okay guys so chapter 10 is the start of unit 3. so we only have two chapters in this unit chapters 10 and 11. so whereas the first unit we had kind of an intro to microbiology as a whole the second unit we kind of looked at how they grow reproduce things like that now we're getting into how we can control their growth how we can treat their growth and how they affect us when they do get into the bodies so starting with chapter 10 with antimicrobial treatments so something that is both good and bad kind of a double-edged sword for most of us is that we don't remember a world before antimicrobials we don't remember a world where one in three children died before the age of five due to some kind of infectious disease that now we can easily treat and then even more children than that were infected with something that managed to survive things like scarlet fever tuberculosis meningitis and ended up having these lifelong debilitations because of those and then grew up with these debilitations if they managed to survive again and then in the 1940s is when we kind of started this modern drug control this ability to kind of counteract this effect of these microbes now we certainly haven't eradicated infectious diseases and we probably never will in fact we're actually at a really kind of dangerous tipping point um known as the post-antibiotic era because most of the antibiotics we currently have have no effect on several different species of bacteria and we'll see why that is and what we're trying to do about it and what can happen if we don't get it figured out but we're kind of at this weird tipping point kind of the end of the antibiotic area at the moment so just some basics before we move on an antibiotic literally just means against life so it's something that's used to kind of fight off a living thing fight off a living microorganism these are actually commonly made by several species of aerobic bacteria and fungi and their job in those organisms is to inhibit the growth of another micro organism so for example a lot of those aerobic bacteria are found in topsoil where they will be growing and then they'll pump out this antibiotic and that process known as antibiosis and then other microbes can't come in and so they don't have to fight for food they don't have to fight for space we took those um from a couple different species we'll see here in a second and we put those to use for ourselves so i do want to know our main origins of antimicrobial drugs so we have two species or sorry two genre of bacteria and two genre of molds a type of fungus so for bacteria streptomyces and bacillus genres and then for molds it's penicillium and cephalosporium and then now we have a lot of synthetic drugs but those four species are where we kind of started this process of finding antibiotics so the goal of antimicrobial drugs seems rather simple you want to give a drug to someone that's infected that will destroy the thing making them sick but not hurt the host unfortunately that's much easier said than done because there are a lot of contradicting factors that are considered when using these drugs so before we get into what most drugs do let's look at what an ideal drug would be of course it would be easy to administer preferably something inhaled that'd be pretty easy to kind of give to a patient but it needs to be able to reach the infective agent anywhere in the body so no matter how it's taken into the body it needs to get wherever it needs to get to it also needs to be toxic to the infective agent but non-toxic to the host because of course we don't want to make ourselves even more sick and then it needs to be able to remain active as long as it's needed but be broken down and excreted from the body when its job is done so in short the perfect drug does not exist instead when we're looking at using drugs to combat some kind of microbe it's more of a balancing act you're trying to find the best one to use in that situation so another big issue with a lot of antimicrobial drugs is that they don't work well on biofilms some biofilms we've talked about before are groups of multiple bacteria living together sticking to a surface and then they start kind of making these different phenotypes they start having different characteristics than when they're free living organisms so when you use an antimicrobial drug it's really hard to affect them because you have totally different characteristics it's also hard just to get into the biofilm so penetrating that and getting deep into it to get to all the bacteria is an issue so typically the strategies we use for treating biofilms are more preventative than actual treatment but when we have a biofilm already in place we try to interrupt that quorum sensing signals that communication between the different microbes that occurs in a biofilm we also add something called dnase dnase basically works to get into those biofilms and basically break down the dna of the bacteria as they're replicating and then also again prevention is probably the best form for biofilms at the moment where we put these devices that have antibiotics on them to start with so we can stop the biofilms before they even begin growing so before we can treat a microbe in some patient we need to know three kind of big things the identity of the microbe because not all drugs work on all microbes so we need to know what type we're working with we also need to know the degree of susceptibility of that microbe or basically the sensitivity of that microbe because not all microbes at this point anyway in the antibiotic era are susceptible there are lots of um antibiotic resistant microbes so we don't want to use a drug that that microbe is known to be resistant to and then we also need to know the overall medical condition of the patient because if they're already kind of on the downhill slope or they have underlying medical conditions we want to make sure we don't use a drug that has some serious side effects that would amplify those other medical conditions now some bacteria require sensitivity testing some do not there are a couple groups right now that we know have several strains of antibiotic resistant microbes such as staphylococcus species niceria gonorrhea streptococcus pneumonia and eurococcus facilis several of those a couple more of those are kind of the big big groups for the moment so we do usually test those for drug susceptibility before we treat them because again we want to make sure we're not dealing with a resistant strain usually we don't need to test for fungal or protozoan infections as they so far have not shown much resistance so one such way that we can test for that resistance is through the kirby bower technique which is something that we have in lab so this might look