might NOT be able to colonize there

         • If can’t get to another better site, won’t be able to stay and will die off

     • What are some examples of when portal of entry not ideal but they find a better site

       • Lots of pathogens get into our mouths

         • Mouths not good sites for many organisms to colonize

         • Mouth gives organisms access to go down into intestinal tracts

           • intestinal pathogens colonizing there now

         • Examples:

           • E.coli

           • Salmonella 

   • What else can occur after colonization?

     • Every time acquire a pathogen, these are all possible outcomes (but not w/ equal probability):

     • Organism becomes transient flora

       • Very temporary, passing

       • Organism stays growing in that body site for only a pretty short period of time

         • Defenses may have killed it off

         • Even though organism able to start colonization, the conditions may not have been good enough for organism to be able to maintain itself

         • In any case, it dies off

       • Time period is too short for disease to occur

     • Organism becomes resident flora

       • Organism can stay a lot longer

       • Staying at site it colonized, living there, multiplying

         • But defenses controlling it

       • NOT HARMING YOU

       • If it’s a significant pathogen, YOU ARE NOW A CARRIER

     • Organism causes OVERT infectious disease

       • Outward signs, symptoms, sick, have disease

       • It is obvious that you have the infection

     • Organism causes SUBCLINICAL infection

       • Means there's no OVERT sign or symptoms, but it is harming you

       • Organism causing SOME HARM but minor enough that don’t have symptoms, aren’t sick

       • Defenses doing a great job containing the organism and defending you against it

         • defenses could be controlling the organism sufficiently to the point that the organisms can’t make the individual sick

       • Depending on organism and how interact w/ body, some people can become IMMUNE to the disease

   • What are some factors that determine whether you will acquire a pathogen ?

     • In every situation in which we acquire a pathogen, what factor determines which outcome actually happens?

     • outcome = virulence + number + portal of entry + traumahost resistance

       • No one factor is more important than the others

       • Virulence: how pathogenic is the organism

         • How great is organism's ability to cause disease 

         • If acquire highly virulent organism, greater chance that organism will become disease

           • And vice versa

         • Covid is highly virulent pathogen

       • Number: literally means number of cells (or virus particles if virus) of microorganism that you acquire

         • Greater number acquire, the more likely the outcome may be disease

         • Absolutely correlated w/ virulence

         • Low virulence organism, needs some humongous number of cells/particles acquired before chance of getting disease

       • Portal of entry:

         • Genitals, eyes, ears, mouth, wounds, skin, etc.

         • Conditions of microorganisms vary at different body sites

           • Oxygen, pH, temperature, nutrients available, attachment sites, presence of various defenses

         • If those conditions are unsuitable for pathogen, then it’s not going to be able to remain there

       • Trauma: even microscopic destruction of cells

         • i.e. When you get a shot, splinter, etc , there’s trauma at that site

         • Any time there is ANY trauma in a place where bacteria growing, there is greater chance that bacteria will exist

       • Host resistance: this is inversely related to the possibility of infection

         • Stronger your defenses are less likely it will be that infection will result when encounter pathogen

         • Immune system is not only defense, also have:

           • White blood cells, proteins in bodily secretions and blood, normal flora

What determines if a particular organism/infectious disease will be communicable?

• NOT ALL INFECTIOUS DISEASES ARE COMMUNICABLE

1. Site of Colonization 

   • (where is the organism growing?) 

     • Is it in the throat, ear, liver? 

2. Portal of exit

   • Place where organism can get OUT of the BODY

   • Examples of portal of entries would also serve as portal of exit

   • Example of when the portal of entry will not have a portal of exit

     • Internal organs (except for stomach or intestine)

     • Bones

     • Brain

     • Heart 

     • Bloodstream

   • What is an example of a noncommunicable infection?

     • SBE (subacute bacterial endocarditis) 

       • Infection of the heart valves

       • One of main reasons not communicable

         • Because sitting in heart valves, unable to get out (no portal of exit)

3. Route of transmission

   • Way for organisms to get from one person to another

   • If an organism can get out of the body, there WILL ALWAYS BE SOME WAY TO GET TO ANOTHER PERSON

     • ALWAYS is a route of transmission

4. Ability of the organism to survive transmission

   • Microorganisms differ tremendously in how long can survive once outside of the body 

     • Some sensitive to temp changes, lack of moisture, etc

     • Others very hardy and could last for a long time

   • Usually going to determine HOW it has to be transmitted

   • What are some examples?

     • Neisseria gonorrheae

       • Depends on how much bodily secretion it is in

       • Cannot survive very long outside body on an object

         • BUT it does NOT DIE INSTANTLY

       • Usually requires DIRECT person to person transmission in order to get from one person to another

     • MRSA

     • Norovirus

       • Very hardy, can stay viable on surfaces as long as two weeks or longer

       • Gastrointestinal infection

       • MOST FAMOUS for causing outbreaks on cruise ships

         • Incidence has declined since they have been doing such extensive cleaning as a result of covid

5. Organism has to get to suitable portal of entry

   • Moving from one person to another is only beneficial to the organism if it enters a suitable portal of entry 

   • Portal of entry must have the required conditions needed by the pathogen to survive and colonize in that area

6. Susceptibility of the “aversion”

   • For those diseases we call communicable, that individual is susceptible

     • DOES NOT need to be compromised host

   • Special circumstance

     • There are some special examples of diseases that are considered communicable caused by opportunistic pathogens communicable among compromised hosts

       • Particular group of communicable diseases caused by opportunistic pathogens 

     • Pneumocystis

       • Parasite that causes terrible lung infection in highly compromised individuals

         • Transplant patients, AIDs patients, immunodeficiency diseases, immunosuppressive drugs 

History of Microbiology

• Microorganisms were the first cells and everything developed from them

• Evidence from ancient writings that diseases have existed for THOUSANDS and THOUSANDS OF YEARS

• Concept of microorganisms and infectious diseases were merely theorized for a long time because there was a lack of developed resources that could help prove said speculations

  • What people THOUGHT were the causes of these diseases being spread

    • Something like “vapors”

• Lucretius wrote about “seeds of disease” (55 BC)

  • There must be SOMETHING that is being transmitted from one person to another

• Cowpox

  • Similar to human disease smallpox

  • Women called milk maids (who milked the cows) didn’t seem to get smallpox when it was in the community

    • Seemed to be protected from having been around the cows with cowpox

  • First attempts at vaccination based upon this idea with cowpox

    • Take lesions from the cow and deliberately scratch material from the cows to person

    • Latin for cow is “vaca” 

• Leeuwenhoek (1679)

  • Hobby of making magnifying lenses (primitive microscopes)

    • Because curious about the things around him

    • Takes specimens like rain water, fly wings, scrapings from teeth

      • Things are MOVING in his drops of water

  • Animalcules 

    • Like little animals

    • Very detailed descriptions of these

  • Communicated this info to others

    • Sent all of this in letters to Royal Society in London

    • Letting others know about the existence of these microscopic things

  • His magnifying lenses only able to magnify 300x

    • Probably looking at protozoa and some large bacteria

  • NOTHING HAPPENS IN THE DISCOVERY OF MICROORGANISMS FOR ANOTHER 200 YEARS 

    • Call Leeuwenhoek the “father of microbiology”

What is spontaneous generation?

• Spontaneous generation

  • Theory (goes back to aristotle) that says that living things could just spontaneously come into existence from decaying organic matter (like rotting garbage)

    • A living organism doesn’t have to come from another living organism, could just come into existence

• What is another example of spontaneous generation

  • If in your kitchen/dorm/home, you left out a plate of meat, etc., a day or two later, discover that it's full of maggots

    • When people believed in spontaneous generation, they thought that that was how these maggots came into existence

  • Experiment that disproved spontaneous generation for VISIBLE organisms

    • Did experiment where used meat and let it sit there

      • Maggots come from flies

      • Eggs develop into larvae which we called maggots

• Why did they believe this?

  • People would make broth (tasty, odorless, and normal-looking soup)

  • However, when left outside by itself, it would become cloudy, smelled terribly, and more = putrefying

  • When inspected under a microscope, they saw billions of microorganisms 

  • MANY CLAIMED THAT THE MICROORGANISMS SPONTANEOUSLY DEVELOPED FROM THE ORGANIC MATTER

• Where did those microorganisms come from?

  • Some say they spontaneously generated from organic matter in the broth

• What was done to disprove spontaneous generation?

• Who is Louis Pasteur

  • Invented swan necked flasks

    • Made a broth in them and boiled it

    • End is open so oxygen can get in

    • Could sit maybe forever and aren't ever going to be organisms growing in it

    • Boiling argument could still exist

    • Show that flask can allow microorganisms to grow by letting them in

      • Could break it and let air in

      • Could tip flask and let broth go into neck and then tip back

  • Proved two things

    • No such thing as spontaneous generation (even for microorganisms)

    • There are microorganism in the air

  • Pasteur and the wine problem

    • Saw yeast in unspoiled wine

      • The yeast is what actually makes the wine

        • In right conditions, yeast take in sugar, and produce ethanol

    • In spoiled wine, saw bacteria

      • Turning the ethanol into acetic acid (vinegar)

    • How to prevent bacteria from spoiling it?

