MHAAM Lecture: Johannes Krause on Ancient Pathogen Genomes

research center for the archeo science of the ancient Mediterranean pronounced in Germany as mom and the United States as mmm or sometimes mayhem and under the aegis at Harvard of the initiative for the science of the human past and with the support of the departments of human evolutionary biology and the Standing Committee on archeology our overall project aims to bring together the power of the advance sciences and the questions and inspirations of the humanities and the social sciences to illuminate the human past and the microbial past in which our present is whether we wish to acknowledge it or not so deeply embedded in its initial research program the new Research Center between Max Planck and Harvard is focusing on one hand on reconstructing ancient migrations in the Mediterranean the peopling of the Mediterranean Basin from the genetics of the ancient DNA of those people and on the other and reconstructing and studying ancient pathogens and their evolution and the historical impact in our inaugural meeting in LA at last October at which some of you were happy enough to be present lucky enough to be present we heard a lot about ancient genetics we heard the first genetic evidence about cultural groups who have been archaeologically identified as Mycenaeans and Minoans we heard about one of our favorites Yersinia pestis and more today we focus on ancient pathogens and on another ancient pattern pathogen tonight is a special occasion in the life of our project for this presentation offers the early fruits of a human collaboration between our Harvard scholars our Max Planck scholars and scientists and scholars from other institutions as well it offers the very practical fruits of this unprecedented collaboration across the ocean and across the borders on our own continent the devastating impact of the invasion of European life forms on the naive populations of the Amer cos are well-known in a general way and some of the terrible later outbreaks for instance of smallpox in these regions are historically well documented but much remains completely unknown or controversial because historical accounts are incomplete misleading or ambiguous the new archaeological science is now identifying ancient molecules of specific pathogens and assessing their impact this is essential to reconstructing what really happened at various moments in the Columbian encounter and to weighing its historical consequences these terrible events were tragic beyond tragedy for those who experienced them and obviously of grave importance for historians and archeologists I would say even for citizens for they continue to affect in some way direct or indirect those of us who live in the societies that have emerged from this historical and biological crucible but it is also of import for the modern-day life sciences and I hope we'll hear more about that as we go forward evolution is not something that started with the rise of microbiology the pathogens that afflict us today continue constantly to evolve in the unending war between old drugs and new bugs many things many think that the bugs are beginning to get the upper hand in that context it is a more than historical interest to identify and understand the genomic details of the past pathogens how did they get to be the way they were and how do they differ from what they are today what lessons does past evolution of pathogens hold for their future evolution and forms and for our future medical responses tonight we'll hear from my co-director of the German end of our magnificent new transatlantic collaboration my treasured friend and colleague professor johannes causa founding director of the Max Planck Institute for the science of human history at Jana who needs little introduction to most people in this room because this is the fourth time in fort months that I've had the honor and pleasure of opening a talk by him to open the discussion we will be privileged after Johannes has made his presentation to have from this side of the river a member of the steering committee of the initiative for the science of the human past the land and clay professor of scientific archaeology Noreen shiraz from across the river we are thrilled to have dr. ed Ryan director of global infectious disease harvard school of public use but at MGH professor of Medicine got too many titles here HMS professor of human ology and infectious diseases Harvard School of Public Health who works on enteric infections cholera typhoid fever particularly in Bangladesh we're no less thrilled to see so many distinguished colleagues from the medical school and from the School of Public Health and we know that your presence here will nourish some wonderful questions and subsequent discussion not just in this room but in the hours when we hope the days and weeks and months that lie ahead as always we'll conclude with a short reception where our conversation can continue but with no further ado let's hear from the main act professor johannes causa who will be talking to us tonight about death by contact ancient pathogen genomes from epidemics in early mexico please welcome Johannes just five seconds for setup here work mr. microphone working can you hear me in the back okay wonderful so first of all I would like to thank Mike for the invitation to speak again here kind of a constant visitor here themes I'm very excited to be here this is work today that I'm presenting which is actually not so much part of the max planck hobbit research center for the ocular signs of the angel Mediterranean but it's actually a collaboration which we already started before we actually initiated that Center I'm together with marine - Russ who will speak to you also after which is a project where we wanted to study and find out more about the pathogens that were present in the 16th century in Mexico that caused some of those traumatic epidemics that diminish the Native American population in this part of the world as many of you know and before I talk about this results and this investigation I would like to introduce you to our Institute because that is an institute which we just inaugurated also just a few years ago in 2015 in fact which is an interdisciplinary Institute that nicely shows how different disciplines from the bio archeology are actually working together it's an institute that has I guess that does work on this surface so we have three different departments archaeology linguistics in archaea genetics that work together there in the interdisciplinary approach to look at the signs of the human history similar to the signs of human past initiative here which basically means in our case that we are using scientific approaches to classical questions that you might have from archeology or history which often involves the Natural Sciences something like genetics proteomics isotopes to address questions and that can be for example mobilities to settlement history from the past using genomics or isotope work for example and we're also looking at climate ancient environmental change so how do humans for example get affected by environmental change in how humans for example also changed of course the environment over time looking at sediment cores for example ice cores and we're also doing a lot of work on human modification with the ecosystem so we have a research group that is quite interested in how humans for example modified the rainforests over the last ten thousand years for a lot of people it's not quite clear that the rainforests have actually been affected by human activity over a very long time period or modified also by humans using again genomics as well as very carbon dating we have Department linguistics and cultural evolution that has a strong focus on language diversification and the history of languages and how language is evolved and diverged from each other so they're using actually tools that come from bioinformatics from Philo genetics and apply them to languages through computational linguistics