familiar or will look familiar but this is basically an auger diffusion test where you grow the microbes on a auger blade basically this kind of just flat jelly-like surface where we spread the bacteria and let them grow at the same time we put these discs that have antibiotics infused into them around and so essentially the idea is if the microbes grow it means that they don't care about that antibiotic disc versus if you get this kind of ring where the microbes are not growing around that disc that's known as a zone of inhibition and that just shows that that drug was effective so it's a good way to tell us whether or not a drug is effective or not but it also tells us what drugs are more effective so for example in the top image there you can see the one farthest the bottom one farthest to the left on that top half of the image is the most effective because it has the largest zone of ambition inhibition but the antibiotic disc right above it and then two to the right of it both of those had no effect on the microbe because you can see that kind of hazy discoloration of the agar that's the growth of the growth of the bacteria even though the antibiotics are there another technique is known as the minimum inhibitory concentration or the mick test this gives us kind of more quantitative results it tells us more sensitive results essentially what we do here is we take a drug and dilute it and then microbes are added to several tubes that have basically a weaker and weaker and weaker and weaker strains or sorry weaker and weaker and weaker concentrations of the antibiotic so this is nice because it not only tells us which antibiotics are effective but it also tells us which concentrations we need to inhibit growth so it helps us determine the smallest effective dosages of a drug which is good because again some of these drugs have pretty serious side effects so the less we can use and still get the job done the better so in the bottom half of that image there basically what you're seeing is the little discs that are pink colored are ones that are still showing growth and then once they turn purple kind of bluish-colored that means the microbes have been killed off and then the ones with x's are just the first ones that have the smallest amount of bacteria growth or the dead bacteria so even if you do the susceptibility tests even if you think you have the best drug available sometimes treatments do fail usually if that antimicrobial drug fails it's due to one of the following first it could be an inability of the drug to get to the proper area of infection maybe the microbe is solely in the skin so it can't get to the skin maybe it's in the brain can't get to the brain needs and the joints can't get the joints whatever it is second it could be that there are resistant microbes in the infection that didn't make it into the sample that was collected for testing so maybe you thought you had a strain that wasn't resistant but it actually is or at least part of it is resistant third it could be an infection caused by more than one pathogen some of which are resistant or minimum it could be they're just different enough species that one drug won't be effective because again not every drug works for every microbe or for outpatient problems there's usually the highest possibility is this one that the patient didn't take the microbial correctly or sorry antimicrobial correctly either didn't take their full course that's pretty common where they stop treatment because they start to feel better so they stop taking them start taking the antibiotics and try and save them for later or something all that does is kill off the weak microbes and then they grow back stronger so if therapy then does fails usually you have to switch to a different drug do some kind of combined therapy with multiple drugs or some different method of administration could be used and that's typically only if it's that first issue inability of the drug to get to a certain area of the body so there are lots of things that play when you're trying to pick out the right drug to use how toxic the drug is how much it'll affect the host different drug interactions if the patient is on other drugs at the same time the patient history patients other health issues all these things kind of combine and make it really hard to decide sometimes what drug is necessary to treat a certain infection so a lot of times we'll use what's known as the therapeutic index or ti this is a ratio that compares the dose of drug that's toxic to humans compared to the dose of a drug that has that minimum effective dose generally what you do is you take the toxic level divide it by or put it over the minimum effective dose and the closer those two numbers are the smaller the ratio the higher likelihood that you'll have some kind of toxic drug reaction so for example in the little image at the bottom there you have two drugs one on top and one at the bottom the top one has a toxic dose of 10 over a therapeutic dose or sorry a minimum effective dose of 10 roughly those were rounded so you end up with a therapeutic index of 1 to 1 which is a pretty small number especially when you compare it to the drug underneath that has a toxic dose of 10 with a minimum effective dose of one giving it a therapeutic index of 10. so the riskier choice would be the one that's that one-to-one ratio versus the 10 to 1 on the bottom there so now we're going to look at drug interactions starting with how the drug interacts with the microbes and then later on we'll look at how the drug interacts with our human cells so when we're talking about the goals of an antimicrobial drug what we're really talking about is this term known as selective toxicity which is the ability of a drug to kill or at least inhibit the molecules of a microorganism but not vertebrate cells because we don't want them to affect host cells because we ourselves are vertebrates most antibiotics target prokaryotic cells those bacteria and our kale cells this is because there are lots of differences in the makeup of a bacterial cell compared to a human cell for example they have peptidoglycan we don't they have those 7ds ribosomes we have ads so there's a lot of quote-unquote easy targets for the drugs to go after that will for sure attack the prokaryotic invader cells and not affect our eukaryotic host cells but in other microbes like protozoa fungi and helmets those are a lot harder to kind of treat because those are also eukaryotic cells so there's a lot fewer targets that are safe to attack because it means they'll also attack our host cells and then viruses are their own kind of tricky business because remember they use the host cell machinery to reproduce so there are very few things to actually target on the virus