      • Heat the stuff at a much lower temp than boiling which will kill bacteria and not the yeast

  • Pasteurization: gentle heating designed to kill pathogens but does not sterilize

    • Milk  

    • Non Refrigerated milk products are pasteurized at higher temperature so sterilized until carton is opened

    • Kegs are not pasteurized, so they need to be kept cold

  • Pasteur invented autoclave

• What is the germ theory of disease

  • Idea that some human diseases are caused by microorganisms

• Who worked with the germ theory of disease in mind?

  • Joseph Lister (1860)

    • Surgeon who developed interest in “pus of surgery”

      • Something some patients developed after surgery, after compact fractures

      • The site got red and pussy and patient got feverish and sick and sometimes died

    • Hypothesized that microorganisms were entering the wound and putrefying the human tissues

      • Gets idea after reading about Pasteur’s work, putrefaction of the booths

        • Thought to self maybe microorganisms in air that fall into patient’s wound and putrefy the human tissue

    • What did he do to prevent this?

      • Introduces practice of antiseptic surgery

        • Anti = against

        • Septic = infection

        • First person to introduce any kind of practice to try to eliminate/cut down infections occurring in his patients 

        • Phenol sprayed in air around surgical table

          • Phenol is very toxic (even diluted) and going to kill all the organisms

  • Semmelweis 

    • Interested in childbed fever (puerperal sepsis). 

      • Illness developed in many women after giving birth in the early 1800s

      • Bacteria was evident in the blood of women who died while giving birth (bacteria was introduced to the women through the residents)

    • Semmelweis took blood from some of women and looked at it under microscope and saw bacteria

      • Proposed that those bacteria were CAUSING the disease

      • He decided that there were some observation he made in hospital

        • In the maternity hospital, there were always young doctors in training responsible for taking care of women in labor and delivery but ALSO responsible for performing autopsy

          • When these doctors were not in hospital, the incidence of disease went down

          • Women who stayed at home to have babies didn’t hardly ever get this disease

      • He had all the doctors in training who examined the women, wash their hands extensively between patients and between doing autopsies and going in for examinations of women

        • Kept detailed records

        • The incidence of the disease went DOWN

      • Perhaps it was caused by bacteria seen in microscope 

        • Women were getting the bacteria from the doctors in training who were going from autopsy area into the labor and delivery area

    • Semmelweis was first to suggest handwashing as way to prevent infection

    • This disease still exists today, but with a very low incidence

      • When it occurs today, it's always an ENDOGENOUS INFECTION

        • From bacteria in the vaginal flora that get into the uterus and bloodstream and cause the same illness

Who is Robert Koch?

• First person that carried out lab experiments to prove (through ANTHRAX) microorganisms cause certain diseases (1876)

• His theory was based on Henle (a student of Darwin)

• What is the importance of Koch’s Postulates?

  • First time that experiments were done to PROVE that a certain microorganism caused a certain disease

    • Proving the germ theory of disease

  • He read work from Henle

  • When a new infectious disease arises today, the way to prove that certain microorganism is the cause, you carry out Koch’s Postulates

• What are the four steps of Koch’s postulates?

1. Organism MUST be found in EVERY person with the disease

   • HOWEVER, “not found in people who don’t have the disease” excludes carriers which is incorrect 

     • They have the disease, they just don’t show symptoms

2. Isolate the organism in lab through pure culture 

3. Take organism and introduce it to a suitable laboratory animal (once in a while, done with humans)

   • Suitable:

     • Not all animals are susceptible to the same pathogens

     • May have to experiment with how animal is GIVEN to animal

   • They have to get the SAME disease

     • Trying to prove that this organism causes this disease

4. Isolate the organism again (out of animals) and get it in pure culture

• Isolate the organism again (out of animals) and get it in pure culture

  • Have to get it out of animals to prove it was really there

• NOT A HISTORIC THING, SOMETHING WE STILL USE TODAY

• Example of postulates

  • When determining that HIV is cause of AIDS, 

  • Couldn't’ find an animal species that got the same disease

  • Until proven, still some scientists who thought something else was the cause

Golden Age of Bacteriology

• 1875-1900s

• During this time that organisms discovered that cause a huge number of bacterial infectious diseases

• Up until this point, no one knows about VIRUSES

• What happened in 1892 that led to discovery of viruses?

  • Tobacco mosaic disease

    • When plants get this disease, the leaves get discolored in mosaic pattern and then die

    • Farmers are the ones in trouble

  • Questioned if a microorganism be the cause

    • Took a whole bunch of leaves from plants with disease

      • Put them in blender to make mush

    • Took the ground up material from infected plants and put it through a special filter

      • This filter (kind of like filter paper) is special because the PORES are TINY, TINY, TINY

        • NO bacteria, no protozoa, no fungi, and no algae can get through these pores

    • Took the sap and put it on new plants

      • The new plants got the disease

        • Means it CANNOT be bacteria, fungi, algae, or protozoa

        • Not a protein that came out of the plants

    • Started to realize there was a microorganism there that they had not known about before

      • It had to be EXTREMELY small in order to go through that filter

        • Called them ultrafilterable viruses

          • Virus to them was used to apply to anything that was visible and harmful

            • No idea what an actual virus was

  • Two reasons why not discovered before this time

1. So extremely small that they can’t be seen with (what we call) a light microscope (like one in our lab)

   • Can’t see something as small as virus

   • Wasn’t until electron microscope 

2. In 1800s, early microbiologists were growing cultures in primitive labs

• ALL VIRUSES ARE OBLIGATE INTRACELLULAR PARASITES

  • Obligate = have to be this way, no alternative

  • Intra = inside cells

  • Parasite = general term used to refer to these harmful organisms

• Bacteria in body are ON YOUR CELLS

• Viruses on body are INSIDE YOUR CELLS

How can viruses be cultured?

• Cell culture for viruses

  • Test tube/bottle/flask that has some kind of living cells in it

    • Patient specimen put into it

      • Viruses will go inside the cells and the cells will replicate the viruses

• When nurses have to collect specimens for viral cultures, it’s different than for bacterial cultures

• Norovirus

  • Example of virus that could remain in tact for almost two weeks or longer on surfaces

  • Different virus remain in tact and infectious for different periods of time when get outside the body on surface

Who discovered antibiotics?

• 1929 Fleming

  • Some of his petri dishes got contaminated with a mold (fungi)

    • The staph aureus seemed unable to grow where the mold was on plate

      • But could grow where mold wasn’t on the plate

      • Thought that the model was producing something that affected the staph aureus 

    • The particular mold that was on there was Penicillium

    • Set out to purify whatever substance it was producing that kept the staph from growing 

      • Substance became known as Penicillin

      • Wasn’t until mid-late 1940s that Penicillin was actually able to be used 

      • FIRST ANTIBIOTIC!!

• What is the big problem with antibiotics today?

  • Bacteria has developed a resistance to these antibiotics

What are the sources of microorganisms in the world?

• If you are a healthcare professional, you have to be concerned about infection control, prevention of transmission, how to protect yourself and others, etc. 

• Throughout whole life, in contact with microorganisms ALL THE TIME

• “we are a source of microorganisms in the world. so, what needs to be known if we’re interested in infection control?”

• 1. Humans

  • Can get “germs” (microorganisms) from other people

  • Not all of the pathogens that we are worried about getting come from other humans, but a lot do

  • Details need to know for humans

    • Site of colonization of that pathogen in the other human body

    • Portal of exit: how organism going to get out

    • Route of transmission

    • What would be a suitable portal of entry into you

  • Want to know how to block all of the above

    • How to protect yourself and your patient

      • Important in pathogen control

• 2. Animals

  • Details to know for animals

    • What pathogens really get from animals

      • There are only CERTAIN pathogens that we get from animals

        • Examples:

          • Rabies 

          • Salmonella 

          • Equine encephalitis (from horses)

    • Site of colonization of that pathogen in the animal

    • Portal of exit: how organism going to get out

    • Route of transmission

    • What would be a suitable portal of entry into you

  • Isn’t any pathogen that we get from animals that is present in ALL ANIMALS

    • There's only certain species of animals that could have that pathogenic organisms

  • Something we can get from cats

    • Toxoplasma gondii 

      • Opportunistic pathogen (affect compromised hosts)

      • Pregnant women should stay away from cats and cat litter 

        • If she gets it, and it gets to the fetus and infects them, it could cause severe brain damage

• 3. Insects & arachnids

  • Vectors: a living transmitter of microorganisms

    • Human, animals, insects, and arachnids would all be vectors by technical definition

    • But when most talk about vectors, talking solely about insects & arachnids

    • Different microorganisms have different vectors and different microorganisms live in different areas of that vector

  • Details need to know about vectors

    • What are the vectors

    • How does vector give it to us

    • How can we protect ourselves from vectors?

      • Protect self from vector physically

        • Long sleeves, long pants, nets over bed, etc.

