Microbiology Lecture 13 Diagnostic Microbiology by Dr. Tierno
Slide 1 Diagnostic Microbiology Tierno: To identify the so called etiologic or causative agent of infection in the oral cavity likely, and youll have to submit that to some sort of diagnostic center or laboratory for identification of the microorganism or organisms present, and their antibiotic susceptibility profile. Its important for you of course to develop an ability to treat empirically, in other words youre looking at the oral cavity, you know the flora of the oral cavity, and youre going to treat to cover those organisms that are likely to cause infection. But you will not know the susceptibility pattern, antibiotic susceptibility, and thats why its always good to submit the culture, confirm the identity of the organism, and get the specific antibiogram or antibiotic susceptibility pattern, which will be provided to you from the laboratory that you submit your culture to. Nowadays, you are lucky that diagnostic microbiology involves molecular methods. In fact, we have a couple of methods in Tisch that can identify a bacterium in ten minutes as opposed to days that it would normally take someone to identify an organism. So youre going to be privy to that. But, you still must know classic diagnostic microbiological methods. And thats what Im presenting today, and I will touch upon some molecular methods, and this lecture was split I think we have part two tomorrow. And tomorrow I will be giving you chemotherapeutic agents, antibiotic agents, thats a two part lecture also, so one part will be tomorrow and the next part will be I think the following week. After that, I will talk to you about laboratory susceptibilities, how the laboratory generates susceptibility patterns on the organisms that are identified. And then the final lecture that I will give will be on antibiotic resistance. Its been only sixty-somewhat years since antibiotics were presented for use in therapy, probably maybe 70 years from world war 2 when penicillin was first utilized in the 40s. And we have come to a point where we have almost made antibiotics useless. And thats coming back to square one, well talk about that over time. But today lets concentrate on diagnostic, sometimes its called clinical microbiology.
Slide 2 Top Killers of Man Tierno: Now, before we get into actual culture methods, we have to talk a little about the gestalt, to understand where things are. Youll look at this chart, back in 1900, life expectancy was between 43 and 45 years. That was considered old age at that time and the average person might have had his end of life at that point. In the year 2014, the number one killer in the world still germs. Microbes, and we use the colloquial phrase germs to cover all types of microorganisms: bacteria, viruses, rickettsia, algae, everything you can imagine is placed in that category germ. Its the number one killer worldwide. And life expectancy, I should have said that before I mentioned the germ thing, is approximately 78 years in America, its higher in some other countries, and that 78 year mark was because of three things. Vaccines, hygiene, and antibiotics. But keep your eye on antibiotics. Also vaccine use has been getting a bad name, people are fearful of autism. There is absolutely no evidence whatsoever that autism has to do with vaccine preparations, administration, or thimerisal which was used, which is a mercury product in miniscule quantities only in the flu vaccine currently. There is evidence that the genes for autism are many, and have been identified. And there are various types and variations of autism so I wont go there. So weve increased life expectancy. Germs, I said, was the number one killer across the world, but industrialized nations have relegated germ death to third place after heart disease and cancer. But if you look closely at cancer and heart disease, you will see that you have many cancers, well start with that, like human papilloma virus causing cervical cancer. We even have a vaccine for that cancer. What about human herpes virus number 8? Kaposis sarcoma. We used to think it had to do with a cultural thing, now we know theres a virus involved in that cancer. Were all familiar probably with the hepatitis B and C giving rise, if you get a chronic infection, to a hepatic carcinoma. And then there are overtly cancerous viruses called oncoviruses that can give rise to cancers. And of course Epstein Barr virus has been Transcribed by Sofiya Khazanovich July 24, 2014
associated with lymphomas and on and on, you get the point that some of these organisms can give rise to carcinogenic processes including bacteroides and colon cancer. There are even studies that show that the microorganisms indirectly can be involved in carcinogenic properties by taking beef products and breaking them down to quinidine and other materials that were chemicals that are carcinogenic and can cause inflammatory processes. Now if you look at the other side, the heart aspect, the cardiovascular disease, many of you have read about periodontitis. Porphymonas gingivals, which is part of the normal flora of the oral cavity, can give rise to a cardiovascular event. And even effect immunity. In fact there are some organisms in periodontal disease that are able to set the stage for inflammatory processes as well as give off certain types of chemicals that can clot blood. But a lot more research is needed, but clearly periodontal disease is a problem. We have done some work at the dental school where patients who have died of a stroke or other clotting events, we do a microbiomic analysis of the clot and we do a microbiomic analysis of the gingival sulcus in patients who have periodontal disease, and same flora is in both whether one is a cause, or whether one is the effect remains to be determined. We think its the cause. There are other bacteria that can give rise to inflammatory responses which can set the stage for a cascade of events that occur and give rise to both cardiovascular problems as well as carcinoma. Any chronic condition where the cells die and are reborn can give rise to an oncogenic property. You may have been familiar with chlamydia pneumonia, this organism is related to chlamydia trachomatis the STD, and that particular organism is found in arteriosclerotic processes. Again, were not 100% certain whether its a cause and effect, which way it goes, or is it just the product of having the plaque that you accumulate that organism, or does that organism cause arteriosclerotic processes? So keep in mind we may not have relegated to third place, microorganisms. Microorganisms that can cause disease.