that won't also target the host cells so when a drug gets into our system there are generally five ways or five mechanisms that that antibiotic is going to work so first you could have inhibition of cell wall synthesis this is the most common mechanism and it's usually things like penicillin our largest group of drugs usually do this where they affect the building of the cell wall of that of that microbial that we're trying to kill second is it could be inhibition of nucleic acid synthesis something that's going to target transcription or dna replication of that prokaryotic cell could be inhibition of protein synthesis which remember this is process of translation this is the second largest largest clast um usually it targets things like the 7ds ribosomes in the prokaryotic cells versus our ads ribosomes in the host cells it could also just change the cell membrane in some way that could make them weaker more susceptible easier to lyse or pop and then the last one inhibition of metabolite synthesis this basically means that it will affect those essential nutrients those things that are needed such as folic acid ion things like that so the microbe can't make it and will eventually die because of lack of it the problem with this one is usually it affects metabolite synthesis both for the microbes and for us so these ones usually have some pretty significant side effects um on top of the normal side effects so just a quick look at these so for example we said inhibition of cell wall synthesis at the top there this is just listing some of those different antibiotics that can do this i don't need you to memorize them don't worry about that then you have our two groups that can affect transcription versus translation inhibition of protein synthesis would be translation inhibition of nucleic acid replication that would affect transcription as well as replication there could have inhibition of those metabolites in the bottom right or something to kind of break down that cell membrane or that plasma membrane in the bottom center there so there of course are tons and tons and tons of different drugs that are available to use for this antimicrobial purpose we generally group them into two main groups and we'll see there's kind of a third here in a second but we generally group them into either broad spectrum drugs or neurospectrum drugs and this just determines basically how many microbes they generally affect broad spectrum drugs tend to affect more than one group of bacteria a lot of times these are detrimental because they can also kill a lot of our normal microbes that are in our body such as tetracycline which if you don't know what microbes you're working with these are good but again it also affects our normal microflora or normal microbiota narrow spectrum drugs on the other hand target a specific group so these are better in the long run as long as you know what you're trying to treat so this is something that will help you more when you get into like nursing programs health care field things like that but you could also have this as a exam question picking out a broad versus a narrow spectrum antibiotic so if i give you an image like this you can see we have five groups of prokaryotic cells the mycobacteria gram-negative gram-positive yadda-yadda ya and then in the kind of brackets we have different antimicrobial drugs and so what it's showing is the different groups that are being affected by that drug and so out of these of course the biggest broad spectrum drug is going to be those tetracyclines because you can see it spans across four it almost four complete groups of microbes versus something like those polymixins they only affect a small category of gram-negative bacteria so those would be considered a narrow spectrum so the other sort of kind of third group that i mentioned earlier are penicillins so this originally just started as one drug penicillin which was a narrow spectrum drug that really only affected a small group of gram-positive bacteria problem was it was susceptible to counter attacks by microbes because it was actually made by one of those species of fungi penicillium so it had been around for a long long long time so lots of different microbes had developed kind of defenses against penicillin since we first discovered it it's been improved over many many years many many times to kind of overcome these limitations so now penicillin itself is kind of its own group of drugs where we have several different types we have several narrow spectrums that affect different types of bacteria we also have a couple broad spectrums um things like that so we've already mentioned this but remember biofilms when microbes are in a biofilm they behave differently than when they're free living sometimes called planktonic so oftentimes they're unaffected by the same antibiotics in a biofilm versus free living mostly this is due to a lack of penetration ability they can't get in and actually attack all of the microbes but also those different expressed phenotypes and again no obvious solution yet there's the idea to interrupt that quorum sensing to disrupt communication and then also preventing biofilms is probably the best one but it doesn't work in tissues to prevent a biofilm because you can't just constantly be taking antibiotics so things like middle ear infections that are caused by biofilms we don't really have a way to kind of prevent those in this instance so now moving on to some of those eukaryotic organisms that are difficult to treat starting with fungal infections so these are eukaryotic cells so again they have their own special problems when we're talking about antimicrobial or chemotherapy because most drugs are designed for bacteria and those are all ineffective against eukaryotic cells on top of that fungal cells are very similar to human cells so a lot of drugs that are toxic to fungus are also toxic to us currently there are very few anti-fungal agents right now there are really just four main groups that are listed below and that's kind of what we run with for the moment protozoa infections um so we have two big groups of these because malaria is such a huge worldwide issue not so much here in the u.s but such a huge issue worldwide we have a whole group dedicated to malaria and then we have other protozoan infections so anti-anti-malarial drugs these are again we have a couple different ones but for the most part we actually use what's known as artemisian combination therapy or act which is multiples of these drugs at least two of these drugs used at the same time and this is because there are actually several different species of plasmodium that can cause malaria in addition they also have several life cycle stages and there's no single drug that's effective for