by for example reconstructing then family trees with languages like the indo-european languages trying to find out when for example was the common ancestor of all indo-european languages or Austronesian languages and doing similar things also for cultural evolution we have a strong focus also on the coevolution of genes and culture so how did basically culture influence genes say practices subsistence strategies such as agriculture for example then lactase persistence spreading within a population and then that will be the focus today of my presentation as we are also interested in the spread and diversification of human associated microbes which can be basically the microbiome so microbes that live in you and on you but also in fact just diseases which are killing you at the end so if we talk about infectious diseases we have to actually go not too far back into human evolution so the history of most infectious diseases is starting sometime we think in the early Neolithic so about eight to ten thousand years ago when humans started to settle down so humans kind of kind of basically changed the subsistence strategy from hunting and gathering to agriculture with that came basically a type of living in settlements which caused them to settle down and this kind of larger population sizes that came out of that then caused basically very good breeding conditions for pathogens to emerge within the human population and what also happened is that humans started to domesticate animals and it is thought today that from those domesticated animals many pathogens actually then moved into the human population that's a process which is called zoonosis and there are many examples of that such as measles smallpox flu tuberculosis plague leprosy or pertussis where today we find the closest relatives of those human diseases or pathogens that are found in the human population in those domestic animals for example then when the human populations grew in size so large civilizations emerged those pathogens found even better breeding conditions and they caused massive outbreaks so that caused epidemics on a larger scale continental wide scale for example that we then called pandemics so large outbreaks which are done also found in historical records some of them I'm listing here where for example the first and kind of earliest records we have are coming actually from ancient Greece from the 5th century BC that was the so-called plague of Athens which was a major outbreak that happened during the Peloponnese war actually killed the king of Athens at the time Pericles it's not really clear what pathogen cost this plague of Athens thought it could have been measles based on the historical accounts but we don't really know for sure and then there's two large outbreaks of pandemics that happened in the Roman Empire so the Antonine plague as well as the Justinian egg plague the Antonine plague some people think has actually stopped the expansion of the Roman Empire so again had a strong impact on human history and the justinian ik plague which mike is actually an expert on in the 6th century ended maybe the Roman Empire was one of the reasons that ended the Roman Empire it certainly marks the transition from antiquity to the Dark Age the medieval time and that is one of the few then dynamics that we know from ancient history where we actually know what was the culprit we actually know what pathogen costs it likely that was a senior pastors causing bubonic plague because we've actually done genetic research on that quite actively over the last few years and then there's two more that I would like to mention one is the Black Death which is probably the biggest pandemic that we know of human history they killed about half of the European population in the middle of the 14th century again they're based on genetic research but partially also historical research we have no good understanding what pathogen caused the Black Death that was again your senior pestis causing you bubonic plague pandemic and then a pandemic which is actually not over yet so some people say it's still ongoing which is the white plague that started in the 16th century which is basically tuberculosis spreading within the human population starting in Eurasia and then also spreading into other continents which is caused by tuberculosis or Mycobacterium tuberculosis except of tuberculosis many of those pathogens that might be involved here bubonic plague we have leprosy measles smallpox especially small pox which is actually Radek ated sound a bit like something from the past and you might actually think that infectious diseases are more something from back in time in history and not so much more a topic of modern day medical research and this is actually what also a lot of researchers thought in the mid of the 20th century is in the mid of the 20th century there were many medical researchers that were actually thinking based on vaccination programs based on antibiotics that were developed that by the end of the 20th century we will not have infectious diseases anymore within the human population of course today we know that this was not true you know that things have actually gotten pretty bad and grim because we actually see new pathogens emerging since the 1980s just partially due to the globalized world partially also due to antibiotic resistance that some of the infectious diseases are actually coming back so we have newly emerging infectious diseases many of them you of course know HIV Beulah hunt as ours and so forth but we also have this antibiotic resistant bacteria like multi drug-resistant tuberculosis for example which are becoming more and more a problem in the health sector so infectious diseases therefore are still very much in the focus of a lot of medical research when I started to work in this topic I actually noticed however that even though it's a very hot and widely debated and important topic we know surprisingly little about the evolution of pathogens so we know little about evolutionary rate so mutation rate so how fast do pathogens change over time so how fast do the accumulate mutations for example we also know surprisingly little about host-pathogen interactions so how does the animal pathogen that was a pathogen in cows or pigs or dogs become a human pathogen so what what has to happen to this to this pathogen and surprisingly also we don't know so much about what pathogens cause epidemics and pandemics in the past right we don't often know what was actually the causative agent of a past pandemic and the reason why we know so little about that is largely because if you want to study evolution you usually have to look at fossils right so if I want to study the evolution of humans I can look at Neanderthals or Homo erectus or australopithecines if I want to look at the evolution of elephants I can look at mammoths or some other type of purpose idiom but if you want to study bacterial evolution you don't really have fossils from the past if you have a fossilized bacterium it's just a round shape in a piece of stone or something like that it's not really something that tells you something about the kind of larger biology of past bacteria and this is when we then started this new field of research that we call ancient paths Genomics so we are basically creating a molecular fossils from ancient pathogens by going back in time taking skeletons from the past and extracting the DNA of pathogens from those ancient skeletons and this is something then we do in our department for your genetics where we work with bones in clean rooms where we dress up with protective clothes to avoid contaminating those ancient bones that we're analyzing with our own DNA and we get this DNA out of those bones by just drilling in little holes that can be into bones that can also be into teeth depending what type of DNA that you're looking for so if you're looking at the DNA from the individual itself from whatever the human or the mammoth or the bear that you're interested in you would just look at the