Slide 3 General Microbiology Tierno: Now, our topic today is diagnostic microbiology, or clinical microbiology, which is different than general microbiology. Youre probably familiar with general microbiological methods, or at least the concepts where youre studying all types of microorganisms, structure, reproduction, genetics, all aspects of microorganisms, and how theyre distributed in nature and relationship to other living things, and the physical chemical changes they make in their environment. All organisms on planet Earth, whether they're trees or whether they're animals, fish, doesnt matter what, has its own normal flora. Its own passport of germs, microorganisms. Theres not one organism on earth that does not have a companion of many microbes including the human body. It is important to know that because you have to know, when you take a culture of the oral cavity, there are some 500 organisms that are normally present there, and they wax and wane, but theres a certain number that are always present. So you have to know what normal is to know what abnormal is. And sometimes you have to use quantitation to determine or to differentiate the two.
Slide 4 Clinical Microbiology Tierno: So well come back to normal flora in a minute. Lets define clinical or diagnostic microbiology. Clinical microbiology involves two processes. Youre dealing with microbes that are the cause of an infectious process. The so called etiologic agent of a disease. And we have to identify those organisms either by growing them out in the form of bacteria, or using cell cultures to grow out viruses, or use similar methodology or different methodology, molecular techniques, as I said to you, you can actually identify bacteria in ten minutes in the lab with something of, Ill show you what the machine is, its called the Malditof. And Ill talk about that in tomorrows section of the lecture. But right now we have to get the identity of an organism and second what antibiotic specifically can be used to kill that organism in a person. And of course its not a simple task, cause you still have to take into consideration the person and his or her background health situations. You can also indirectly identify the presence of an organism. many of you have had measles, so in order to determine whether you have had measles, Transcribed by Sofiya Khazanovich July 24, 2014
you can do a blood serology to test whether you have antibodies to a microorganism whether its the measles or some other organism, and that will indirectly tell you that you have had that organism. Theres also something you can do in a real time circumstance, where you have a particular viral disease, and if its past the point where you can isolate the virus, you can do an acute serology blood test to look for antibodies, IgM. And then you wait for convalescence and you do IgG should be detectable. And that could sort of phase the course of the disease and the convalescence. But serology is retrospective. Were looking for better than culture even. We want real time microbiology. Theres no reason why a patient cant come into an emergency room and present with certain circumstances and cultures are taken, submitted to the lab, and within the 2 hours you will get the genus and species of a microorganism causing that patients infection as well as the antibiotic susceptibility pattern by probing the genes of resistance both chromosomal and extra chromosomal, and therefore you can prescribe directly for the patient the specific antibiotic instead of using empirical methods and instead of using the old classic microbiological methods which you have to know anyway which take days. So thats where were coming from. Also in your purview will be the practice of real time molecular techniques for identification of these organisms. And we will talk more about whats available tomorrow. Now lets get back to clinical microbiology.