all of those species and all of those life cycles so we usually use a combination if someone does get malaria and then for those other protozoan infections there's a big variety we'll just use kind of look at one because we don't really care but the most widely used one is an amoeba side which remember amoebas are just a specific type of protozoa but these are typically ones that cause hepatic and intestinal infections and our final eukaryotic group are those helminths remember the worms these are especially challenging mostly because they're larger parasites and their cells are very similar to our own more so than even fungus or protozoan cells another big issue is that blocking reproduction like stopping more eggs from being produced has no effect on adult worms so the most effective drugs that we have have to immobilize disintegrate or break down and then inhibit the metabolism of all stages of the helmet thick life cycle so the eggs larva and then the adult species again a couple different groups of drugs for this one mostly based on what type of helmet you're looking at for example we have some broad spectrum roundworm drugs we have some specifically for tapeworm and fluke infections and then we also have one that specifically used was was specifically used as a veterinary drug but now we use it in humans for nematodes against two diseases specifically stronghold diocese and onco uh on cocercosis sorry more commonly called river blindness and then last but certainly not least viral infections remember these are acellular so these are not prokaryotes these are not eukaryotes but they do present their own unique challenges because mostly they use our host cell to do all of those functions like reproduction and metabolic functions so if we disrupt the virus metabolism it means we most likely are going to disrupt our own host cell metabolism as well the good thing is that vaccines have helped significantly for several diseases including polio measles mumps or bella smallpox all of those but there are still several viral infections that we need to get some kind of prevention for such as aids influenza common cold even right now we have flu vaccines right for influenza but some of you especially in the past two or three years if you've had a flu vaccine you've probably still gotten it because they just weren't very effective because there are so many strains of the flu vaccine and they have to make it so early that sometimes they guess wrong on which strains will be kind of most common but when we are able to treat a viral infection typically those antivirals are going to target very specific points in the infection cycle for those viruses they will either block penetration of the virus so stop it from getting into the host cell to start with they will block transcription or translation of the viral molecules specifically or they'll prevent maturation of those viral particles and again it's important to have these treatments but we really don't have very many treatments actually most of our kind of fighting viruses has been through vaccines but even those are not very common right now we really only have treatments for hiv hepatitis b and c and then herpes virus those are the ones that we routinely treat we also have treatments for influenza but they're not really effective so a lot of times people don't even know they exist so the positives of using antimicrobials is that they do tend to treat a lot of microbial infections but the downside of using antimicrobials is a lot of microbes have adapted to these by developing drug resistance drug resistance is just when a microbe begins to tolerate at least a certain amount of a drug that normally would be inhibitory for that microbe for example resistance to penicillin developed in some bacteria as early as 1940. now that's not as impressive until you hear that penicillin was discovered in 1940 so you can see this is a very quick process as soon as we kind of discovered antibiotics we started discovering hey they don't always work by the 1890s and the 1880s we started seeing large scale treatment failures so drug resistance comes about either through genetic versatility basically the ability of microbes to adapt their entire populations to a drug it could be some kind of intrinsic nature of a microbe intrinsic nature just means that resistance is a fixed trait of that microbe basically it's not something that would normally harm that microbe for example all microbes are intrinsically resistant to antibiotics that they produce themselves for example penicillium species they're not affected by penicillin by itself because they make it so of course they're not going to make something that would hurt themselves or they could get drug resistance through acquisition of resistance this is the one that we'll focus on mostly because it's kind of the scary for scariest for us at the moment so how does drug resistance develop contrary to popular belief antibiotic resistance is actually an ancient phenomenon and it doesn't always occur solely due to drug exposure that has certainly helped matters or i guess and when we're talking about us it's made matters much worse but for microbes it's helped them but it's not always needed for example in 2012 they opened up a cave in mexico that had been cut off from the surface for millions of years and they found several species of bacteria inside the cave 93 of those species had actually developed resistance to several antibiotics that we currently had on the market which seems kind of weird you're like how would they get antibiotic resistance if they'd never been exposed to antibiotics well that's because they had been exposed to antibiotics remember the first antibiotics that we discovered were made naturally by two groups of fungi and two groups of bacteria so resistance those antibiotics was a survival strategy for the microbes that was needed way before humans ever discovered them so when we're looking at acquisition of resistance microbes are going to become newly resistant to a drug after one of two events either a spontaneous mutation in some critical chromosome that's going to give them resistance to that antibiotic or acquisition of entirely new genes through some kind of horizontal gene transfer remember those conjugation transformation transduction that will never go away so let's first look at that spontaneous mutation um this is pretty rare remember most mutations are harmful or at the very least neutral very few actually give a benefit to the microbe so a lot of the times just getting a mutation in general is pretty rare event on top of that not only do you get some kind of random mutation but the chance of it giving resistance to a specific drug is even more rare but every once while this does