bone if you want to study the pathogens we're actually not looking at bones but we're looking at teeth because teeth often still have dried blood inside and then the dry blood you would find the black borne pathogens if you want to study the oral microbiome you might look into dental calculus which is still stuck on the teeth so it really depends what type of DNA you're interested in that depends then which material you're sampling and then from those basically little bone powder that you might drill out from those ancient bones to extract the DNA simple DNA extraction protocols and then it gets turned into DNA which can be manipulated sequenced as you will later on see also captured or enriched for the type of DNA that you're interested in and then at the very end that DNA gets sequence and those wonderful modern sequencing machines which as many of you know have kind of tremendously improved over the last decade or so so the throughput of those machines has increased by 100 million fold in just about 12 years right which allows now human genomes to be produced for several hundred dollars which 15 years ago was two billion dollars for the first human genome so it's really amazing how this throughput um has increased and it's very useful also for our ancient DNA because the sequencing length that comes out of this machines is actually perfect for our DNA that comes from the ancient fossils because DNA after thousands of years is broken into small pieces and those machines can only sequence short DNA molecules but fast that's not a problem because our DNA is already short but by then extracting the DNA from those ancient bones we can then get those ancient pathogen genomes and that then really gives some sort of molecular fossil record for ancient pathogens so we can really look how did certain pathogens certain bacteria or viruses look 500 years ago five thousand years ago fifteen thousand years ago we can look at long time mutation rates so we can directly calculate the mutation rate of the pathogen because we have a radiocarbon date of this pathogen so we know how it looked like a thousand years ago we know how it looks like today we can measure the number of mutations that happened in a thousand years which is something that's very difficult to do if you just look at modern bacteria for example we can look at host-pathogen interactions through time so we can see how did the pathogen change whether certain mutations that had to happen that it kind of adapted for example to new hosts or that virulence factors actually emerged so this is something that we've specially done a lot for a senior pestis which was the main focus of our research over the last few years and then of course we can give some very interesting information to the archaeologists the historians we can learn what type of pathogens were actually present in the past that cost was large epidemics so the type of question that for example Mike might have what caused the dressed in Yannick plague queen connections and take skeletons from this large outbreaks trying to find out what pathogen were present or Rhian that had that important question about and what happened in the 16th century in Mexico where we can then try to identify what pathogens are actually present in those ancient skeletons and from Central America and we've done that on a number of projects together with some of the group leaders in our department so first we started with a senior pestis as I mentioned before this is was we the main focus of our research over the last few years where we were able to reconstruct it from the black death so from the 14th century as well as then from the 6th century and then later centuries and we've even traced back the history of his pesters now into the Stone Age so the oldest genomes we now have are more than five thousand years old from all over here Asia and we can actually really reconstruct the genetic history of the senior pesters quite well now even looking at when it emerges as potentially a human pathogen from some sort of pre bubonic form to the bubonic form which is very exciting it also looked at ancient leprosy medieval leprosy most lived that we reconstructed from medieval skeletons from different sites all over Europe for leprosy or my chrome lab was actually quite exciting now that we see that there was a very large genetic diversity of leprosy in the past in Europe actually the the same diversity that we find in the world today which currently makes us think that at least Western Eurasia maybe even Europe itself could be where leprosy actually merged in the first place which is a pretty crazy idea if you think about it because today it's not fountain Europe anymore but in the past it was present in Europe and was extremely diverse actually many different strains quite some genetic diversity and there but we are not only looking at human pathogens we have been also looking at plant pathogens in the past so we for example reconstructed p2 after infestans which is causing potato blight so it's actually plant pathogen and this plant pathogen caused one of the biggest migrations in human history from the last 200 years there was the Irish potato famine that cost a lot of Irish people to actually leave Ireland that happened in the mid 19th century we were actually able to use a barium collection so leaves that were in herbaria to reconstruct from those leaves from the mid 19th century this all my seeds were fungus-like organism and then compare that to modern potato apply to modern feet after intestines to see how it changed over the last hundred fifty years what we actually found was that the one that was causing the potato blight in the 19th century it's actually extinct it doesn't exist anymore was actually replaced by another one because potato actually got resistant against the one from the 19th century at the end of the 19th century and then a new one was basically introduced at the beginning of the 20th century which is now present and potatoes again actually causing a lot of to loss in the world like this one from the 19th century is actually extinct because it was basically not as well adapted we've been also looking at Hilo back to pylori so the bacteria that can survive in your stomach that can cause an ulcer for example or stomach cancer and we have been able to reconstruct them you might wonder how do you get ancient stomachs there is actually one really nice preserved ancient stomach that comes from this gentleman here which is the Iceman so the Iceman that was stuck in the ice in the clay sure of the Alps for about five thousand five hundred years was discovered in the 1990s early 1990s we had actually access to the dried stomach of freestride stomach of this mummy and we could indeed reconstruct yellow-backed a pylori from this ancient Iceman and we've also done some work on microbiome tuberculosis there's a project I was actually thinking maybe to kind of cover today in the presentation but I think there would have been too much but this is also a new world and pathogen that we have here reconstructed but this is not post contact this is actually pre contact and that was very exciting because for a lot of time people did not think that tuberculosis was present in the Americas before contact and that is because if you today look into North and South America and the tuberculosis you find the native populations as well as kind of population from today is they have usually M tuberculosis of the European type so tuberculosis or microtubules has very different types in different parts of the world this is a sort of fighter geographic pattern is a European version is Asian version there's a lot of different African versions their highest genetic diversity is in Africa but what you find in the new world is all basically the European type and because we know that the Americas have not been settled pre-contact at least from Europe but actually from a jet was kind of strange that you find just the European type and therefore people assumed that tuberculosis