Slide 5 In the beginning was the germ Tierno: Lets go back to the beginning. The reason why we have normal flora. If you look back historically, of course we dont have evidence about 4 billion years ago of microbes per se that were preceding the microbes that we have in the fossilized rock 3.5 billion and the indirect evidence for 3.8 billion years ago. There were probably micelles, these were cell wall-less organisms that were sort of gathered in a particular geometric pattern just as chemicals group together, but lets start with our 3.5 billion year old fossilized bacterial cells in the rocks in Australia. And there are many other similar findings elsewhere, especially at hot water vents, which have been untouched basically for a long time, and as theyre assayed they find evidence of fossilized bacteria. If you look at the first prototypical cells that were totally independent and viable, they came later, the first prototypical cells that were completely independent were cyanobacteria. In fact the cyanobacteria which are sometimes erroneously called blue green algae exist to this day. And theyre the only 100% independent microorganisms. These are found in the waters of the world. So theyre pretty plentiful. And well touch on that, and the reason I mention this is because its important to understand as I said, everything that has evolved.
Slide 6 Origin of life forms Tierno: Everything has its own complement of microorganisms. And therefore no matter what the organism is, over time including the first human ancestors and humanity to this day has a complement of microorganisms.
Slide 7 Image Tierno: There is an ability to understand what gave rise to eukaryotic cells, you know there are prokaryotes and eukaryotes and the prokaryotes besides the bacteria, there are the archae, the old bacteria. And they're separate, one was thought to come from the other and its not the case, but we know one of the bacterial forms and one of the archae had a common ancestral combination that gave rise to the eukaryotes which would include protists, plans, fungi, and animals. And that just gives you a general perspective based on what we now know.
Slide 8 Role of Microbes Transcribed by Sofiya Khazanovich July 24, 2014
Tierno: There is a role that microbes have in general. If microbes did not exist, no life on this Earth would exist as we know life today. So somewhere down the pipe, maybe within your lifetime, someone will discover something on another planet or another area and right now this is what we know. Cyanobacteria are at the bottom of the food chain and in fact the majority of plankton approximately 100,000 cells per milliliter occur in the waters of the world, and in fact they are serving right now the astronauts when they go right now to the space station, they take with them dried mats of cyanobacteria that are eaten because they're very high in protein. In fact its the highest protein source you can get, and they're very easy to transport. They may not taste so good but at least they will sustain life. Microbes are also responsible for converting the nitrogen around this planet to nitrates, and thats most important because plant life requires nitrates to grow. And even though were bathed with nitrogen as a planet, we dont utilize it. What utilizes it are the nitrogen fixing organisms and they convert nitrogen to nitrates. They also produce 90% of the Earths oxygen. If you look back in the evolutionary trail, oxygen was produced only after plants came on planet Earth and it is because of that that we had this burst of evolutionary processes. And its not the trees that are producing the bulk of the oxygen, its the water that has cyanobacteria in it. And the sunlight allows those organisms to take the carbon dioxide out of the air and produce oxygen as you know by photosynthesis. And thats why were worried about ozone layering being lost, big holes in the ozone, UV radiation can strike these waters and actually disrupt many of those organisms by killing them and reducing oxygen. Decomposition of organic, there is no organic material that cannot be broken down by one or another microorganism. So they are the decomposers, the recyclers, its very important for these organisms to recycle any organic material. Anything that dies is recycled. The carbon is reutilized, all of the elements are utilized. So without microbes
Slide 9 If there were no germs Tierno: Basically no food, no oxygen, no nitrates, no recycling, no life.
Slide 10 Image Tierno: Now we use the sun of the ultimate source of our energy, the sunlight that shines down. As you can see from this and you probably know without me going into it, green plants serve as food stuff to herbivores, herbivores can serve as food stuff for carnivores, or omnivores eating both plants and animals, and everything has parasites, and everything dies to be decomposed and recycled. Its a very important aspect of the chain of life in the world.