happen solely because of the huge numbers of bacteria in populations and the amount of bacteria on the planet at any given time the end result of these spontaneous mutations varies it could be something just like a slight change in sensitivity where maybe you need a larger dose of a drug or a longer dose of a drug all the way to complete loss of sensitivity where they're completely resistant resistance through horizontal gene transfer though this is much more common generally this originates from plasmids called resistance factors through conjugation transformation or transduction basically these traits because of this horizontal gene transfer are termed line and weight basically that just means that they're basically just available and any opportunity that comes around those resistance factors can be passed to an entirely new species and then give that new species that ability to be resistant on top of that a lot of species have those transposons these are basically called jumping genes where the resistance traits on them are passed between new species as well as stain in the old species a lot of times when you have conjugation transformation transduction the new microbe gets that resistance but the old one doesn't so sometimes you actually lose resistance not often but sometimes with transposon with transposons sorry they all get resistance we've also very recently discovered these groups of microbes called persisters this is essentially a phenotypic trait or a physical trait not something in their chromosomes not something in their genetic makeup where some microbes have the ability to essentially go to sleep when exposed to a drug until the concentration diminishes and then they can wake up this shuts down their metabolism which means the drug isn't able to work if it doesn't have access to the working parts it's not going to be able to do its job this is one of those phenotypic differences that we see in a lot of biofilms compared to their free living counterparts and so in the image in the bottom there you can see the red or those persist persister populations versus the blue or sensitive populations when you have a group of microbes like to the far left you start treating them with antibiotics most of the sensitive population or all the sensitive population will get killed off but those persisters are able to hang out until the antibiotic is gone then they go through basically essentially resurrection which is called recirculation so basically they can just keep growing and then they can cause other microbes to come back in start replicating doing all this kind of over again we've also recently found several species of fungi that can become resistant whenever they need and these are due to small regulatory rna pieces called interfering rna or rna i that can basically temporarily bind to a genetic sequence when they bind to that this gene is silenced and they typically do this to a gene that job is to make a certain protein the protein in this case is the one that's going to be the target of the antibiotic so when it's silenced when it has this rna i bound to it the antibiotic doesn't work anymore because it no longer has a target which means that fungus is now temporarily resistant to the drug then once the antibiotic is gone or the concentration is low enough the silencing is reversed and the gene starts producing its protein again as normal so this is known as an epi mutation and an epigenetic event where the epi mutation is the actual silencing of the gene and the epigenetic event is the entire mechanism where they can silence and then unsilence the gene as needed so when a microbe does get drug resistance there are typically five mechanisms and again these are different five mechanisms on how that microbe is now drug resistant so our previous five mechanisms were how drug actually worked these are how the micro becomes resistant to that drug so the first is that it could start producing new enzymes that make the drug inactive typically this occurs through acquisition of new genes through that horizontal transfer it could reduce permeability or uptake of the drug into the bacterium this usually is a mutation not so much horizontal gene transfer it could be that the drug is immediate immediately eliminated from the cell could be that it gets in but then the cell immediately pumps it back out usually this is acquisition of new genes maybe binding sites for the drug are decreased in overall number or the affinity of those binding sites is lowered so the drug isn't taken up as easily this can be either or it could be due to mutation or it could be due to that horizontal gene transfer that acquisition of new genes and then finally it could be that one of the metabolic pathway pathways that's affected is either shut down and then in an alternative pathway is used instead so basically if it affects some form of pathway that keeps the cell alive it'll just use a different pathway or just shut that pathway down if it's not vital typically this occurs via mutation specifically a mutation that alters the original enzymes in the cell so so far we've seen how drug resistance occurs at the cellular or molecular level how one cell can become drug resistance but really in terms of human health the problem with drug resistance is at a population level it's entire groups of microbes so let's see how we go from one cell being resistant to an entire species that can become resistant so i actually stole this image from the cdc naughty naughty but it's fine on how antibiotic resistance happens so starting off you have lots of germs and some of them could be resistant to antibiotics in this case in step one there the ones that are resistant are in orange the ones that are not are in blue step two occurs when you introduce antibiotics you kill the bacteria that are causing the illness but you can also kill good bacteria protecting the body from infection you basically kill any microbe that's affected by that drug so you can see in this case all of the blue microbes are gone but those ones that were resistant and orange are still there then in step three those antibiotic resistant bacteria now that they have all kinds of space all kind of food they are going to grow up crazy big and strong and then you usually have an entire population of just antibiotic resistant microbes there may be some like the one little blue guy hanging in there but most of them are going to be that antibiotic resistant and then step four is where we're at currently that's kind of the scariest for us is that then some of those antibiotic resistant microbes can pass that resistance onto other bacteria sometimes completely different species causing more problems where that's where we can see that horizontal gene transfer that