      • Try to control the population of the vector

  • Two kinds of vectors

    • Biological vectors: insects/arachnid that has the microorganisms IN THEIR BODY

      • Living in them

      • Does not harm the vector

      • Examples of diseases from insect vectors: 

        • Malaria

        • Zekka 

        • West nile

      • Examples of diseases from arachnid vectors:

        • Spiders do not have pathogens in them that humans would get from them

        • Lyme disease

          • Ticks are the biological vectors

          • Get from tick biting you

        • Typhus 

          • (not typhoid fever)

          • Microorganisms that cause it are carried by lice

            • Lice have it in their intestinal tracts

          • Transmit to humans 

            • When the infected lice are on skin, transmit through their feces

            • The insect bites the skin, it gets irritated and the human inoculates it through scratching

    • Mechanical vectors: land on something that is contaminated and pick up the microorganisms on their FEET

      • Fly off and land someplace else (food, wounds, etc.)

      • All insects

      • All the mechanical vector does is TRANSPORT the microorganism on the outside of their body

• 4. Fomites

  • Fomite: An inanimate object from which we can acquire microorganisms

  • What are special fomites within a hospital setting?

  • Fomites vs. reservoir of infection

    • Reservoir of infection: can either be a living organism OR it can be an object which has sufficient moisture such that organisms are able to stay alive on it for some period of time

      • i.e. an ice machine or water fountain 

      • Has to be enough moisture for organism to be able to stay alive

      • Living things are reservoirs, we are reservoirs

    • Fomite examples - desktops, tables, etc.

      • Dry, no moisture

      • Not a reservoir

What are the Modes (routes) of Transmission

• Direct contact

  • Going from one person to another

    • EITHER by respiratory secretions going out into the air, touching, sexual contact

  • PERSON TO PERSON

• Indirect contact

  • Object that gets contaminated by one person w/ the pathogen

    • Then another person comes along and picks up the pathogen from the object

      • Object examples:

        • Door handle

        • Cup, water bottle

        • Sink faucet

        • Sheets

      • One way people acquire the dorm disease

• Insects and Arachnids

• Direct inoculation

  • Some kind of situation in which the organism is put through the skin or—in a terrible case—into a person’s bloodstream

    • Can get tetanus from a thorn pick

    • If given an injection and skin not properly disinfected, organisms are going to go through

    • If given IV fluids or blood transmission that is contaminated by bacteria, it is going directly into blood vessels

• Common vehicle

  • A common vehicle is usually food or water source that is contaminated w/ a pathogen

    • Some number of people get that pathogen by INGESTION

      • Number of people doesn't have to be large but it could be

  • One of the BEST examples

    • City of Milwaukee had a problem with Cryptosporidium

      • Parasite found in water supply, but usually in small numbers that do no harm

      • In Milwaukee, the entire city’s water supply had high numbers of  Cryptosporidium

        • Interesting that what happened in the city is EXACTLY what will happen when people get exposed to pathogen like that

          • Many didn’t ge stick at all

          • Some got mild illness

          • Some (mostly compromised hosts) got serious illness and were hospitalized

          • Some died

What are types of symbiotic relationships?

• Symbiosis: two living organisms existing together

  • Sometimes having impact on each other BUT NOT ALWAYS

• 1. Mutualism

  • MUTUALLY benefiting

  • Relationships btwn microorganisms in body in which BOTH the microorganisms and us are benefiting

  • Every microorganism living in/on body is benefited

    • In mutualism, WE are also benefiting 

  • Examples:

    • Bacteria in intestinal tract ASSIST in digestion

    • Vitamin K

      • Needed for blood clotting mechanism

      • Bacteria in intestinal tract produce this necessary vitamin K

    • All of normal flora on mucous membranes are all part of defense against other organisms

      • New organism comes in and has to come with normal flora for nutrients, attachment sites

      • Not foolproof – still get infections

• 2. Commensalism

  • Relationship where one organism is benefitting while the other is in a neutral state, merely existing.  

    • Organisms that live on our skin benefit from us through the environment and nutrients we provide, but they are not doing anything for us at all

  • Organisms on skin aren’t really doing anything for you

    • They're just there

    • The human is not benefitted

• 3. Parasitism 

  • One of living organisms is essentially living off the other and CAUSING HARM

  • Exact same thing as giving definition of infectious disease

    • Parasitic relationship is the same as having an infectious disease

What is normal flora in relation to symbiotic relationships?

• Normal flora are all the bacteria, protozoa, fungi that inhabit our bodies living in mutualistic and commensalistic relationships

  • SOME of which may become parasitic if 

    • They get to body site where don’t belong

OR

• The normal balance of organisms is disrupted

OR

• Balance between normal defenses and organisms is disrupted

• E.coli in intestinal tract

  • Common example of organism that causes infection when gets to body site where doesn’t belong

  • Especially causes harm in urinary tract

    • Urinary tract infection

• Staph. aureus

  • Lots of people 

What is epidemiology?

• The incidence/occurrence of infectious disease

  • They also study the causes of diseases, specifically infectious diseases in microbiology

• 1. Endemic

  • Always present in specific geographical area 

    • Means there is ALWAYS going to be some cases of the disease

  • Pathogen LIVES there

  • People who live in area may possible become immune

    • IN SOME CASES; not true for all pathogens and people

    • People who travel there risk becoming exposed to pathogen and getting its disease

  • Examples:

    • Malaria 

    • In Mexico – a kind of E.coli (not the type in intestinal tract)

      • Located in the water

      • Things cannot do 

        • Brush teeth

        • Eat raw fruits

        • Drinks with ICE

• 2. Epidemic

  • Outbreak of MORE THAN THE USUAL number of cases of a particular communicable disease

    • Doesn’t have to be huge 

      • Could be a mini epidemic

  • Almost YEARLY there is an influenza epidemic in our country

    • Practices taken to prevent covid minimized the number of influenza cases temporarily

• 3. Pandemic

  • Epidemic has spread so far that it is essentially worldwide

  • Examples:

    • Covid

    • 1918 influenza (spanish flu)

      • Worst thing that had ever been seen

      • The particular influenza virus had some unique abilities

        • Typically influenza impact young and old

        • This pandemic struck hardest for people in OUR age group

• 4. Sporadic 

  • Disease that occurs sporadically; meaning there are VERY FEW cases occurring in a given year

    • Unrelated to each other

    • Not being transmitted person to person

  • Example:

    • Plague

Other important terms

• Morbidity rate

  • Expression of HOW MANY CASES of disease are occurring

• Mortality rate

  • Expression of HOW MANY DEATHS have occurred from the disease

How is infection control in the hospital setting?

• All of this collectively means lots of problems with nosocomial infections

• We have more susceptible hosts to worry about IN the hospital than in the community OUTSIDE

  • Not every patient in hospital is compromised host but many are

• Lot of SOURCES of microorganisms

  • Patients themselves

  • All the people who work in the hospital

  • All the visitors

  • Impossible to eliminate ALL sources

• MANY different routes of transmission

• Hospitals are accredited by specific agencies

  • In order to maintain accreditation, must do a lot of things that are related to infection control

    • Education of ALL PERSONNEL in the hospital

      • Annual trainings 

      • Educated about infection control

    • Infection control department and infection control committee

• What are the specifics of an infection control department and committee?

  • Nurses (and staff members) play the biggest role in overseeing the monitoring of infections. 

  • The committee is composed of EVERY MEMBER IN EACH SECTION OF THE HOSPITAL (cleaning, nurses, kitchen staff, etc.)

    • This is because all members of a hospital must be educated on infection control as they are all responsible for organism transmission

    • It is everyone’s responsibility to be educated in infection control, regardless of whether they have direct patient contact or not

  • The infection control department and the overseer is responsible for looking over the records of all infections diagnosed in the hospital

    • They must see if any are nosocomial so they may think about how the infection came about (to see if there was a breach in technique and avoidable)

    • If nosocomial, they must determine if it is an isolated patient that needs to be looked at or if it is a situation that can lead to a small outbreak

      • Example

        • Small outbreaks of staph infections within newborn nurseries that are usually traced to a staff member that was a carrier and didn’t follow aseptic technique

        • (extreme example) patient that was transferred to a nearby hospital with a drug resistant organism infecting her

          • Many caught the infection and thus led to the construction of walls which did not prevent the airborne transmissions. 

          • It later overpowered the sinks, which led to the disinfection of the plumbing and the calling it an outbreak. 

        • MDR

          • Infection causing respiratory infections

          • Ultimately found out it was in the sink drains

          • Had to go through whole process of disinfecting

• Certain nosocomial infections are restricted in payments by insurance companies

  • Deemed that these should not occur, medicare, medicaid and other insurance companies will not pay the hospital 

    • Ensures these do not occur 

• Hospital can lose its accreditation if doesn't do what it needs to do to prevent infection

• What is the purpose of isolation?

