8/22

Thursday, August 22, 2019 9:29 AM

First quiz next Tuesday

- Look in Canvas--the relevant assignments, readings, and vocab for each quiz can be found under
quiz headers

This lecture is mainly going to be review

There are 3 domains:

- Bacteria
- Eukarya
○ Fungi, including yeast
○ Protozoa
- Archaea
○ There are no known pathogenic archaea
○ They are still part of our flora, though
○ Some act as secondary pathogens--meaning they create a favorable environment for other
organisms to become pathogenic (these organisms are called primary pathogens)

We will not cover viruses in this course.

Differences between domains affect antimicrobial targets

- Bacteria have no nuclei or organelles. Thus, lots of important processes are open in the cytoplasm
in bacteria, and can be used as antimicrobial targets.
○ Transcription
○ Translation
○ DNA replication
- Also, antimicrobials can be more effective during certain growth phases of microorganisms
○ Stationary phase, log phase, etc.
- Eukaryotic differences
○ Translation happens in the cytoplasm or rough ER
○ Transcription and DNA replication happen in the nucleus
○ This influences antimicrobial choice when dealing with eukaryotic infections (e.g. protozoa,
fungi)
- Also, the enzymes involved in replication, translation, transcription (central dogma systems) are
different in eukaryotes and bacteria--and this influences antimicrobial choice.

Viruses
- Composed of a capsid and nuclear envelope
- Genomes vary a lot in organization
- Nomenclature of viruses is complex
○ Scientists still argue about the correct system of nomenclature
- Phage therapy is an experimental treatment that may be important in the future due to antibiotic
resistance

Human microbiome
- Our knowledge of its importance and diversity keeps expanding
- Companies produce gut microbiome identity tests
- We can almost consider it another organ
- Bacteria communicate within themselves in the microbiome using small molecules

medical microbiology Page 1

 - Bacteria communicate within themselves in the microbiome using small molecules
- Why is this relevant?
○ Antibiotics are usually not very selective, so using them to kill a pathogen also wipes out the
rest of the microbiome
○ The microbiome also serves as a first barrier against other infectious microorganisms
because of competition

How do we identify and distinguish between pathogens?

- Morphology
- Gram stain result
○ Cheap, easy, and common
○ One of the first things done to identify infections
○ We will be looking at some complex gram stains in this course with multiple organisms in
them
○ We will look at some pathogens that do not Gram stain
▪ Chlamydia and rickettsia do not Gram stain because they are generally intracellular
pathogens, kind of like viruses
▪ Acid fast stains must be used instead
▪ These organisms are hard to culture
- MacConkey agar result
○ A selective and differential culture medium
○ Meant to select for Gram negative and enteric bacilli
○ Differential for lactose metabolism
- Oxygen tolerance
○ Majority of pathogens are aerobes and microaerophiles
○ However some are anaerobic, especially in the GI tract
▪ Commonly facultative anaerobes
- Catalase test result
- Hemolysis pattern
○ Specifically useful for streptococcus species

Some organisms are only problematic when they express toxins

- Clostridium botulinum
- Clostridium difficile

Terminology
- Antimicrobial: targets bacteria and/or eukaryotes
- Antibiotic: a substance produced by microorganisms in order to kill other organisms
○ They must be purified in order to be used in humans
○ Not all antimicrobials are technically antibiotics! For example, artificial antimicrobials are
not antibiotics
○ Most antibiotics secreted by bacteria are bacteriostatic, not completely bacteriocidal
- Antibacterial: targets only bacteria
- Antifungal: targets fungi; may also kill bacteria
- Antiviral: targets viruses
○ Typically have a higher incidence of side effects because it is hard to specifically target
viruses, which take residence inside cells
○ Antiretrovirals target reverse transcriptase

Antimicrobial targets:
- Quinolones
○ Targets (inhibits) DNA gyrase
▪ This enzyme is involved in DNA replication in prokaryotes
▪ DNA supercoiling ahead of a polymerase can stall the enzyme, so DNA gyrase untwists

medical microbiology Page 2

 ▪ DNA supercoiling ahead of a polymerase can stall the enzyme, so DNA gyrase untwists
it
▪ The mechanism is in re-ligation step--quinolones inhibit this
○ A single point mutation can cause quinolone resistance, so resistance develops quickly and
naturally
- Beta-lactams
○ Penicillin, cephalosporins
▪ Often used as the first line of defense
▪ Pretty broad spectrum
▪ Empiric therapy: you have to make an educated guess--there is a time and cost
restriction for test results
○ Targets cell wall synthesis (peptidoglycan)
○ Don't penetrate the cell (not good for intracellular pathogens)
○ Requires the cells to be making new membranes (replicating and dividing)
▪ This is why Mycobacterium tuberculosis is so hard to treat--it grows very slowly
- Aminoglycosides
○ Tetracycline, doxycycline
○ Targets translation machinery
▪ Some affect both eukaryotes and bacteria, others only bacteria
□ Ribosome structure is very different between these two groups--specifically that
involving the initiation step
○ These inhibit peptidyltransferase action, inhibiting initiation

Lots of antibiotics can be harsh on the kidneys or liver

- Vancomycin is the last line of treatment for this reason
○ V res enterococci
○ C diff treatment if metronizadole fails

Consequences of antibiotic use (regular or overuse)

- Antibiotic resistance arises
○ Few antibiotics have been introduced in the past 25 years
▪ Why?
□ It is not profitable
 Infections are episodic, not chronic (like high blood pressure or
depression)
▪ Because of this, most antibiotic research is done in academic labs instead of
pharmaceutical companies
- Opportunistic infections due to loss of normal flora
○ Clostridium difficile
○ Yeast infections
- Side effects and interactions with other medications

Where does resistance come from?

- Efflux pumps
- Penicillin binding proteins
- Beta lactamases
- Modification of translation, replication machinery to evade inhibition

Susceptibility testing
- Kirby Bauer method (disks)
- E-strip (concentration)
○ These suggest dose ranges

Hospital acquired infections (previously called nosocomial infections--they changed the name)

medical microbiology Page 3

Hospital acquired infections (previously called nosocomial infections--they changed the name)

medical microbiology Page 4