jumping from species to species so now we start to get into kind of where we're at currently in the antibiotic era and basically that is we are in a bad state so the cdc issued a threat report for the first time in 2013 and they continue to monitor and update the situation um as needed by that i mean all the time because they are currently calling this a potentially catastrophic event it's now predicted that antibiotic resistant deaths will surpass those from cancer by 2050 if something doesn't change very very quickly and this is not a solely united states problem this is a world problem this is a global problem so much so that the united nations actually scheduled a general assembly in 2016 to specifically look at the issue of antibiotic resistance this is actually only one of four times in history of the u.n that a meeting like this has been called due to a health issue the previous ones were due to hiv ebola and non-communicable diseases like uh i just lost what i was going to say it doesn't matter but this is the first time that we're looking at ones based on treating several diseases so the antibiotic era started about 80 years ago really not even that far and the problem with coming up with antibiotics is that we were so confident that they would work and that they would be permanent that we forgot really what the world was like before antibiotics and unfortunately we're at a stage now where it's very likely if something doesn't happen quickly that we're going to go back to that world prior to antibiotics where things like pneumonia had 50 fatality rates where strep throat could kill overnight where infected wounds regularly led to death or minimum amputated limbs so it is a kind of a scary world that we're looking at for a number of reasons but antibiotic resistance is just one of many right now especially in 2020 it seems like we got a lot going on luckily there are several groups working towards this and several large groups for example the world health organization who they started campaign campaigning to combat antibiotic resistance in 2015 um just because of how urgent the situation is so we do have groups working on this so hopefully something will come about so the biggest problem with new effective antibiotics is that they're very slow to come to market one of the biggest reasons unfortunately is just economics coming up with antibiotics that fight short term diseases things like strep throat things like you know flu things like that they're not as lucrative for drug companies they're not going to give as much profit for drug companies compared to drugs that treat long-term or chronic diseases because those are usually taken for a patient's entire life but coming up with short-term versus long-term term drugs are both equally time consuming and equally expensive to develop so they are always going to choose the ones if given the option that treat long-term chronic conditions which leaves us kind of this lull that no one's really as far as drum companies go no one is really researching short-term courses for antibiotics we do have some policy makers that are kind of creating incentives for drug companies to focus on the short-term antibiotics but a lot of this currently is coming out of schools and universities that are studying these themselves which again is very expensive and very time consuming so we said that there are several groups of resistant microbes already so much so that the cdc actually issued three different levels of resistance starting with urgent threats that are the most serious then we have serious threats and then concerning threats the problem with these again is it just takes one horizontal gene transfer and then we can jump these threats up or get new species added in anywhere in here so right now we have three urgent threats these are the worst ones if you're in healthcare already you've probably heard of these c diff cre and then super clap or gonorrhea that is drug resistant but then we have several that are kind of working their way up 12 serious threats three concerning threats and so this certainly is a worldwide problem but we do see issues with this in the us as well for example two million people a year are infected with some kind of resistant bacteria at least 23 000 of them will typically end in death that's a lot of people right especially in supposedly a world power right then on top of that in the fall of 2015 which was five years ago now a bacteria was found in china that had a gene mcr-1 this is a gene that gives resistance to polymixin polymixing is known as the last resort drug for most of those resistant diseases and again the issue with this is that it can easily jump unfortunately this has since been found in humans and animals in the us and if it continues to spread without some new way of coming about to treat resistant bacteria there's a serious possibility that infections will spread that can no longer be treated with any drug which is frankly terrifying so luckily there are several new approaches to antimicrobial therapy some of which are more promising than others so we'll look at those now hopefully a little positive to lighten the mood starting with rna interference so this is where we take small pieces of rna that are used to regulate gene expression and we use them against microbes currently they're being used to try and shut down the metabolism of pathogenic microbes if they go back sit on that dna means they can't go through a transcription translation they can't do what they're trying to do there are several inhuman trials already specifically for hepatitis c and a respiratory virus but they're working on more currently in lab work still that are hopefully going to be in human trials for a couple other diseases in the next year or two the second new approach is defense peptides so a peptide is a teeny tiny little protein chain typically 20 to 50 amino acids long that naturally occurs in all mammals this is actually part of our innate immune system and it's used to fight off bacteria these little guys that go around pow-pow these little bacterial cells we've also found some bacteria to have these as well that specifically fight off viruses so we've basically taken those out of mammals to fight bacteria and taking some out of bacteria to fight viruses and we're trying to use them to fight off infections some of which are actually out already if you've ever heard of fusion this is actually a drug that's currently used to fight hiv and it's a peptide that fights off the fusion of the hiv virus to human cells and this was pulled out of a bacterial cell and now it's used as a drug so some good possibilities here we also have crispr and then drugs from non-cultivable bacteria crispr is probably our most significant