  • Prevent the transmission of organisms 

    • For most types – transmission from one patient to somebody else

    • In some cases – prevent transmission to a specific compromised host

  • Patient only needs to be in isolation for as long as the organism is COMMUNICABLE

    • Example: TB

      • After a few weeks of treatment, tb patient no longer expelling the organism and so don’t need to be in isolation any more

  • Length of time in isolation depends on site of colonization, route of transmission, and portal of exit

  • What are the old terms for the types of isolation?

    • 1. Respiratory  

      • Organisms that are passed in the air

      • Require masks

        • Sometimes gowns

    • 2. Enteric 

      • Have pathogen within the intestinal tract

    • 3. Wound and skin

      • Observed when a patient has a skin infection (surgical incision)

      • If person had infected wound, if it could be covered w/ bandage and no secretions/pus ooze through the bandage then no isolation needed

      • Need isolation if infection oozes through and given an occlusive dressing

    • 4. Strict 

      • Organisms that have MULTIPLE portals of exit and MULTIPLE routes of transmission

        • Multiple ways to pass from one way to another

    • 5. Reverse (protective)

      • Patients who are COMPROMISED and needed to be highly protected from ALL our organisms

      • Masks, gowns, gloves, caps, everything

      • Example

        • Burn patients

        • Certain patients who are immunosuppressed 

  • What are the new terms for the types of isolation?

    • 1. Droplet precautions

      • Infections that are transmitted in LARGE RESPIRATORY PARTICLES that a person expels

      • Similar to AIRBORNE PRECAUTIONS but are distinguished by the SIZE of the respiratory particles excreted from the person

        • Has to do with how far that organism will spread from a person

      • Example

        • Influenza 

    • 2. Airborne precautions

      • Infections in which the organisms are expelled in SMALLER RESPIRATORY PARTICLES 

      • Some of these airborne ones used to be in the strict category

      • Examples

        • Tuberculosis

        • Chicken pox

    • 3. Contact isolation/precautions

      • Could acquire the organisms either by touching the patient directly or certain of their body fluids

      • Examples

        • MDR (Mutli-Drug Resistant organisms)

        • C-diff

        • MRSA

        • VRE (Vancomycin Resistant Enterococcus)

    • 4. Reverse/protective

• Universal precautions vs. standard precautions 

  • Standard is the newer term, universal was older term

  • Universal precautions

    • First came up because of HIV

      • Relates to what is known as bloodborne pathogens

    • If had patient known to have HIV, big sign posted on door that might say “HIV positive”, “universal precautions”

      • Everything sent to lab has fluorescent label 

    • Problem with this

      • Loss of confidentiality 

      • Even if patient doesn’t have bloodborne pathogen, should still take the same precautions

        • You don't know who has HIV or Hepatitis or other blood borne pathogen

        • THEREFORE, have to approach ALL people with the same precautions 

  • Changed to standard precautions

    • These are the precautions you should take for EVERY SINGLE PERSON

      • i.e: occurs in the playing field also, where the trainer puts on gloves to take care of a bleeding athlete to clean the wound

• Opportunistic pathogen taking advantage of compromised host

  • Taking advantage of the opportunity 

• IMMUNE SYSTEM IS NOT THE ONLY DEFENSES OF AN INDIVIDUAL

• Resident flora – could include pathogens can be a carrier for

• Subclinical infections

  • Pathogen is causing SOME HARM in body but so minor that don’t have symptoms; not sick

  • Carrier is NOT BEING HARMED at all by microorganisms

• Broad spectrum antibiotics kill SOME of normal flora

  • Our NORMAL FLORA are part of DEFENSE against microorganisms

    • If we disrupt the normal flora, messing with defense

      • Makes us compromised

Why are microorganisms considered diverse?

• 5 groups of microorganisms: bacteria, viruses, some fungi, some algae, and protozoa

  • Viruses special because not living, not cells, completely different from all other microorganisms

• Each group is entirely different from each other as they have very different characteristics

• Microorganisms live in very diverse environments on this earth

  • There are some really hot areas on earth, some really cold areas on earth, some very acidic, some very basic, some really high salt environments

    • EVERY ONE of these environments has microorganisms in them

      • Your cells could not possibly live or tolerate those extremes, nor could most other microorganisms

  • Each one of those environments have SPECIFIC microorganism that exist in it that have evolved mechanisms to be able to exist there

    • **Organisms CANNOT be taken from their environment and be placed into another

• Diverse array of nutrient sources that different bacteria are able to use

  • Examples

    • Bacteria that can degrade oil spills

    • Bacteria that can degrade pesticides in soil

What is the classification of microorganisms?

• At first only considered to be TWO KINGDOMS of living organisms

  • There were extremely simplistic criteria for what would put a living organism into one or the other

    • Plants

      • Living organisms that were photosynthetic

      • Said to be NOT MOTILE (can’t move)

    • Animals 

      • Living organisms that were not photosynthetic

      • Said to be MOTILE

  • What was the problem with overly simplistic classifications?

    • There are bacteria that are photosynthetic AND motile

    • The living world is not that simple

• Who was Haeckel? 

  • 1866, he suggested the creation of a third kingdom – proposed the name protista 

    • All unicellular organisms or some with just a few cells

      • Wanted to put into that kingdom all microorganisms

    • Therefore, three kingdoms would be: plants, animals, protista

  • What is the issue with Haeckel’s idea?

    • Bacteria are nothing like fungi, fungi are nothing like algae, none like protozoa

      • Became clear that only three kingdoms was not going to work

• Over time (mid 1900s), 5 kingdoms

1. Animals

2. Plants

3. Monera (bacteria only)

   • Now known as prokaryote

   • No longer used today

4. Fungi

5. Protista 

   • Only included microscopic algae and protozoa

What was discovered once the electron microscope came into use?

• This has nothing to do with kingdoms and classification. 

• Biologists used an electron microscope to study cells and their structure

• ALL CELLS OF LIVING ORGANISMS FIT INTO ONE OF TWO GROUPS

  • Prokaryotic: “pro” = “primitive” nucleus

    • No defined nucleus 

    • Do have DNA but not contained in a membrane bound nucleus

    • Bacteria are the ONLY CELLS that are prokaryotic

    • Mucocomplex

      • Very complex

      • In cell wall of bacteria

    • Ribosomes – 70s

    • Bacteria DO NOT have mitochondria

  • Eukaryotic: “eu” = “true” nucleus

    • Defined nucleus

    • Membrane bound nucleus

    • Every other living cell is eukaryotic

    • Ribosomes – 80s 

    • Contains mitochondria (energy production)

Why is this important in infectious diseases and treatment?

• Selective Toxicity: Ability or characteristic of something to be harmful or toxic to specific things but not others

  • Only harms certain things

• What does selective toxicity have to do with antibiotics?

  • Antibiotics: drugs or chemicals that kill or inhibit the multiplication of bacteria

    • If want to have antibiotics that can be given to people for treatment, that have to have selective toxicity

      • Antibiotic has to HARM the bacterial cells BUT NOT HARM your human cells

      • Example:

        • Could kill bacteria in intestinal tract by having you drink bleach

          • These don’t have selective toxicity because will kill your cells as well as the microorganisms

    • Work by interfering with or disrupting a vital structure or process (very general statement)

  • How could antibiotics harm bacteria cells but not yours?

    • Look at differences between the two cell types

      • Want antibiotic to act on something in prokaryotic cells that is not in eukaryotic cells

    • Chemicals used for prospective antibiotics must be able to harm bacterial cells without harming human cells

      • A non-selectively toxic chemical is sulfuric acid, which will kill bacterial cells but will also kill human cells

    • What is an example of antibiotics harming bacterial cells but not your cells?

      • Penicillin 

        • Acts on the mucocomplex of bacterial cells

        • Bactericidal: “cidal” = kill

          • Penicillin KILLS bacteria cells because of how it acts on mucocomplex

          • Help defenses to put an end to the bacteria (no better or worse than bacteriostatic)

      • Erythromycin

        • Interferes with bacterial ribosomes

          • Prokaryotic ribosomes are different than eukaryotic ribosomes

          • Bacteria cannot live if cannot make proteins

        • Bacteriostatic: Inhibits the multiplication of bacteria

          • Help defenses to put an end to the bacteria

          • (no better or worse than bactericidal)

    • What about allergies?

      • *Has nothing to do with how interacts with bacterial cells

      • The way the antibiotic works on the bacterial cells is completely unrelated to the allergy

Why harder to find drugs that could be used to treat fungal and protozoan infections

• Because those cells eukaryotic (like OUR body cells)

  • They are SIMILAR not IDENTICAL

    • Differences between fungi and our cells AND protozoa and our cells

• What are the hardest kinds of drugs to find?

  • Selectively toxic antiviral drugs 

    • Viruses are INSIDE your cells when they are infecting you

    • Your cells (like your ribosomes) are replicating the virus

      • Difficult to find drug/s that could do something to interfere with viral replication that wouldn’t also hurt your cells

What is some general info to know about bacteria?

• They are considered the smallest living organisms capable of existence

  • If with the necessary nutrients and conditions needed for growth, most will: 

    • Take in nutrients

    • Make energy

    • Make the molecules needed to make new cells

    • Be able to live on their own

      • Independent existence

• MOST are unicellular

  • Some live in a community of very few cells

    • Don’t really considered to be multicellular

How is bacteria measured?