Slide 11 Image Tierno: Where can microbes live? Literally anywhere. They even live in the stratosphere in the air. But we wont get into all of that, many of you have had courses in microbiology. But if you look at the temperatures just took a few physical chemical parameters, temperature, oxidation reduction, the Eh levels, pH acid base, and the hydrostatic pressure as well as salinity, those factors, and we can have organisms living at minus 12 degrees centigrade, certain fungi and bacteria, and thats very low and same with above boiling, 104 degrees centigrade, and that is at 1000 atmospheres, sulfur producing organisms. And as far as the Eh oxidation reduction potential, -450 millivolts is very ,very low, the absence of oxygen at a very reduced environment, you can have organisms surviving quite well, and the same with +850 millivolts which is a very oxygenated environment. The intestines for example and the gingival sulcus could be very low Eh an example of where microbes can live in and on your body, as well as the gut and your intestines, -450. [student asks What is Eh?] Eh is oxidation reduction potential, the degree of oxygen present or not present. In a reduced environment you have no oxygen. In an oxygenated environment you have a lot of oxygen, so plus is oxygenated, minus is reduced. Hydrostatic pressure, we can have zero, you get microorganisms that can live, and also at 1400 atmospheres you can Transcribed by Sofiya Khazanovich July 24, 2014
have deep sea bacteria living. Its important for you to know that we live at one atmosphere, bacteria have from 3 to about 15 sometimes even higher atmospheres inside the cell. Thats why when you give an antibiotic like penicillin, the bacterium blows up. You interfere with the rigid cell wall which holds that together and it releases the atmospheric pressure inside the cell and it bursts the bacterium. So, these concepts are important, salinity of course you can have brinish brackish water, you can have double distilled water, you get organisms living in there. For example an organism like legionella pneumophila, the agent of legionnaires disease, can actually live in water with one amino acid cysteine, and one element, iron, ferric ion, and survive, reproduce very well. I think you have a lecture on that I give.
Slide 12 Ecological Patterns Tierno: Now, all of these organisms live in ecological patterns. Whether we use ourselves as an example, it doesnt matter. Any entity can be used as an example. There are basically 3 symbiotic relationships and one independence. I already told you cyanobacteria are relatively independent, however if we upset the atmosphere, they are dependent upon not having UV rays strike them. So nothing is really totally independent, but when we talk about independent in that you dont need another organism to survive, thats what we mean by that term. But lets concentrate on the symbiotic relationships. Mutualism, commensalism, and parasitism. Mutual youre probably familiar with the algae and the fungus on a tree, lichen, youre familiar one gives and takes, one provides food one provides water, or maybe the termite and wood. The termite chews up the wood, gets it in the intestines, the protozoa have the cellulose enzymes to break down the wood to food for both the termite and the organism. So thats mutualism. Each benefits the other. And commensalism is where one takes but doesnt hurt another organism. Many of the textbooks have our microbes living in and on us as commensals. In reality, theyre not commensals, theyre really mutuals. Theres always some mutual relationship that you can dig out, and even the normal flora that coats the skin, you can say theyre commensals utilizing our surfaces of the body, but in reality they compete with transient organisms that may come in by your touching some contamination. Those contaminants dont overcome your normal flora. So in reality its a mutualistic, mutual in that youre giving a place for the organisms to reside and they're giving you some protection. However minimal it doesnt matter. Now parasitism is an extension of commensalism, commensal you take but you dont hurt. Parasitism you take and you hurt. A good parasite hurts very little over a long time, so it keeps the host alive so that it can have its cycles completed. Thats a good parasite. But of course in the end, the host is not very happy because theyve served for a parasite. You can actually say disease is really a parasitic form of an organism living in and on your body.
Slide 13 Physico-Chemical Factors Influencing the Ecology of Microbes Tierno: What physical chemical factors are the most important? No one factor is the most important, but any can be the limiting factor. If you take an anaerobe, put it in oxygen, that one thing can prevent the anaerobe from growing. So any could limit the growth, but you need many of these physical chemical factors to allow growth of an organism. And I wont go into them, its just there for your understanding that microbes depend on many factors for survival.
Slide 14 Normal Flora Tierno: Where is the normal flora on our body? The normal flora in our body is best represented by a donut hole. The outer surface of the donut hole is the skin and the invaginations of the skin like the hairs, the ear canal, the vaginal fold, those are external to the body. They are invaginations of the skin, and thats where youll find whats called normal flora varying depending on pH and well talk about that and other factors. The inside of this donut represents the mouth to the anal pore. Thats where youll normally find microorganisms. Mouth to the anus, that whole tube in a tube, youll find organisms. Transcribed by Sofiya Khazanovich July 24, 2014
Theres one little caveat that were now learning, as I was about to say, in between is sterile. Well, we have to qualify that. The methodologies we used in the past told us that we couldnt culture anything between those two lines. So we would say things like the lungs, the placenta, the bladder are sterile. But theyre not. With the new research, microbiomic research where you can identify microorganisms using molecular methods, you can identify their presences without having the ability to grow the organism. There are many organisms that we cannot grow, we have no idea how to grow them. So keep that in mind. Using molecular methods we can identify organisms, and doing that has allowed us now to understand that microorganisms exist in places we thought were sterile, especially things like the bladder, all things being equal, Im not talking about a person who has chronic urinary tract infections, Im talking normally. So in between there are some organisms associated. Well talk more about that.