came with the Spanish in the 16th century to the new world but our colleagues had actually identified that there are human remains from pre contact North and South America that actually show tuberculosis lesions in the skeleton so they have very clear pathology that indicates that tuberculosis was present in the new world before contact and our question then was what type of tuberculosis was that and our so surprised when we reconstructed it the type of tuberculosis that was present in the new world before contact was actually not a human tuberculosis was actually not tuberculosis bacteria you find in humans today it belongs to the micro bacterium tuberculosis complex but it was actually a version that today we only find it pinnipeds so seals and sea lions that was a big surprise to us but it might actually explain how it came to the new world because what we also found was the tuberculosis itself as a complex so all tuberculosis bacteria that are found the world today if you reconstruct their most recent common ancestor because we have those ancient genomes we can now have a good mutation rate we actually know how old super close roughly is it's only about six thousand years old it's very recently kind of spread and infectious disease probably also in the Holocene or last six to ten thousand years and that was always hard to it then imagine how it got from the old world into the new world in the last five thousand years but now we might have a good explanation because those guys of course can swim right so what's basically swimming from africa likely into the americas them and then disseminated in the human population and then the last one and that kind of should be the focus of the presentation today um is the one that we just recently reconstructed in beddows salmonella enterica from the new world so the new world history of course as you all know we are the new world it's a very exciting history but has also seen especially in the first decades quite some devastation in the Native American population and because when the Europeans came to the new world they brought diseases to the new world that those people that lived in the new world had not been exposed to before it is not for for a very long time and we think today that those diseases might have been also facilitated the European conquest because they just killed there were so devastating within the Native American population that this population plummeted and then basically the European had the chance to basically then settle and plesio take over if you want especially North America and Central America so the estimates go that about 95 percent of the Native American population were killed by infectious diseases in this first hundred years after contact some of them we know based on the kind of description from that time period for example like smallpox that was in the 1520's a smallpox epidemic in Mexico which based on the description was very likely smallpox and measles mumps and Forenza have also been indicated maybe in later centuries were responsible for some of this large epidemics that happened but there's still much debate about what other pathogens might have been present in the Native American population in which other pathogens were brought and from the old world into the new world at least from Mexico or Central America we have three major epidemics where we don't really know what pathogen cost them and those are called the coca literally coca literally itself is actually a term from Nahuatl that means just pestilence so it doesn't really tell you what type of pathogen it is it just tells you that there was some outbreak some sort of plague outbreaks and pestilence like outbreak which is not really clear what it was if you look at the numbers you can actually see um how strong those three epidemics influenced the Native American population so we started off with something like more than 20 mil 20 million people that lived in Mexico at the beginning of the sixteenth century and we ended up by the end of the sixteenth century it was about two million or with less than two million so really at more than 90% of the population based on historical accounts were basically killed by those large pandemics and the biggest of them was the great cocolate flea that happened around 15:45 lasted maybe about five to seven years and then there was the second cocoa literally that happening seventy-six and then the third one which was 1590 at the end of the sixteenth century and there's been much debated about what type of pathogen caused them there's some very interesting accounts of your interest from Alexander from whom boiled for example who was debating in the kind of early 19th century what type of disease might have been responsible for it he concluded based on the historical accounts that there was some sort of typhoid like disease which is quite interesting because as you will see that came pretty close at the time typhus and typhoid fever like diseases were not yet differentiated so it was actually interesting that you came to this conclusion so what do we know about the create Co cool it's Li it's a disease pandemic the or epidemic large epidemic and that not just affected Mexico but larger parts of Mesoamerica some people even think that it also went into South America that affected parts of Peru for example in Colombia from the historical records from later time periods you kind of can reconstruct some of the symptoms that people had so there was was some sort of black born fever there was bleeding from facial orifices there was rash there was diarrhea it not just in fact that the indigenous population but it also in fact that the European population so it was not something that was just spreading within the native population but also the Europeans were infected it's not really clear from where it came from so some people think it could be European zone disease that was introduced by the Spanish but there's also people that think it could have been some sort of local origin so some people have claimed that it could have been some sort of virus that emerged from within the Native American population of within the Americas itself and then spread within the population and was actually nothing that was introduced from the outside why don't we know so little about it that is largely because we have very little historical records from the time period if we average you look at the historical records we have directly from the great cocoa literally then this is all we have that's basically the historical record that is this one drawing which is from the codex Delacruz which is just a person that is dying probably with some sort of liquid coming out of its mouth right that's all information we have and if this liquid is now black if this liquid is some other body fluid and is not really clear only in later periods so twenty thirty forty years after the great Coco literally we have some more information some more code Exodus which are mostly drawings and some writings about what happened in the past in the basically twenty thirty years before during this pandemic then you see also colorful images we then have for example blood or some sort of bloody liquid coming out of people's mouths which again looks may be some sort of blood-borne pathogen some sort of hemorrhagic fever for example and we have done also from later on accounts this type of drawings where basically people then report that there was massive amounts of people dying during this time 15:45 1544 445 and based on this limited historical records people have done suggest the different types of pathogens that might have been responsible for the great Coco literally so there was some sort of hemorrhagic fever based on the blood or the kind of bleeding people in still said it could have been some other disease like measles smallpox or typhoid like and diseases for example or use pneumonic plague some people have suggested as well so there's been all kind of hypothesis and what Coco literally actually was and this is then basically