• Measured in units called MICRONS

  • 1 micron = 1/25,000 of an inch

  • Average size of a bacterial cell is 1 micron in diameter

    • They can vary from less than 1 micron (half a micron) to 14 microns

• How many times magnified when looking at a gram stain through a microscope?

  • Bacterial cells are magnified 1,000 times

What are the shapes of bacteria?

• Three basic shapes

  • Coccus, Cocci

    • Round shaped

    • Imperfect – some are elongated

  • Bacillus, Bacilli

    • Rod-shaped

    • Little bit longer than they are wide

  • Coccobacilli

    • Miniscule, rod-shaped cells that are short

    • Tiny, tiny, tiny

• More unique shapes

  • Spirilla 

    • Comma

    • Seagull

    • Corkscrew 

  • Pleomorphic: “pleo” = many AND “morphic” = shape(s)

    • Looks like there’s more than one organism present

    • Example:

      • Microorganism that causes meningitis

What are the basic arrangements of bacterial cells?

• Some bacteria have characteristic arrangement 

  • All has to do with how cells divide or reproduce 

• Chains

• Grape-like clusters

• Sometimes in pairs

  • Organism splits, becomes two, and they remain in similar positions for a bit

What is asexual binary fission?

• Asexual binary fission: process by which bacterial cells reproduce

  • NO SEXES or gender in bacteria

  • Binary fission means bacterial cell that is growing and multiplying has to produce all the molecules necessary to make a new cell

    • Then split into two equal daughter cells

What is generation/doubling time?

• Generation (doubling) time: the time it takes for the total number of bacterial cells in the culture to double in number

  • All bacteria have a genetically programmed RATE at which they multiply

    • Study rate of multiplication in the lab (can’t actually say exactly what’s happening in the body)

  • Example of the rate at which bacteria multiplies

    • 1x10⁵ cells become 2x10⁵ cells

    • E.coli has a doubling time of 15 to 20 minutes

    • Tuberculosis has a doubling time of 24 hours

• What is the relevance of knowing the generation time of bacteria?

  • Urine cultures: when properly done – determine the number of bacteria cells there are per milliliter of urine to properly diagnose UTIs

  • What is one example?

    • E.coli 

      • Low number of cells is normal

        • Considered an infection if at a certain high number

      • Bacteria thrive in urine specimens (considered a culture media for them)

      • If a urine sample is not immediately observed, the E.coli will double every 20 minutes 

      • The sample, when cultured, will then reveal a high number of E.coli cells

        • This prompts a false infection diagnosis

    • How to prevent multiplication of the bacteria? 

      • Colder temperatures slow down multiplication

      • Preservative fluid: keeps down multiplication for about 2 hours

        • If urine specimen culture put into tube from urine culture kit, it has preservative fluid

  • What is another very different example? 

    • Tuberculosis

      • Slower generation time of about 24 hours

      • Could take 4-8 weeks before colonies become visible because bacteria growing so slowly

        • Cannot risk this amount of time for results

          • If individual with overt symptoms and history of possible exposure, going to be put in isolation and on treatment

      • When diagnosing, doctors will look at history, symptoms, chest x-ray information, and acid fast stains

    • What are two other methods developed? 

      • Molecular test: looks for the genes of the bacteria

        • Takes some hours, is expensive, takes certain equipment, not practical

      • Special culture technique: Inoculate specimen into, let grow for couple of days, then do molecular technique looking for organism

        • Done in larger lab that specimen sent to (not necessarily completed in hospital itself)

        • Have evidence of TB within a week

          • If not proven to be positive, it is incubated longer

    • Skin test does not diagnose Tuberculosis

      • Only detecting the bacteria in you

      • Issue with skin test

        • Once get TB organisms in lungs, they stay alive for years and years

          • If anything happens to make you compromised, these organisms can become reactivated

        • Drugs that make you immunocompromised 

        • Some people get vaccinated for TB

          • These people can never get skin test because then they will be positive forever

What is the importance of knowing the gram reaction, morphology, and arrangement of a patient’s organism?

• It gives the doctor and IDEA of

  • What the organism is

    • Even though not giving the exact name

  • What antibiotics to start using to treat the patient

What is the capsule?

• Exterior to the cell wall is a slime layer (thin coating of protein that surrounds the cell) and a CAPSULE

  • Capsule: coating of polysaccharide that surrounds the cell

    • Much thicker than slime layers

    • Important in pathogenicity

    • Only some bacteria have a capsule

• What is the most important function of the capsule?

  • When a bacterium infects us/growing in body, in early times of the infection, the capsule partially protects the bacterial cell from phagocytosis

    • Phagocytosis: Ingestion and killing of microorganisms by certain WBCs 

      • It is a good natural defense mechanism in our body

    • Giving bacterial cells a bit of an advantage early in the infection

• What is an example of a pathogen that has a capsule?

  • Streptococcus pneumoniae

    • Not a pathogen unless it has a capsule

      • If grew in lab under conditions in which it has no capsule, it is NOT A CAPSULE

    • Has to have capsule to get established in body and cause its infection

      • Unusual for capsule to be CRUCIAL

        • Not the case for all other pathogens

          • Dorm disease

• Is the capsule beneficial to us in any way?

  • We make antibodies to the capsule

    • Capsule benefits us too because it helps makes antibodies

      • These antibodies help us to eradicate the organism

  • Several vaccines are made of capsule material to help us make antibodies to the infection

What is the cell wall and its properties?

• Almost all bacteria have cell walls, but animals do not have cell walls

  • Originally, bacteria were classified as plants because plants were only thought to have cell walls

  • This makes our cells different from bacterial cells because we don’t have cell walls

• Bacterial cell has its shape because it is the shape of its cell wall

  • e.g. rod-shaped bacterial cells have rod-shaped cell walls

• What are the important functions of the cell wall?

  • 1. Flagellum – help bacteria to MOVE

    • Cannot work without the cell wall being present

  • 2. Responsible for Gram reaction of bacterial cell

    • Gram positive or gram negative happens because of the cell wall’s composition

      • Gram positive is sensitive to certain antibiotics because of the composition of its cell wall that differs from that of gram negative

• What is important to know regarding the mucocomplex of cell wall? 

  • Penicillin – disrupts mucocomplex of cell wall

    • In Gram positive bacterium since wall is mostly mucocomplex, if mess it up there is nothing else to protect cell membrane against osmotic pressure

      • Cell will rupture

      • NOT ALL are sensitive

    • Gram negative may disrupt mucocomplex, but it will not really hurt them

      • They have so much else making up the cell wall

  • Lysozyme: enzyme that your body produces and serves as part of your defense against bacteria

    • In all body fluids – saliva, mucus, urine, tears

    • Defense because lysozyme breaks apart the mucocomplex molecules

    • Gram positive cells are sensitive; it will affect these cells

• What is LPS (lipopolysaccharide) 

  • Breakdown of LPS

    • “lipo” refers to chemical substances like fats or lipids

    • “polysaccharide” refers to sugars

  • AKA endotoxin – “endo” = within; “toxin” = harmful to us

    • A harmful substance found within the bacterial cell called LIPID A (part of its structure)

    • Lipid A free in bloodstream interacts w/ proteins in blood

      • Triggers whole series of very bad physiological events

        • Blood clotting, affects cardiac output, affects kidney output, affects all smooth muscle

        • Said to be in “state of shock”

          • There are 4 or 5 different types of shock, including shock from blood loss

    • Can lead to endotoxic/gram negative shock (interchangeable)

      • Can also be called septic shock (but we don’t like this term bc not specific enough)

      • Hard to treat all the things going on at once

        • Leads to high fatality rate 

      • How does endotoxic/gram negative shock occur?

        • Starts w/ infection in body due to a gram negative organism

        • Infection gets bad and bacteria gets into bloodstream

          • Releasing LPS into the bloodstream

• 3. Cell wall prevents bacterial cell from bursting/rupturing

  • Absolutely essential to life of the bacterial cell

    • If take away cell wall, then the cell would burst

  • Inside the cell, there is a high concentration of molecules as compared to outside the bacterial cell

    • Outside of the cell, the concentration of molecules in the normal environment is much lower

    • There is REAL OSMOTIC PRESSURE present

      • Real force being exerted inside the cell

      • Osmotic pressure is pushing against the cell membrane 

  • Cell membrane, which is not a strong structure, would not be able to withstand the force without a cell wall

What is the cell membrane?

• Important structure that is inward of the cell wall

• No matter the cell, all have membranes

• controls everything that goes in and out of a cell

  • Nutrients go in through the cell membrane, end products bacteria don’t want go out through cell membrane

• Has a part known as the mesosome

  • Where the cell membrane folds onto itself

  • Was thought to be a place where energy production occurred in the bacterial cell

What is flagella?

