2Nosocomial Infections A Nosocomial Infection is a hospital- or clinic-acquired Infectious Disease.Nobody goes into medicine in order to prevent Nosocomial Infections.Nevertheless, to practice medicine you must be able to prevent Nosocomial Infections.To prevent Nosomial Infections you need to have some understanding of microbiology.Oh yes, and Infectious Disease, in general, is kind of important to medicine, too.At the very least, you should be striving to Do No Harm!And avoiding harming by infection requires some reasonable knowledge of microbiology.Nosocomial Infections
3Microscope of Antony van Leeuwenhoek (1632-1723) Microbiology, b. 1674Microscope of Antony van Leeuwenhoek ( )
4Microscope of Antony van Leeuwenhoek (1632-1723) Note that images will dissolve in if you are responsible for them and/or I’ll circle or “square” in blue the parts of these images you are particularly responsible for).Microbiology, b. 1674Note that “blue” text you are very responsible for, “black” less so, and “red” only in the form of bonus questions.Microscope of Antony van Leeuwenhoek ( )
5Microbiology is the Science that studies Microorganisms. Microorganisms, roughly, are those living things that are too small to be seen with the naked eye.Microorganisms cannot be distinguished Phylogenetically from “Macroorganisms”For example, many fungi are microorganisms, as well as all bacteria, all viruses, and most protists.Microbiology is more a collection of techniques:Aseptic techniquePure culture techniqueMicroscopic observation of whole organismsA microbiologist usually first isolates a specific microorganism from a population and then cultures it (i.e., in pure culture).What is Microbiology?
6Microbiology b. >3 billion BC “It is generally believed that microorganisms have existed on earth for several billion years, and over time, plants and animals have evolved from microorganisms.”Microbiology b. >3 billion BCAbove is a fossil cyanobacterium that is 950 million years old.“Microorganisms are… very diverse in all their aspects: appearance, metabolism, physiology, and genetics. They are far more diverse [in these terms] than plants and animals.”
8Origin of Microbes: Spontaneous Generation Myths Snakes from horse hairs in stagnant waterMice from grain and cheese wrapped in a sweaterMaggots from rotting meatFleas from hairFlies from fresh and rotting fruitMosquitoes from stagnant pondwaterEels from slimy mud at the bottom of the oceanLocusts from green leavesRaccoons from hollow tree trunksTermites are generated from rotting wood
9Pastuer (1861) Refuted Spont. Gen. Pasteur filtered air through cotton plug showing that filterable particles cause contamination of sterile broths.Swan-necked flask experimentsPastuer (1861) Refuted Spont. Gen.
10Origin of Microbes: Pasteur’s Swan-Necked Flasks
11Origin of Microbes: Pasteur’s Swan-Necked Flasks Remains sterile.Bacteria, fungal spores, and dust adhere to glass.Contamination of cultureHeat to sterilize (doesn’t always work).Broth turbidity indicates bacterial growth.
12Origin of Microbes: Pasteur’s Swan-Necked Flasks No Turbidity w/oContamination!Remains sterile.Bacteria, fungal spores, and dust adhere to glass.Contamination of cultureHeat to sterilize (doesn’t always work).Broth turbidity indicates bacterial growth.
13Pasteur was fortunate to have worked with broths prepared from non-soil or -plant associated substances (e.g., hay).Those substances contain bacteria that can form endospores, not all bacteria can.Endospores represent a bacterial durable state and are very difficult to kill.John Tyndal (1876) discovered that there exist differences in the ability of heat to kill different kinds of bacteria-containing cultures.Ferdinand Cohn (1876) showed that this difference was due to endospores and Robert Koch (1877) showed that the bacterium Bacillus anthracis forms endospores as part of its transmission.Problem of Endospores
14Types of Microorganisms Bacteriaa.k.a., eubacteria (“true” bacteria)a.k.a., domain BacteriaArchaeabacteriaa.k.a., domain ArchaeaSingle-celled members of domain Eukarya.ProtozoaMicroscopic AlgaeMicroscopic FungiViruses and other AgentsTypes of Microorganisms
23Binomial Nomenclature (1/3) Examples: Escherichia coli, E. coli, Escherichia spp., and “the genus Escherichia”The genus name (Escherichia) is always capitalizedThe species name (coli) is never capitalizedThe species name is never used without the genus name (e.g., coli standing alone, by itself, is a mistake!)The genus name may be used without the species name (e.g., Escherichia may stand alone, though when doing so it no longer actually describes a species)When both genus and species names are present, the genus name always comes first (e.g., Escherichia coli, not coli Escherichia)
24Binomial Nomenclature (2/3) Both the genus and species names are always italicized (or underlined)—always underline if writing binomials by handThe first time a binomial is used in a work, it must be spelled out in its entirety (e.g., E. coli standing alone in a manuscript is not acceptable unless you have already written Escherichia coli in the manuscript)The next time a biniomial is used it may be abbreviated (e.g., E. for Escherichia) though this is done typically only when used in combination with the species name (e.g., E. coli)The species name (e.g., coli) is never abbreviated
25Binomial Nomenclature (3/3) It is a good idea to abbreviate unambiguously if there is any potential for confusion (e.g., Enterococcus vs. Escherichia)These rules are to be followed when employing binomial nomenclature even in your speech. It is proper to refer to Escherichia coli as E. coli or even as Escherichia, but it is not proper to call it coli or E.C.!Failure to employ correct binomial nomenclature on exams will result in the subtraction of one point (on 1000-Point Scale) per erroneous usage—don’t let this happen to you!!!!!!When in doubt, write the whole thing out (and underline)!