where we started off together was Noreen who had actually been working with colleague from Mexico son le hablas Garcia who had been excavating a site that is called Tempest kula you Kunda which is a site that is a former Miss tech site which is in Waka in Mexico and they had actually excavated the site and when they excavated the site they actually found a large mass burial in the center of this former Native American town so this was a cemetery which is actually here present on the Grand Plaza which was a cemetery where more than 800 individuals were buried they were buried in a very interesting way people had basically dak holes long rows basically entombed those people but hadn't really closed those holes so this marketplace was basically full of big holes when the people left so it didn't even fill it up so was never used as a marketplace again actually the town was even given up so the site was abandoned just after this epidemic and was not used again they actually moved the entire town to another place so it was such a big event that happened here doing this cocoa literally probably so many people died that they actually gave up that town and moved somewhere else maybe the author thought there some sort of bad spirits not really clear but people abandoned the site and we then analyzed human skeletons from two different parts of the site so first of all from this mass burial from actually the only mass burial that we have from the great cocoa Leslie and from this then time period 15:45 to 1550 as well as human remains from the so called churchyard which is actually a pre-contact cemetery which was also present in this village so we got skeletons from the pre-contact side as well as from the post contact site to see what type of pathogens we might actually find in those individuals and my student ash was actually working on the analysis she then looked at those ancient samples who she used teeth again because as I mentioned before teeth have the dried blood where we can then extract DNA that DNA can then come of course from different types of origins and in this case of course unlike for example for the black death where we might have had some idea what pathogen might be present in those individuals we had no idea what pathogen we could actually look for and therefore we chose an approach which we call a shotgun approach where we extract the DNA from those teeth and then looked for what organism what bacteria those DNA fragments that we can extract from the ancient teeth can actually come from and this in principle should be straightforward but it's not completely easy because you're usually producing with this next generation sequencing quite a large number of DNA molecules like millions that we produce from each tooth and then to kind of identify what organism those DNA fragments are coming from is quite challenging because it's just computational and not completely straightforward and therefore we use the tool that we had developed in our lab which is called mold which is really fast way of basically identifying what organisms those DNA fragments come from and this is a tool which is called Megan alignment tool so Megan is a metagenomic software that the people at no metagenomics might have used before and it's actually quite a fast rapid tool for aligning DNA fragments to a reference database so you can use thousands of genomes in this case we used about 6,000 bacterial genomes we have now also used all of GenBank which has actually also mammalian genomes as well as viral genomes and you can in parallel visit we screen all the DNA fragments against this large database and it's quite fast as you can see here it's about 200 times faster than Plast plus this for the people that don't know plus plus is kind of the gold standard alignment I kind of taxonomy identifiers that people have been using in the past so it's a bioinformatics tool this for example of available in in the web where people if they have a DNA sequence blast the DNA sequence to see what organism that's coming from so there's something that's been around for more than 20 years now but this is quite a bit faster and allows you rapidly to screen a lot of DNA sequences so then the idea is basically we take the DNA from those ancient skeletons and then just shotgun sequence that and look with this algorithm how it looks like so this is just the principle of this algorithm I don't want to go too much into detail here but what we basically have is our raw sequencing reads we compare that to the mall database and you can choose whatever database you want to have in our case we looked at all bacterial genomes because we're interested to see what tide pathogens might be present in this data set and you then get some sort of output files which can be in different formats that you can then for example feed in to Megan so Megan again Desmet metagenomic alignment tool where you can basically see what type of DNA comes from what type of organisms inside your sample or you can also have some output files same format which is a standard and output file that people use for alignment so it really produces a DNA alignment so for people that do bioinformatics it's like bwa or some other lineman focus really produces alignments that you can actually look at which is quite different to Kraken or some other method genomic tools that people am are using currently and it's yeah it's it's very fast quite efficient because what it actually does is it kind of produce some sort of hash tables which is loads into the working memory of the computer so you need actually a computer which has about 2 terabyte of work memory which is not the normal computer that most people have but still most bioinformatics centers have such a computer available and it can process about 1 billion reads in less than 24 hours which is extremely fast if you would have done I will work with a different kind of algorithm not with that type of approach it would have taken months but in this way it only took hours to screen basically this larger data set from this cocoa literally size the output that you get looks like this which I guess hard to see in the back it's even hard to see in the front so this is a gigantic phylogenetic tree um so basically each note here is a different bacteria that you can find this just for some random sample and that we had from tuberculosis screen and what you see is actually thousands of bacterial kind of clusters that are supposed to be present in this sample from this bone that this DNA has been extracted from it can also zoom in and it looks like that this is just for micro bacteria and then you see that you have supposed to have all those different types of micro bacteria present here so not just micro bacterium kind of in general but bhavas caneta tuberculosis leprosy in this one sample and this is true for almost every metagenomic sample so if I take dirt from the table here or from the backyard you always find all kind of DNA from bacteria that is similar to bacteria and larger databases and that is largely because most bacteria in the world have not been sequenced yet right there's probably billions of different of tactile or to use how they're called and from bacteria and but there's only about 6,000 that were in this database I think there's a pond at 12,000 that are sequenced so far and so it's a very small number of bacteria that are actually known most of them are human pathogens because that's where our main interest is in but we are not sequencing a lot of environmental bacteria for example so if you take an environmental sample and you compare that to a database you will find all kind of human pathogens but there's actually not the true human pathogens that are in this sample this is actually largely false positives was just some similar bacteria that have 90% sequence identity 85 percent sequence identity but are not really truly that type of pathogen so it doesn't mean if you find this here that it's there so you have to have some other criteria to make sure that this