• Flagella described as a long and wavy appendage

• If a cell has flagella all around, then it is extremely motile

• Only some bacteria have a flagella which allows them to move 

  • Some bacteria are not motile at all

  • Some bacteria have other structures/features that make them motile

• Bacteria use their flagellum to:

  • Move toward good thing

  • Move away from bad things like toxins 

• Number and arrangement determined by the GENES of its species

  • For each genus that has flagella, every cell has the same number and arrangement of flagella

What is pilus/pili (fimbriae)?

• Short, wavy appendages that come off the main body of the cell

• Located all over the cell

• What is important about them?

  • One function is that pili help the bacterial cell attach to surfaces

    • If bacteria in body – surfaces attaching to are our epithelial cells (like on mucous membranes)

    • If bacteria that live in pond or lake – surfaces attaching to may be like a rock

  • If they cannot attach, they will not be able to colonize

    • Bacterial cell will be swept away and will lose its chance to colonize

• NOT ALL BACTERIA HAVE PILI

  • Some bacteria have them, some don’t

  • Bacteria that do not have pili have other things that will help them attach to cells

• What is the F Pilus

  • (F = “fertility”)

    • HAS NOTHING TO DO WITH FERTILITY/REPRODUCTION

  • F+ = bacterial cell that DOES have F Pilus

  • F– =  bacterial cell that DOES NOT have F Pilus

  • What are its properties? 

    • Looks completely different than other pili

    • Long tubular structure made of protein 

    • Only f plus cells can make f pilus

    • The “F” stands for fertility

      • Has nothing to do with fertility/reproduction

  • What does the F pilus do? 

    • Allows the cell to attach to another bacterial cell known as an f minus cell

      • “f minus” means that it is unable to make an f pilus

    • The F+ cell’s pilus must have a means of recognizing the F– cell to attach which probably includes surface charge, etc. 

  • What is the importance of the F pilus? 

    • Has to do with DNA (plasmid)

What is important to know about bacterial DNA

• Bacteria has 1 chromosome

  • Circular in shaper

  • Its chromosome is humongous compared to bacterial cell itself

    • To fit the BIG chromosome into the SMALL bacterial cell, chromosome is very very tightly coiled

• What is a plasmid?

  • Completely separate from chromosome

  • Very small compared to chromosome

  • Made of DNA so there are genes on plasmids

    • These genes are not essential to the life of bacterial cell

  • Can have multiple types and multiple copies of each type

  • Special type of plasmid

    • R Factor (R = resistant)

      • Makes bacterial cell resistant to several antibiotics 

Thursday, October 20, 2022

What is an R Factor?

• R = “resistance”

  • These plasmids have genes that will make the bacterial cell resistant to several antibiotics

  • How R Factor could make bacterial cell become resistant to an antibiotic? 

(penicillin example)

• Plasmid may have a gene that allows the cell to produce the enzyme penicillinase

  • Penicillinase: “-ase” means“breaks down”. 

• When that bacterial cell is in the presence of penicillin, the enzyme will break down penicillin molecules

  • Makes the antibiotic ineffective (resistant) against the cell

What is conjugation?

• Conjugation: a process that involves the F+ bacterial cell attaching to an F- bacterial cell

  • Only goes in one direction → an F- cell provides nothing to the F+ cell

    • Two F+ cells cannot conjugate

  • Bacterial cell can only conjugate with bacterial cell it is related to

    • Cannot pass R factor to ALL bacteria

• How does conjugation occur?

  • The F+ cell will make a copy of its plasmid to give to the F- cell

    • This process makes the F- cell equally resistant to the several antibiotics that the F+ cell has the genes for 

  • The F- cell then conjugates with another F- cell and that F- cell gives the plasmid to another and so on

    • Why is conjugation a bad thing?

      • Have millions of cells that are all conjugating and actively reproducing

        • Number of resistant cells is increasing rapidly

• What is a “hyper-exaggerated” example involving conjugation?

  • Assume someone has intestinal infection and the doctor gives them antibiotic penicillin to treat it (wouldn’t actually get penicillin for intestinal infection)

  • At the outset, few of the cells have the plasmid and are resistant to penicillin

  • Sensitive cells are being killed by penicillin early in the infection

  • Resistant cells have been conjugating and replicating within the intestinal tract during that time 

    • Thus, the R factor has passed onto other cells while being multiplied

    • This only leaves cells that are resistant to penicillin left

      • Process called selecting for resistant cells

What is selecting for resistant cells?

• Selecting for resistant cells: sensitive cells have be killed off by the antibiotic and all that is left are cells with the plasmid that are resistant

• Eventually, notice that person not getting over infection

• Cultures and sensitivity tests will be done

  • Patient will need new antibiotics to fight the infection

• What has contributed to the development of antibiotic resistance? 

  • Use of human antibiotics in cattle feed

    • Cattle are given antibiotics to prevent them from obtaining certain illnesses and make them grow faster. 

    • Antibiotics contribute to the development of bacterial cells in the cattle making them resistant to antibiotics

    • Antibiotics do not just stay in the cattle

      • They would enter the environment, meat, and humans

      • Spreading antibiotic resistant bacterial cells 

  • Overuse of antibiotics in people

    • When use antibiotics too much, actually instigating some bacterial cells to become resistant to them either through R factors or other means

      • Fostering the development of antibiotic resistant bacteria

      • This is a problem bc there are some bacteria that are resistant to all or almost all antibiotics

    • What are some of the causes for this problem?

      • Physicians tend to use broad spectrum 

        • Should treat with narrow spectrum because then exposing bacteria with smaller range of antibiotics

      • Physicians give patients antibiotics to treat respiratory, viral infections 

        • Antibiotics do not work for viruses

      • Many people do not take their antibiotic prescription the way they are meant to (not on time or stop use prior to schedule)

      • People tend to use leftover antibiotics/share antibiotics 

        • e.g. the taking of a roommate's antibiotics 

      • Pediatricians are often pressured and pestered to prescribe antibiotics by crying parents who just want their child to get better

        • Doctors must now sign up for programs where they make money by limiting the amount of antibiotic prescriptions they make

        • Parents do not know that parents cannot harm viruses, which is what their child might have

What is a transposon?

• Transposons: “jumping genes”

  • Piece of DNA that makes a bacterial cell resistant to ONE antibiotic

  • When bacterial cell has transposon, a COPY can be made and sent to another bacterial cell

    • Now have two cells that are resistant

      • Continues to occur and multiply

• Bacteria involved do not have to be related to one another

• NOT A PLASMID, just a piece of DNA that can be found in the chromosome and then be shot out to another cell

• Not necessary to bacterial cell’s life force; not life essential

What are spores and when do they occur?

• Created when conditions are poor for the growth of bacteria

• Forms inside and creates a cell wall

• Not multiplying, metabolizing, growing, etc.

  • It’s just there

• What is so important about spores?

  • Because of the very thick wall, they are extremely heat resistant (temp) and very resistant to chemical disinfectants

    • Temperatures that might be used to kill regular bacteria do not work for spores

      • Can only be killed using the autoclave temperatures (252 Fahrenheit/121 Centigrade)

    • Chemical use (even around the hospital) do not kill spores

      • There are disinfectants that are sporicidal 

Thursday Lab, October 6, 2022 – UTI’s

• Pages that relate to urine cultures, urinalysis – page 35-38

What are UTI’s?

• UTI’s are extremely common type of infection

  • True in hospital patients, nursing home patients, and in the community

• Urinary tract doesn’t have too many tracks so easy to look at

  • ALSO very clear cut what part should have microorganisms and what parts should NOT have microorganisms

• What does the urinary tract consist of? 

  • Two kidneys

  • Two ureters

  • One bladder

  • One urethra

  • The ONLY PART that should normally have the bacteria would be the most exterior part of the urethra (nearest to the outside/to the urethra meatus)

    • All the skin area around urethra meatus is loaded with bacteria

      • Lot of them are intestinal organisms

• What are two types of urinary tract infections 

  • Kidney infection: pyelonephritis  

    • Kidney infection is more serious because kidneys perform vital function for body

      • If infected, that infection is disrupting some of the function of the kidneys

      • If bacteria infecting kidney, lots of little blood vessels that the bacteria could get into bloodstream through

  • Bladder infection: cystitis 

    • EVERY bladder infection has the POTENTIAL of having the bacteria go up to one or both kidneys

      • This is the case for any average normal person who gets cystitis

      • No way to predict whether this will occur or not

    • Still an infection with symptoms

      • Some can get really sick with bladder infection

  • Urethra infection: urethritis

    • NOT considered a urinary tract infection

    • Considered urogenital 

• What is the difference between ascending vs. descending UTI’s?

  • Ascending: going up

    • Infections in which the bacteria go up through the urethra and get to the bladder

      • Maybe get as far as the kidneys

    • MOST COMMON urinary tract infections

  • Descending: going down

    • Infections in which the bacteria causing the infection are first in the kidneys and go down

    • How could bacteria get to the kidneys other than going up?

      • The bacteria was in the bloodstream and got deposited (dropped off) into the kidneys as blood flowed through them

        • How do bacteria get into the bloodstream?