Slide 15 Of Microbes and Men Tierno: Depending upon who you read, there are ten times more bacterial cells in and on your body than there are human cells. The ratio is 10:1. So ten percent of you is you. 90% of your cellular makeup are your bacteria. This occurs for many organisms. Dogs, cats, squirrels, you name it. Whales, you name it. There are more bacteria in your intestines, one teaspoon of your intestines, than there are or were men who ever walked the face of the Earth since the beginning of time. As Carl Sagan used to say, billions and billions, try trillion. Approx. 2.5 pounds of your body weight is actually your bacteria. Thats the sum weight. There are more bacteria.. I say tablespoon, I meant teaspoon, so in case youre on a quiz show or something. Combined weight of microbes on planet Earth is greater than all other forms of life. Thats a kicker. Cause microbes exist in the environment also, in soil, rocks, the air.
Slide 16 Metagenomic Research Tierno: You get the picture. Now, this metagenomic or microbiomic research will be changing as new research occurs, but its important for you to know that it is changing. Currently, over 1000 species live in the gut. Now, this was up only about 170 at one time half of which is shared by everyone, this is about 2, 2.25 at any one time, about half are shared by everyone. So each individual actually has different flora in addition to the, by the way I have this lecture I gave it to Dr. Boylan to post in case you dont have it, I think they posted an older one before I added these slides. So thats important, but not that important. Its important for you to know there are normal flora and many microbes, far more than we ever realized that are part of the human body. In fact, it was one of the researchers at NYU, Dr. Marty Blazer, he did one cubic centimeter of skin on the arm, the underside of the arm on the right side and left side, and found common organisms but different organisms also. Thats how dynamic your flora is. It is mindboggling. The microbial world on any creature is mindboggling. Were only now revealing all of the intricacies that we didnt have the capacities before. Now as far as the human genome, the entire human genome, approximately 20,000 genes, and we are subject therefore to the proteins made by our genetics on our genome, however just using 124 people he collected genes from stool. It turns out that there are many bacterial genes and viral genes that are actually being utilized by humans. In the neighborhood of 2 million, far outweighing humanitys genome. Also university of Washington found many viruses intestinally, we found them in the lung, in the bladder, we dont know the function theres no isolation technique, only molecular methods to help us identify. 80% of these organisms were previously unknown. This is very important for you to understand. When you take a culture from someone from the oral cavity and submit it to the laboratory and say AHA! Here it is, this is whats causing the infection, heres how I can treat it, and its done, you have to understand the depth and dynamic of these organisms that are in and on us. While it is true your etiologic agent may be the predominant organism thats isolated by the laboratory and therefore youre probably right, that is the culprit and you treat accordingly, you still need to know this. Composition of gut viruses are unique to Transcribed by Sofiya Khazanovich July 24, 2014
every single individual, even identical twins. Obviously we have a lot to learn and Im telling you this upfront so you dont think you have a handle.
Slide 17 Image Tierno: Heres another way of putting it. The New York Times, for every human gene in your body there are 360 microbial genes. You have that gene, and you have 360 for every one of yours.
Slide 18 Image Tierno: That to me is breathtaking. Where are the bulk of organisms? I already talked about. They're really in two places. Anybody have an idea? Number one you know, Im talking about on people. Gut. Correct. The bulk are in the gut, I just told you this, a spoonful. I will tell you something and just to give you perspective. Most microorganisms are harmless to the body but there are overtly pathogenic organisms that can kill people. You can literally, all things being equal, in a normal individual without any pathogens present in the gut, spoon eat human feces with no deleterious effects. Thats how powerful your immune system is and how harmless most bacteria are. Dont take my word for it, dont try it. However, there are in the gut
Slide 19 Image Tierno: We discussed the 10:1 ratio. And dont worry about this chart, its just there for you to know that in various areas of the body there are different genera but this this pales in the present day because we now know that there are more organisms. I dont know if any of you ever looked at Bergeys Manual for Determinative Microbiology, we get all of the organisms that are known, its a companion I think, its 8 volumes, its a lot of organisms. So there are many more organisms that cannot be identified that would be on this list in various places. So its a wide variety of organisms, you dont have to know the names of all of them obviously.