is indeed the pathogen that you might be looking for that it's a true positive hidden it's not a false positive we then established a pipeline which is actually not published at which we call our May extractor which takes the output file from this mold and then there's a number of steps to make sure that the DNA that you have found with some sort of toxin ID is indeed from a pathogen that you might know of and it's not some sort of close relative and one way to look at that is edit distance edit this Angeles means the number of basically mutations away from the DNA sequence you have so if you take your DNA sequence that you have you compared to the reference sequence how many basically substitutions how many mutations how many steps away is the DNA that you're studying and if you have zero it means it's identical if you have one it means it has one substitution 2 3 4 into and so forth and if you have something that's very similar it should have an edit distance plot that kind of looks like this if you have something that is more different has a lot of substitution you have something that more looks like that which then tells you it's a false positive so that's one way to look at it we can also look at the redistribution so what you want to have is if you have a reference sequence of a genome you want to have that your fragments actually fall all over the genome and not just in one particular part of the genome that is highly conserved there elements inside bacteria that are conserved between many different bacteria and if all your reads end up in this one place you actually know it's not that pathogen that you have there but just a close relative that happens to be similar and this part of the genome can also look at DNA damage I will come to that a bit later and you can then also take the DNA which is damaged so this is DNA which has changed over time because it's old its ancient and you can then look at this ancient DNA and then look at the added distance of this ancient DNA at the DNA which is actually old and it should also have this type of pattern here and not kind of some sort of normal distribution if you take this different filtering steps you can then screen also larger data sets we've done it in this case for about two thousand eight hundred and human samples so from different time periods so this is DNA now not just from the pre-colombian or post Colombian but this is actually from all over the world even the and of Tata in your Paleolithic Mesolithic all kind of samples that we have been screening to just see what type of pathogens we have in here if we apply the small tool if we apply those filtering steps we found in this case about 132 depending which filter actually many drop out to no filters you have three hundred twenty thousand pathogens which is probably mostly false positives but then based on which filtering steps you see actually this number goes quite a bit and down and then to get an overview of what is in there we we have this kind of kind of plots heat maps where you have the pathogens here and then this is all the samples this is just kind of part of those samples that come from the late Neolithic Bronze Age so they are about 5,000 to 4,000 years old basically then those are the four different filters so the kind of warmest color your red means it's a good positive likely positive hit and if you have something that is blue then maybe it's a candidate but you should evaluate that more maybe a mapping to that genome for example or specifically zooming in and you can actually see that we have quite a number of seems to be ancient bacteria which are good candidates good positive hits present in those for example five thousand-year-old human remains most of those are not really pathogens per se when they are actually commensal pathogens the bacteria that live for example the oral cavity because most of those samples are teeth and then you often have something like Treponema identical our streptococcus mutans which can be pathogens but they also live in your mouth so those are for example like this guy here which you can actually see many of them and other guys but you also see some of the pathogens that we are interested in for example this row here is a senior pestis and there's actually quite a number of samples here from the bronze age from about 5,000 years ago that have positive history a senior pastor so they give us some indication a senior pastors was present in those samples and that is then actually something we followed up in this case we were indeed able to reconstruct his senior pastors from those Bronze Age individuals but coming back to a tip off our side from Mexico from ancient Mexico we did the same approach the molt approach for the tip off site we had about 1 million DNA sequences that we compared with this large database and then again you get this massive tree which is actually quite huge at the time when we had that we didn't have this nice filtering tool that are just presented but actually ash the student had to go manually through that list kind of look at every node and see if there's one note that is bigger than the other notes which might indicate there's more DNA of that particular pathogen which was a lot of work that's why we invented this other kind of new tool and approach because it's kind of manual approach takes a lot of time and what she found what basically stuck out is that there was a large cluster of reeds that were mapping to Salmonella enterica subspecies enterica serovar parrot ivy emcee and that was quite interesting because a very specific type of of Salmonella which was seem to have been present here and it was quite a number of reeds it's just 600 700 some large numbers but it's still big enough that you might wonder if that could be the pathogen and that was responsible for the death of that person we actually found three samples and had several retreats and then about seven that had a lower amounts of reads if you then look at the summary for all the samples that she screamed you could see that in the samples in the post contact Grand Plaza were about ten samples that had actually pretty high fractions compared to the other bacteria that we find in those inch zuman's that came from Salmonella enterica Parata if you see based on this analysis if you look at the pre contact site you can actually see that none of them was positive so there was no indication of salmonella enterica present in the skeletons from the pre-contact site we also had one sample here that was actually a sample which comes from sediments who were sediment DNA we just wanted to make sure it's nothing that comes from the environment so that also came from the Grand Plaza but in the sediment we actually didn't find anything that looked like Salmonella enterica so it was a good indication that Salmonella enterica was present there and we wanted to then and follow this up one problem you have if you then have an indication of that DNA that might be present you want to make sure that the DNA from this ancient pathogen that you're interested in is indeed ancient that it's indeed DNA that comes from the past and nothing that could have contaminated the site maybe there was some sort of people were fertilizing with for example feces of pigs which is quite common that often carry salmonella so we really wanted to make sure that this DNA that we have here is not from the present but it's actually from the past and to do that we look at something we call DNA damage I mentioned it before it's basically when the DNA gets old it breaks into small pieces and it's not only breaking into small pieces and it also accumulates chemical damage so that the basic chemical structure of the DNA changes there's something that we call a mist coding lesion where for example one base of the DNA gets chemically so modified that during the DNA sequencing or the amplification we actually read it as a different base so one example is cytosine so the C in the DNA which can get deaminated and when it gets DNA it turns into uracil