          • When you have bacterial infection anywhere in body, there's ALWAYS a chance that the bacteria can get into the bloodstream

          • Bacteria in mouth get into bloodstream every time brush teeth and get dental work done

            • Defenses should kill them very quickly and nothing happens

          • Intestinal bacteria can get into bloodstream

            • Defenses should kill them very quickly and nothing happens

            • Evidence of this in elderly 

• For whom is it more common to get a UTI?

  • In almost all age groups, UTIs are more common in FEMALES

  • When is it common in males?

    • Little toddler boys (maybe 2-3)

    • Males over 50 

      • Over age of 50, many males experience an enlargement of prostate gland

        • Predisposes them to bladder infections

  • What are predispositions to UTI?

    • Predispositions: make something more likely to happen

      • For example: pregnancy

    • Why are females more predisposed? 

      • Many of bacteria are intestinal organisms like E.coli

        • Those are the exact organisms that cause MOST urinary tract infections

        • In females, the urethra meatus is surrounded by the very bacteria that if it gets in, it has the ability to cause UTI

          • The supply is right there

      • Female urethra is about 2 ½ times shorter than male

        • Far less distance for the bacteria to move through

        • In males – organisms that might get into the urethra have a longer distance to go and might not actually make it to the bladder before they get killed or flushed out 

What are urine cultures and how are they used to diagnose UTIs??

• Some doctors and microbiologists wanted to determine how to use urine culture to diagnose UTI

  • Had idea that urine was sterile

    • Thought that all they had to do was culture and if find bacteria then means that person has UTI

    • Proved to be untrue

• What is the difference between bacteriuria and significant bacteriuria? 

  • Bacteriuria 

    • Presence of bacteria in urine as detected in a culture

      • Learned this was wrong because EVERY ONE of these specimens grew bacteria whether individual healthy or not

        • All organisms around urethral opening

    • Everyone has bacteriuria

  • Significant bacteriuria 

    • Presence of bacteria in urine that IS indicative of infection

• How to determine the difference in the urine of uninfected people and infected people?

  • Very carefully collected urine specimens and culture them

  • Unifected

    • Mixtures of organisms

    • In “low” numbers

      • Numbers = the number of bacterial cells per mL of urine

  • Infected 

    • Only 1 or maybe 2 different bacteria (at the same time)

    • In “high” numbers

      • Numbers = the number of bacterial cells per mL of urine

        • Bacteria are multiplying at great extent in urinary tract

    • Almost never is a UTI caused by more than 2 organisms at the same time

      • Typically only happens in person with abnormality of urinary tract

• What is quantitative urine culturing?

  • When urine is culture, has to be done in way that lets you not only see how many different bacteria present but how many cells of bacteria per mL of urine

  • Example:

    • E.coli going to be in most female urine cultures

      • Also the MOST COMMON cause of UTIs

    • Only way can tell the difference btwn E.coli that is just near the meatus and one that is in urethra causing infection

      • When causes infection it will be in a high count

What is colony count?

• Colony count: number of bacterial cells per mL of urine

  • Not actually the number of colonies

  • Helps in determining if individual has an infection

• What is the meaning of colony counts?

  • ≤ 10,000 cell/mL

    • Uninfected or “normal”

    • Midstream urine culture will show mixture of organisms in LOW numbers

      • No way person has an infection

      • These are normal urethral and skin organisms

  • ≥ 100,000 cells/mL of urine as long as only 1 or two organisms present indicates infection

    • Infected 

      • Urine culture have growth of one organism or sometimes two together, but rarely is it due to more than two

        • More than two only happens in people with abnormalities of urinary tract

    • When organisms present, they are in HIGH numbers

  • 50,000 – 99,000 cells/mL of one or two organisms

    • **There are people with infections that get lower counts

    • These lower numbers probably mean infection as long as only one or two organisms

  • 11,000 – 49,000 cells/mL of one or two organisms

    • Unlikely that individual has an infection

    • Doctor should always look to see if patient has symptoms

    • Look at urinalysis results

• What is the first thing doctor should do if they suspect UTI?

  • Urinalysis: has parts that can suggest UTI but it cannot prove the way a culture can

  • Great aspect of urinalysis – parts give evidence of diseases that have nothing to do with infection

    • Broader application than culture

      • Example:

        • Can reveal if individual has glucose in urine as a result of diabetes

        • Kidney disorders (not infections)

  • Good because can be done quickly

• What is the importance of the 1 or 2 organisms?

  • Get cultures with more than two organisms growing in high counts

    • Two possible explanations

1. Very RARE situation in which individual does have that kind of mixture cause infection

• Result of abnormality of urinary tract

2. Very COMMON reason is that the urine was not properly collected

•  If this occurs, have to take another specimen

  • Must be sure that the specimen is very properly taken 

• What is the importance of a midstream urine collection kit?

  • Very often a NURSE who is responsible for giving patient directions or helping them if they need assistance

    • Must use words that patient can understand

  • What is a critical part of collection?

    • Not to collect first part of urine that comes out

      • This will hopefully flush out some of urethral organsims

      • Then move the stream into the cup

  • What results if specimens are not collected properly?

    • Could get high mixture of organisms

    • Results could make it look like patient has infection when they don’t

What are the predispositions to infections?

• Predispositions: something that makes an individual more likely to acquire urinary tract infection

• Any bladder infection can become kidney infection, but may be rare

1. Urinary retention: condition in which one cannot empty all of the urine from the bladder

   • Predisposition to BLADDER infection

   • Normally, when a person urinates, there is very little urine that is left in the bladder

   • With urinary retention, a person has little or much more than the typical amount that remains

     • Anything above the normal amount of urine left in bladder

   • Sometimes leads to the person being unable to urinate

   • Why is it not good to have this extra urine in the bladder?

     • Defenses on lining of bladder (enzymes, macrophages, wbc) that when bacteria do get into bladder, these defenses should be able to kill off right away

       • When urinary retention, defenses unable to work as well

     • Bacteria goes up into the bladder frequently 

       • Bacteria enter the bladder in small numbers, but are eliminated by its mucus membrane (defenses) 

       • When a person has urinary retention, the bacteria uses the remaining urine as a culture medium to better multiply

       • While in the urine, the defenses on the mucous membrane are unable to kill them

   • Who is predisposed to urinary retention?

     • Pregnant women

       • Unable to fully urinate because of the growing uterus and the pressure it places on the bladder

         • Gives woman sensation that makes her feel like has to urinate frequently

         • When does urinate, uterus still pressing on bladder

           • Cannot get the sensation of knowing whether the bladder is fully empty

     • Children in a hurry

       • Kids tend to hold their pee or use the bathroom too quickly

         • Desire to continue playing or go back outside as soon as possible

         • Tend not to empty their bladder entirely

     • “Elderly” (>50) males

       • As men get older, their prostate glands commonly become enlarged

       • The prostate surrounds the urethra, so it impinges against it as it enlarges

         • The flow of urine is then impeded and slows down, causing the person to not fully empty their bladder

     •  Anatomical problems

       • Any anatomical thing that obstructs the flow of urine through the urethra 

         • Individual can either be born or develop this abnormality

       • Example: Urethra

         • Some born w/ narrow urethra (urine doesn’t flow through as well as it should)

           • May have to have the urethra stretched as treatment

         • Urethral stricture

           • Stricture: something that narrows a tubelike structure in the body

           • Every time mucous membrane is infected, it’s also inflamed

             • One of last stages of inflammation is formation of scar tissue

               • New cells made on mucous membrane to replace cells damaged by infection

           • Buildup of scar tissue partially blocks and narrows the urethra

       • Example: general anesthesia

         • It is very common for patients to be temporarily unable to urinate

         • May cause urinary retention if lasts longer than 2-3 hours (short term)

           • Some surgeons may choose to catheterize patients before anesthesia or wait until after surgery to avoid urinary retention

2. Ureteral reflux: 

   • Predisposition to KIDNEY infection

   • “Reflux” means something that is flowing upward when it’s not supposed to

     • e.g. acid reflux, where stomach acid is flowing up the esophagus

   • Sphincters are tight closures that prevent urine from going from bladder upwards into the ureters

   • Who does ureteral reflux affect?

     • Pregnant women

       • Hormones of pregnancy relax the sphincter

     • Little kids

       • Their sphincters are not fully developed

       • If believed to have weak sphincters, the child will be placed on antibiotics for a year until they develop 

         • If they continue to get infections, they will get surgery to tighten the sphincters

3. Obstruction 

   • Predisposition to KIDNEY infection

   • Any tubular structure in body has been obstructed, very likely to be an infection above the blockage

     • Very general statement

   • Examples of things that obstruct/block ureter

     • Kidney stones (most common)

     • Tumor (very uncommon)

       • In or around ureter in some way that it is blocking

4. “Honeymoon Cystitis”

   • Predisposition to BLADDER infection

   • Refers to females who tend to get bladder infections after intercourse

     • Not STD

       • Endogenous infection (from her own organisms derived from intestinal tract, most likely E.coli)

   • Irritation to the urethra during intercourse can cause organisms like e.coli to be in the urethra and make their way to the bladder

   • Is rare event for some, but is a constant event for some women that happens every time they have intercourse

     • What to do if an individual gets it frequently?