Slide 20 Image Tierno: They vary in places of the body. For example, a gingival crevice is another place where you have the same concentration. In feces, there are 10^12 colony forming units per gram. In the gingival sulcus, there are 10^12 microorganisms or bacteria per gram. There are more grams of stool than there are of gingival sulcus material, but most of those are anaerobic. The anaerobic ratio in both the gingival crevice, thousand to one anaerobe to aerobe, and in the colon, 1000:1. Whats the number one organism of the GI tract, the feces? Not E. coli. Its really a bacteroides type organism. Bacteroides. And this, thats why its 1000:1. Bacteroides is anaerobic, E. coli is facultative. So thats the predominant. And skin has lesser amounts. But yet in different areas of the body, there are different types of organisms present.
Slide 21 Man vs. Microbe Tierno: So it is always a dynamic struggle between man vs. his microbes. And I mean man and woman and man. Its a see saw relationship every day of your life. Everything you do to your body affects the flora, whatever stuff you put on your face or in your hair or on your body, all your soaps, whatever you use, affects the flora. Keep that in mind.
Slide 22 Ubiquity of Organisms Tierno: The two main sources of microorganisms, certainly the air is but were not really worried about that as much, although its listed in the environment. So I generalized it to environment as well as humanity. There are three body sites where we display our organisms or transfer our organisms to each other. One is the oral cavity, we talk, we cough, we sneeze and that can spread organisms. Or we kiss, Transcribed by Sofiya Khazanovich July 24, 2014
thats direct transference. 80% of all infections are transmitted by direct and indirect contact. I just gave you direct, coughing talking sneezing kissing. Thats direct contact. You can understand how that can impart germs. Indirect contact is like touching a door knob, an elevator, keyboard, microphone, whatever. Thats indirectly. So 80% of all infections are transmitted that way, direct and indirect contact. The other 20% are transmitted by vector, like lets say mosquitos, ticks, or by common source like contaminated water or food, or by airborne. The true airborne is like a tuberculin organism which is less than 5 micrometers in diameter and can fall to the earth very slowly if at all. It can be sustained for quite some time with currents of air movement. Now, the normal flora of the body versus transient versus pathogenic. You know you have normal flora, you know they can be transient organisms like picking up dog doo or whatever and your hands are contaminated. Thats transient, which may or may not take hold and may or may not transfer to you dependent upon you washing your hands, very important. Then there are overtly pathogenic forms like salmonella, shingella, campylobacter. Organisms youve heard that can give rise to disease, and if you look at a virus, norovirus is the stomach flu, the vomiting diarrhea virus that can be transferred very easily to people. So after the oral cavity you have, you can spread by touching things, skin, and you can spread by passing feces that you may contain one of these pathogen organisms, youre touching the doorknob and then some people touch that and their mouth, ears, and nose, which are the conduits of entry into the body, or an open wound anywhere on your body. Thats the way organisms infect you. As far as pathogenic organisms, they have two particular properties. Most important is their virulence. Virulence is expressed in terms of invasive ability. Some organisms can invade your intact skin and these organisms are said therefore to have certain enzymes that allow them to get through layers of your body. Organisms are also said to be toxigenic. Staph aureus, toxic shock syndrome, staph aureus can give rise to a toxigenic course rather than a true infection and kill a person. Many of you are aware of tampon related toxic shock. Theres also toxic shock related to group A streptococcus pyogenes. Now, the mouth is an area that many individual researchers have been working on especially at this center, and some of the toothpastes we develop we develop because of an oral ecology. Theres a toothpaste called Colgate Total, it has something triglycan, which seems to mimic hormones and may be taken off the market, but it had the ability to prevent epiphytic growth of plaque on the teeth. Triglycan. You know how organisms adhere one to the other? Is there a star in the back? Oh, class ends, is that it? Wait, let me just finish that. So um oh you have lab? Okay, Ill finish it when you come back tomorrow.