and uracil is retinas timing so a C actually becomes a T in the DNA sequence and that is something that happens especially in the ends of the DNA because the ends of the DNA it's often fingers trended so the DNA is broken so you don't have the double strand but you have the single strand and then you accumulate that damage especially in the single strand because it's not protected like the double strand DNA and if you look at long a DNA fragment so this was for example Neanderthal DNA we analyzed and some years ago you can see that the damage is especially strong at the beginning of the DNA fragment so this is the five prime end of the DNA so we see a lot of c2 T's so the red line here's C's that have become T's and then it goes down and actually on the other side of the strand we see G's that have become A's when we first thought that we were not quite sure why have we see two T at one side of the DNA and g2 a at the other side of the DNA but that has something to do with how we sequence the DNA we actually have a step where we fill in the DNA we're actually filling in this part of the DNA and during this fill in step we're basically putting the reverse complement base into this part of the DNA sequence so if you have a c2 T on this side you get a g2 a on the other side so what we actually see is C 2 T on both sides but here we have the reverse complement strength of the DNA and that is something that we see in ancient DNA like this is Neanderthal this is 40,000 years old but we also see that in DNA which is hundreds of thousands of years old but where we do not see that is in modern DNA so for example this Neanderthal was contaminated with maybe my DNA or anthropologist or somebody else and the modern DNA the contamination doesn't have that so it's basically completely flat we also looked at that through times this is time here on the x-axis and this is the amount of DNA damage on the y-axis we actually sees a very nice correlation so the older the DNA gets the more damage it accumulates so if we have for example DNA that has 20% damage you can be pretty sure that it's older than 100 years so it cannot be contamination this is something that we have been using over the last ten years or so to really then authenticate if we have DNA from the past whether that DNA has this damaged pattern if it does not have that damaged pattern we have to assume it's modern contamination because all ancient DNA we have analyzed so far has this damage usually more than 10% many cases more than 20% and if you look at the DNA then from the 10 individuals that were positive for um part I if you see we can actually look at the power type you see and you can actually see those nice patterns here we sometimes call this smiley plot because they make us very happy and they kind of look like a smiley and you can actually see that all samples have this smiley they have this damaged pattern which is typical of ancient DNA so we can be rather sure that this Salmonella DNA that we have present here is coming from the past so then the next step we wanted to do is not just see what type of DNA is present but actually trying to reconstruct the entire genome of that ancient Salmonella that's something that we have been pioneering in this first paper where we looked at the black death genome and that's why we use probes which are bound to little pieces of glass so capture arrays to fish out the DNA that you're interested in so basically what we have is a DNA capture array little class light with DNA that is synthesized on the surface of that piece of glass that's something that companies can do for you you can actually design those probes yourself they're about 60 base pairs long and you can have millions of them on the surface of this piece of glass in this case we used more on Salmonella enterica diversity so you can actually see the probe design here for modern Salmonella enterica so 24 different genomes from the whole the diversity of Salmonella so not just enteric enteric up and even close relatives and put them all on this piece of cleft so then incubate that DNA from the ancient skeletons with his piece of glass the complementary fragments will bind to the DNA on the surface of this piece of glass and you can wash away the background and then sequence the DNA in the next-generation sequencing machine and that actually works quite well so if you look at the amount of Salmonella DNA that we had before enrichment was very very low just a few hundred sequences we had per million DNA sequence if we had sequence but then it was about 30% so one hundredfold in Richmond this is something that we are doing quite routinely on all kind of pathogens with this kind of capture it also has the wonderful property that capture and like for example PCR allows for sequence mismatches so with PCR you often have the problem that if there is a basically substitution and the priming site you don't get a product but with hybridization even if you have 10% divergence even if the DNA sequence you would like to fish out has 10 percent differences for the DNA that you use as a probe it would still bind and you could still fish it out which is actually quite nice and doing that we got from five of the ten samples genomes was pretty high coverage so between four and a half to one hundredfold coverage which means we have seen 100 fold coverage for exam we have seen every position of the ancient Salmonella genome about a hundred times so there's actually pretty good qualities of the genomes are pretty much complete and we have a very high confidence that the DNA sequence we have from them is actually the true DNA sequence is not affected by damage for example by the old age so it's basically as good quality as modern Salmonella DNA that you would get from the next-generation sequencing approaches what you can then do is family tree you can actually see how those ancient Salmonella genomes are related to modern Salmonella genomes and this is now all kind of Salmonella genomes here so this is a parrot I fee for example then kind of out groups like this Arizona I'm Sarah are here typhimurium here so something that you find it in mice for example so all kind of different types of Salmonella and you can actually see up here on the very top this is where our t-posts samples fall in the family tree of salmonella they are falling very closely to power typhi see just a few hundred substitutions and mismatches or differences and that is on the other hand and very close to cholera sues which is actually a type of Salmonella you'll find in pigs which can affect humans is actually pretty severe of humans catch it as a disease but it's usually found within peak populations and also cause some people to then propose that actually pig gave this type of Salmonella this type of power type feces Salmonella into the human population so there was some sort of zoonotic transmission from pigs into humans that happened maybe a few hundred or a few thousand years ago I don't have much time to present some new data that we now have from other ancient Salmonella they actually suggest and it was not given from pigs to humans but actually Youmans gave it to pigs but something maybe we have time to talk about them afterwards so similar to tuberculosis were actually we gave it to cows and cows gave it to us like a lot of people have thought so this power type you see that we have here is actually just one out of four Salmonella enterica serovar that cause this type of enteric fever so which is called power typhoid view or typhoid fever so there's more than 2,600 serovars so different types different strains of Salmonella but most of them are not causing some sort of enteric fever they can cause some gastric disease but they're not entering basically the bloodstream they're not basically causing some sort of septic State so they are staying outside or kind of inside the gut but they're not entering the human body it's quite rare today apart a few see we don't find it at all in in in Europe except of tourists that actually bring