discovery in terms of what it can do but it's problem is that there's legal battles with it right now on who discovered it um so who has property rights to it who can use it so it's kind of stuck in this like lawsuit thing where it's not actually doing a lot of good but once it gets out of that it's going to be huge so this is basically a system that was found in bacteria that allows the bacteria to make very specific cuts in genes like can go down between between two two nucleotides and cut exactly where it wants to and in bacteria this was normally used to fight off viruses but now we've turned it into a genetic tool where we can cut out genes wherever we want and put in new genes wherever we want one just one use of that is that we could cut out genes that are giving bacteria resistance but we've also used it for things like kind of ridiculous things for example we've used it in pigskin we've cut out the things that make it quote-unquote pig skin and then we've used that skin that was grown on the pigs and we took out all the pig genes from it and then we can use that skin that's harvested as skin for like burn patients and things like that we've also used it for stupid things like if you've ever seen the little glowfish in like petsmart or something the ones that you put the black light on they're like neon pink neon green all that that was through not specifically crispr but genetic engineering where we put a glow gene in these fish that didn't normally have it um so it's actually very cool the different things that we can do huge possibilities here again we just need to get through the legal right then drugs from non-cultivable bacteria um so most bacteria in the world can't be grown in a lab in fact 99 of bacteria can't be grown in the lab the possibility then on what we could find if we could grow those bacteria in a lab is huge remember our first four groups of antibiotics were found from bacteria and fungi in a lab so if we could grow all these bacteria that we haven't seen who knows what we'll find in fact a group of scientists in massachusetts actually created this special chamber that allowed them to grow a specific form of bacteria specific species of bacteria and they discovered texobactin which is an antibiotic that was has so far not been how do i wear this hasn't been able to have any resistance from it or if it is the resistance that bacteria are growing seems very very slow so so far it seems kind of like the new super antibiotic if we get it out into actual human trials right now it's still in the lab work and then last but not least bacteriophages um so these are not really a new approach to an antimicrobial therapy but more a renewed approach um because we actually discovered these before antibiotics so in the 1930s early 1940s in the former soviet union patients were actually being treated for bacterial infections with mixtures of bacteriophages remember those are viruses that specifically attack bacteria and so they were doing mixtures of these basically these little viruses to attack the bacteria that were causing the illness now when we discovered antibiotics again we were so confident that they were working research pretty much just like got thrown out the window with these but now with so much resistance it's been picked back up currently there are several human trials the largest currently with pseudomonas aeruginosa which is pretty common to cause ear infections by making biofilms which makes them even harder to treat we also see several instances that are currently used for example a lot of wound dressings are pre-treated with bacteriophages that are used to basically fight off any incoming bacteria that would infect the wound we also see it used in food processing facilities and places like that to decontaminate food as well as to treat salmonella on like poultry and things like that so there's a huge benefit to bacteriophages specifically because the specificity of the virus is so small it will only attack that one type of bacteria so these are really nice because we automatically know they won't affect our host cells and something else that we're seeing is having big effects not as not so much for treating but more preventative our probiotics and prebiotics so probiotics are preparations of live microbes that are fed to both animals and humans to improve intestinal microbes or intestinal microflora microbiota these are nice because they can replace microbes that were lost during like antimicrobial therapy if you were given like a broad spectrum antibiotic to fight something it will replace those good microbes you can also just augment the microbes that are already there nice thing about these is they're safe and effective it's all good bacteria it's really nice for managing food allergies a lot of times sometimes people develop allergies to food because they their gut flora is mixed up they don't have the proper microbes that they should versus when you get the proper microbes that food can be broken down and it doesn't hurt you anymore or at least the reaction is slowed down now once you have severe food allergies i'm not saying like if you have a peanut allergy you can eat some yogurt and you're good right nobody do that kabosh that idea but sometimes it can lessen those kind of less severe reactions especially if it first gets started and then prebiotics are basically nutrients that encourage the growth of those good microbes those beneficial microbes so a lot of things like fructans a type of sugar found in a lot of fruits those encourage things like bifidobacterium in the large intestines which grows up really big and strong and kind of fights off a lot of pathogenic growth we find these in a lot of kind of healthy foods things like garlic jicama tomatoes leeks things like that but you can also buy like packages of prebiotics so much so you can even get it like to sprinkle in water and drink it type thing but these are really nice because if the good bacteria is there there's less food less space for those bad microbes so even if they get in they have a harder time kind of growing up digging strong and making you sick all right and then the last tidbit i want to look at are interactions between the drug and the actual host organism now so roughly five percent of patients that take some kind of antimicrobial experience some kind of adverse reaction there are several groups of side effects but most of them fall into one of three categories either direct damage to the tissues of the host through toxicity from the drug could be an allergic reaction or could be disruption in the balance of normal microbiota the normal microbes that live in the system some of these are short-term and reversible some of them are permanent and they can range from you know