26Types: CyanobacteriaDescription: also called blue-green algae, cyanobacteria are a kind of bacteria (more specifically, a kind of eubacteria)Types: photosynthetic aquatic procaryotes, green lake scum, cell wallsNutrient Type: photoautotrophsDurable state: ?Diseases: none
27Types: AlgaeDescription: photosynthetic aquatic eukaryotes, cell walls, both unicellular and multicellular typesTypes: brown, red, green, diatoms, dinoflagellates, euglenoidsNutrient Type: photoautotrophsDurable state:?Diseases: Some poisonings associated with unicellular types: Alexandrium causes Paralytic Shellfish Poisoning (PSP), Dinophysis causes Diarrhetic Shellfish Poisoning (DSP), Pseudo-nitzschia multiseries causes Amnesic Shellfish Poisoning (ASP) [some would describe some as protists]
29Types: HelminthsDescription: Flatworms (platyhelminths), roundworms (nematodes)Types: metazoan (multicellular animal) parasites, engulfers and absorbersNutrient Type: chemoheterotrophsDurable state:?Diseases: trichinosis, hook worm, tape worm (pictured are scolex-heads of), etc.
30Types: Protozoa (Protists) Description: Unicellular and slime molds, flagellates, ciliatesTypes: eucaryotes, parasites (most not), engulfers and absorbers, wet conditions, no cell wall, ~30 human pathogensNutrient Type: chemoheterotrophs (some classifications include some photoautotrophs as well)Durable state: cysts (some)Diseases: malaria, giardiasis, amoebic dysentery, etc. (shown are harmless--to us--protist components of pond water: Amoeba, Blepharisma, Paramecium, Peranema, & Stentor)
31Types: VirusesDescription: Viruses are not cells but some viruses do have lipid envelopesTypes: acellular, obligate intracellular parasitesNutrient Type: not applicableDurable state: virion particles, some can encase in durable state of hostDiseases: common cold, flu, HIV, herpes, chicken pox, etc.
32Types: VirusesSmallpox is a Diseasewith a Viral Etiology
34Microbes & EcologyMicrobes are produces—they provide energy to ecosystems, especially aquatic ecosystemsMicrobes are fixers—they make nutrients available from inorganic sources, e.g., nitrogenMicrobes are decomposers—they free up nutrients from no longer living sourcesMicrobes form symbioses (such as mycorrhizal fungi associated with plant roots—though somewhat macroscopic, the bacteria found in legume root nodules, etc.)Microbes serve as emdosymbionts (e.g., chloroplasts and mitochondria)
36Microbes & IndustryIndustry: Fermentation products (ethanol, acetone, etc.)Food: Wine, cheese, yogurt, bread, half-sour pickles, etc.Biotech: Recombinant products (e.g., human insulin, vaccines)Environment: BioremediationEach carton of Bugs+Plus provides easy to follow step-by-step instructions, containers of specially-formulated wet and dry nutrients and a container of microbes cultured for their ability to digest oil and other petroleum derivatives.
37Microbes & Disease Microbes both cause and prevent diseases Microbes produce antibiotics used to treat diseasesThe single most important achievement of modern medicine is the ability to treat or prevent microbial diseaseMost of this course will consider the physiology of microbes and their role in diseaseThe Germ Theory of Disease = Microbes cause disease!(yes, it wasn’t so long ago that humans didn’t know this)Nevertheless, most microorganisms, including most bacteria, do not cause diseases in any organism (including in humans)
38Impact of Infectious Disease Infectious diseases are diseases caused by microbes200,000 deaths per year in U.S. from infectious diseases~20 million died from influenza (a disease caused by a virus) in 1918“New” infectious diseases still being discoveredImpact of Infectious Disease
39Normal FloraThese are the ~harmless microorganisms found on your body.Every part of your body that normally comes in contact with outside world (deep lungs and stomach are exceptions).