       • Visit a doctor

         • Be sure that there is no other predisposition occuring

       • Practicing good hygiene after bowel movements

       • Drink a glass of water before and after intercourse

       • May possibly be given standing order for antibiotic

         • Take after intercourse

       • Drink cranberry juice 

         • Not a preventative but a treatment

5. “Trauma” 

   • Predisposition to BLADDER infection

   • Trama usually means damage to some tissue, but include irritation of a mucous membrane

   • What can be responsible for irritation of the urethra?

     • Catheterization

       • In-and-out

         • Put in to get urine and then taken out

       • In dwelling 

         • Catheter left in place in the patient

         • The whole time the catheter is in place, it’s irritating the mucous membrane

       • The longer the catheter is left in, the more an individual is predisposed to bladder infection

     • Sensitivity to dyes and perfumes

       • In soap, toilet paper, bubble baths, certain foods

What are the signs and symptoms of a UTI?

What are certain treatments for UTIs? 

• Treatment has to evolve around getting culture done, organism isolated, sensitivity test

• The prescription of antibiotics

  • Prescribed based on UTI symptoms and which organisms are most likely to cause them

    • Sensitivity test is done afterward, when the specific infection is determined

• Drink a lot of cranberry juice 

  • The more you drink, the more you urinate

    • Every time pee, flushing organisms out of urinary tract

  • Cranberry juice lowers the pH of urine

    • Makes it less habitable for bacteria

  • Chemical found in cranberry juice is antibacterial 

• Drink large amounts of liquids (NO CAFFEINE as it will irritate the bladder) 

  • Makes us pee more often

    • Causes the organisms to flush out of the urinary tract

  • Dilutes the urine

    • Makes it less favorable for the bacteria

What are the different types of urine specimens?

1. Midstream urine cultures

   • Most common form of urine specimen collection

   • What are the advantages of a midstream urine collection? 

     • Easy to do

     • Does not require medical personnel to collect the urine specimens

       • Can do it at home, on own

     • Noninvasive procedure

   • What are the disadvantages of a midstream urine collection?

     • Simple, detailed, and explicit instructions must be given to the patient so they may understand proper collection

       • Using words patient understands

     • If midstream urine is not collected well, it could lead to terrible cultures

       • Two reason so many are poorly collected

         • Nurse didn’t give clear directions 

           • Some nurses may not know how important it is that specimen must be properly collected

           • Some nurses may be embarrassed by what they have to say

         • Patient didn’t understand/didn’t follow directions

     • Cannot sit around

       • Will multiply like crazy if do

     • Some people cannot give a midstream urine specimen

       • Elderly

         • Lack mobility and cannot manipulate their bodies in ways to obtain specimens

       • Children

         • It is easier for little boys because they have a special collection apparatus

       • Extremely obese

       • Coma

       • Someone mentally challenged where cannot follow the directions

     • Culture has to be done quantitatively 

       • Use colony count to distinguish bacteria and significant bacteriuria

2. Catheters

   • In and out catheterization: put in and then taken out

   • In dwelling catheterization: left in place

   • What are the advantages of catheters?

     • People who struggle with midstream urine collection

   • What are the disadvantages of catheters?

     • Specimens obtained through cather still contain urethral organisms

       • Must be cultured and interpreted exactly same way as midstreams

         • Quantitative culture

     • Catheter causes irritation and inflammation of mucous membrane

     • Nurses have the burden of ensuring a good catheter insertion via aseptic technique

       • Daily catheter care

         • Cleanse the urethral meatus area. 

         • Check for any blockage/debris buildup in the catheter

     • While the catheter drains into a bag, the urine in said bag can never be used for a urinalysis or urine culture specimen

       • For a urinalysis: 

         • There is a special procedure that must be done in a 

         • Certain locations along the tubing. 

         • A needle on a syringe is used to aspirate the urine out of the tubing, not the bag

     • Longer a catheter is in place, it is more and more likely that the patient will receive an infection

3. Supra Pubic Aspiration (SPA)

   • “Supra” means “above something”

   • Insertion of needle on a syringe through abdominal wall into bladder

   • Only performed on little babies

   • What are the advantages of SPA?

     • Obtains the urine directly from the bladder

       • Never through urethra, no urethral organisms, no skin from urethral meatus

     • Urine is sterile if there is no infection

     • Quantitation DOES NOT need to be done

       • Clear cut – there either is or isn’t growth

       • Specimen has growth if the patient has a kidney or bladder infection

   • What are the disadvantages of SPA?

     • Patient is exposed to potential dangers when putting a needle or tube into the body cavity

       • Invasive 

     • It is not an appealing process

       • Some people are fearful or do not want the procedure done

     • Requires the direction of medical personnel and their time

4. Cystoscopy

   • Minor surgical procedure

   • This procedure is not done just to determine if the patient has a UTI

   • A scope tool is used to see if the tissue of the urinary tract has abnormalities

     • Cystoscope: an instrument with cameras at the end that has tubes that are inserted through the urethra and up into the bladder 

       • Sometimes the doctor will use an instrument that will let them get into the ureter as well

       • Different from inserting a catheter

         • Outer tube touches urethral microorganisms

         • Inner tube going further up the urinary tract and never contacting the urethral microorganisms

   • If the doctors see something they believed needed to be biopsied, they will clip the tissue and take it back to the lab

     • Unrelated to UTIs

   • When is a cystoscopy done?

     • If the patient has had repeated episodes of UTIs

     • There is some suspected problem with the patient’s urinary tract and the doctor needs to look at it

   • What are the advantages of a cystoscopy?

     • Minor surgical procedure

     • Provides 3 specimens that can reveal what body part is infected: 

       • Left ureter

       • Right ureter

       • Bladder

     • All three specimens should have no growth if there is no infection

   • What are the interpretations of the 3 specimen combinations?

• What are the disadvantages of cystoscopy?

  • Invasive

    • Instrument is causing trauma to the individual

  • Time and money

  • Anesthesia 

  • The design of the instruments does not provide a culture of the skin organisms

What reports can you get from midstream/catheterization?

1. No growth (<1000 cells/mL)

   • Absolutely NO BACTERIAL COLONIES grew on culture

     • Use very small volume of urine

       • If specimen really well collected, than there could be >1000 bacterial cells and nothing may grow on plate

2. One organism, maybe two

   • Each has to have colony count high enough to be considered bacteriuria

   • Antibiotic sensitivity test

3. Mixed bacteria (>100 cells/mL) 

   • Mixed bacteria: at least 3 organisms present

   • Two explanations

     • Common – not well collected specimen

     • Rare – patient w/ abnormality of urinary tract

   • What should be done?

     • Recollect the specimen carefully

4. “No significant growth”

   • Some growth but doesn;t indicate infection

   • NEW PHRASE USED

     • May just list a “low colony count”

       • Doesn’t specify organisms, etc.

What organisms most likely cause UTIs? 

• Gram negative rods (GNR)

  • Most common cause

  • Family enterobacteria

    • E.coli 

    • Proteus

    • Enterobacter

    • Clyptyella 

  • Pseudomonas 

    • Not likely to be cause of UTI in common people

• Gram positive cocci

  • Normal intestinal organisms that can get into the urethral opening

    • Enterococcus

    • Group B strep

• A yeast

  • Candida albicans, a UTI and not a vaginal infection

  • Special cases

    • May be on antibiotics

    • Individual could be diabetic

What is the proper evaluation of a UTI?

• 3 aspects to diagnosing urinary tract infection

1. Documentation: proving the individual actually has a UTI and not something else

   • Bacteriuria: 

     • Initially thought that if bacteria was present that indicated infection

       • Found this to be false because bacteria is PRESENT IN ALL CULTURES regardless of whether an individual has infection

       • Why always find bacteria?

         • The very anterior part of urethra has bacteria

           • When pee in cup, going to have bacteria in the specimen

   • Significant bacteriuria + quantitative urine culture

     • The very same organisms that are going to be in urine specimens from urethral organisms and urethral opening (E.coli) ARE the ones that commonly get into the urethra and cause infection 

     • How can you tell the difference between bacteriuria and significant bacteriuria?

       • Colony count in conjugation w/ how many different organisms present

       • See previous notes about what certain colony counts mean

2. Identify which site in the urinary tract is infected

   • Determine whether bladder or kidney

   • Symptoms can SUGGEST whether bladder or kidney is infected, but not PROVE

     • Aspects of urinalysis that can suggest KIDNEY infection

       • Certain things that can be present when kidney infection that are not present in bladder

     • What is the only way to PROVE urinary tract is infected?

       • through urine culture

         • Cystoscopy: 

           • Only done if multiple repeated UTIs

           • Not routinely done

         • Basis of whether kidney or bladder more likely done through symptoms and urinalysis info

   • Why is it important for doctor to get an idea of whether kidney or bladder infection?

     • The treatment is different for a kidney and bladder infection

3. Detect any predisposing factors that may exist in patient

   • Whether minor or serious one

     • Ex: Repeated UTIs

   • Doctor needs to see if there’s any predispositions present