mild cosmetic reactions like a rash hives things like that to lethal reactions like anaphylactic shock so first looking at toxicity to organs so there are obviously lots of organs in the human body but typically the ones that are most commonly affected are things like the liver the kidneys the gastrointestinal tract cardiovascular system nervous system respiratory skin teeth and bones which yes is pretty much all of them so that's fun moving on to allergic reactions these typically occur because the drug acts as an antigen in the host body an antigen is just some kind of foreign material that is going to stimulate the host's immune system this is going to provoke a response it could be either from the entire drug or substances made by the breakdown of the drug very common with several drugs but the most common are penicillin and sulfonamides allergic reactions then are kind of strange because typically the first encounter doesn't really have a reaction so a lot of times the patient doesn't know they're allergic to something the first time around but then after the first encounter with a drug the patient becomes sensitized which means the body's now looking for that drug again looking to react then when they encounter the drug a second time that's when the body is going to produce a reaction such as hives respiratory inflammation sometimes anaphylaxis anaphylaxis if you don't know is kind of an overwhelming allergic response that occurs very very rapidly and it can be fatal because it can actually close airways basically just cause the body to go into shock and then looking at the possibility of suppression or alteration of that microbiota so your normal microbes are could be called your biota your microbiota your flora your microflora whatever you want to call it the normal microbes in your body typically kind of cover every body surface both internally and externally most of these are harmless at a minimum some of them are beneficial like the ones that produce vitamin k to help us with blood clots or break down food that we normally wouldn't be able to eat every once in a while though there are a few pathogens in there the problem with this is that when you do get sick if you are given a broad spectrum antibiotic remember they just attack pretty much any microbe that they can including your normal healthy microbes when we do that we leave our body open to super infections super infections are where microbes that were once small in number like those few pathogens that were possibly hanging out can now overgrow because they have tons of space tons of food and they just kind of go crazy there are tons of examples of super infections the two most common though are utis caused by the treatment of e coli so for example lactobacilli are normally found in the vagina but can be killed by the broad spectrum antibiotic cephalosporin when those are killed you also typically have candida albicans in the vagina that starts to overgrow and it can cause a yeast infection infection or can cause oral thrush neither of which are pleasant you can also have antibiotic associated colitis this is where again you take a broad spectrum antibiotic kills off your normal flora this time in the colon the problem with the colon is that sometimes you have clostridium difficile hanging out in the intestinal lining when all the other stuff dies off clostridium difficile can actually kind of go to sleep it's one of those kind of persisters one of those ones that can produce endospores and just kind of go into hiding until the mic until the antibiotics are gone and the microbe can start growing again when it does it grows up thick and strong because it has tons of space tons of food on top of that it releases toxins that can cause things like fever diarrhea abdominal pain this is what causes c diff all right and then last but not least i want to briefly talk about how we got to this point where we are almost to this post-antibiotic era where we're almost to the point that antibiotics are no longer a thing the biggest issue is that we have a worldwide problem of drug management antibiotics are typically seen as a cure-all from anything from a cold to acne most often the drugs actually have no effect or sometimes are even harmful for whatever they're being taken for and this is again not just a u.s problem but looking just at the u.s here for a second there are nearly 200 million prescriptions written in the u.s for antimicrobials every single year 75 of those are pharyngeal sinus lung or upper respiratory infections that are viral in origin now remember antibiotics attack prokaryotic cells viruses are not prokaryotic so they're taking these drugs that have nothing to do with the actual disease all it's doing is killing off their normal microflora and not actually killing the virus on top of that for a long time doctors used what's known as the shotgun approach using broad spectrum antimicrobials for minor infections instead of wasting time and energy doing tests they were just like meh take a broad spectrum antibiotic you know come back if you still feel sick the problem with this is it led to super infections and other adverse reactions it also caused the development of a lot of resistance in what's known as bystander microbes microbes that weren't really causing an issue but they were in the body so when you again expose them to that drug there's a chance that they could become resistant luckily there is growing awareness for this so there's a big reduction of this practice but you still have a lot of old school doctors doing this and a lot of doctors in other countries doing this that maybe aren't as informed and then another huge issue is that tons of these drugs are actually leaving the u.s to countries that don't have as strict kind of control on their antibiotics for example it's very common for individuals in latin america and asia to self-medicate with antibiotics they can actually walk into any pharmacy like a walgreens or a cvs and get an over-the-counter antibiotic they don't need prescriptions in fact when i went to mexico last year one of my friends that was on trip with us she bought like a big bag of antibiotics and brought them back to the u.s because they were cheaper and she didn't need a prescription for them even though i yelled at her she did it anyway but when it's used in this way again drugs are largely ineffectual and it leads to drug resistance because you don't know what you're treating it could be viral in which case you're doing nothing so this is really important and the reason we kind of harp on this for you guys is a lot of you are headed into the healthcare field and you should be aware of both positive and negative effects of these antimicrobials but otherwise that's it for chapter 10.