it when they have been in Asia but especially in Southeast Asia in Africa it's actually still common today but it's just a few thousand cases per year so it's actually not as as common as it might have been in the past I mentioned it before we have been looking for it now in our large dataset I showed you we screened more than 2,000 human skeletons from the past we've actually found it going back to 8,000 years in the past and actually besides your senior pesters one of the most common causes of death that we can reconstruct in skeletons from the past so it seems to have been very common in the past not so much more on the present its transmitted fecal-oral maybe hygienic conditions have improved over the last few thousand years I would hope so at least and that's probably why we don't find it so common today today anymore but it seems to have been quite common in the past so cause some sort of fever body rash as well as diarrhea in the mild cases but it can all to cause death if untreated force antibiotics today it doesn't cause so many casualties anymore because mostly people get treated with antibiotics but it can still be quite severe and untreated cases has a pretty high mortality and there's also quite a number of people that answered some Tata carriers so basically kind of the typhoid mary kind of case I guess people have heard about it like a person that was carrying bacteria over basically her entire life in the beginning of the 20th century she was an asymptotic carrier so she had those bacteria but transmitted them without getting sick herself and that's something that happens also quite in a few cases where people and have this particular strain of Salmonella enterica so concluding remarks then what can we say we've seen that about 10 of the 24 individuals that we looked at from this epidemic cemetery I'm carried Salmonella enterica the others also had wreaths to map to of Salmonella enterica but not in large numbers so it could be that all of them died of it but it seems that at least half of them died of Salmonella enterica so it's a very good therefore candidate agent for the great cocoa literally epidemic I say here candidate because we cannot exclude that there were other pathogens present during that time the study has been widely discussed and widely criticized also what's always good to get critique but people have busy set why do you say now what salmonella couldn't it be still some hemorrhagic fever or something else of course it could be we can only say that for this one epidemic outbreak in this town of T post we have the presence of Salmonella enterica it could be that there were other strains of other pathogens that were present in the larger region of Mexico during the time all that it was even a virus that caused a kind of hemorrhagic fever such as the filovirus like Ebola like that was present what some people have argued based on the historical records so we cannot really rule out that the pathogen actually existed before in the in the New World so that it was not brought in by Europeans but that there was some sort of local origin of it but there's one very interesting study which is actually published yet but it's available on the bio archive which looked at Vikings and actually identified Salmonella enterica in 12th century Norway so they have a strain of Salmonella enterica on 12th century Norway so this is work by mark Ackman and colleagues from Warwick University and interestingly if we compare this Salmonella enterica from the Y Kings that fortune is already available and we compared to our Salmonella enterica from a tea Post in Mexico is actually very closely related so they're falling kind of very closely together suggesting that the very close relative of the Salmonella has present in the 12th century in Norway and then of course everybody knows that why Kings have made all its way into America in the maybe 11th century or something like that so they could have introduced it before but we think that's an unlikely scenario because there has been only one settlement in Newfoundland but likely it was present in all of Europe during this time we've also found in southern Europe actually in the past and the Spanish likely then brought it over because it's very unlikely that the strains that we have in the new world and teapots are removed 20,000 years from this waiking strain because they're too closely related so as we have it in Europe pre-contact who likely was brought in by the Spanish in the 16th century so there was of course a lot of trade a lot of people arriving there was also a lot of livestock that was brought by the Spanish into the new world like pigs for example I mean as you know most native population didn't really have a lot of domestic animals except of turkeys and Yama's and guinea pigs there wasn't a lot of domesticated animals in the new world but then they introduced cows introduced horses that introduced pigs and it could even be that because of this introduction that the pathogen actually came with this animals into the new world and probably also changed the whole way and how people interacted with animals in among each other what I've also shown you is this wonderful new tool mold that at least for the people that do metagenomics work is actually quite a nice too it's extremely rapid it's quite sensitive so you can really detect small amounts of DNA that match to a certain reference genome and it really allows now to find all kind of candidate pathogens from ancient skeletons that we or others might be interesting what I also want to mention is if you look at where do we have genomic DNA from ancient skeletons in the world right now you can see that we have a very strong bias on Europe because that's where most of the laps are actually based and also where most of the samples are coming from the people have been analyzing but you can actually see there's large parts of the world we don't have a lot of ancient DNA that we can look at for ancient pathogens so there's a lot of work we have to do so there's a lot of basically future investigations for pathogens that might be present and other parts of the world can also see from Mesoamerica and North in South America that's actually quite a small number of samples I mean it's still quite amazing to see that it's about three and a half thousand or so human samples that have been analyzed over the last few years given that when I did my PhD about 10 years ago was fun to Payable we worked for five years in one genome that was a Neanderthal genome which was pretty low quality and was the first um archaic human genome that was produced it took us five years cost 10 million euros was a big project and now we have actually thousands from all over the world so we have made break a great progress but still there's a lot of work to do and maybe we can even do some of that work with some of you together so by that I would like to thank of course all the people that did the work and not just talked about it like myself so the graduate students the postdocs Alexander Hagen Kirsty Basra Joe group leaders now in our department Nerine of course as well as Tina was a professor in our department and anneli who provided us with the samples the rest of the team west of our department and all the funding sources and thank you for your attention thank you very much your house let's begin with the first comment from my friend and colleague Noreen Shiraz I just have really two points to make one of which Johannes has made beautifully I just want to stress this is really the first project where the pathogen was completely unknown there was no morphological indication there was there was only guesses based on historical records which turned out not to be very helpful this changes everything and frankly this is what I have been waiting for the search for Athan ancient pathogens that are associated with morphological change or with a good historic record are wonderful but this is an order of magnitude different and this is what we need to solve the issue of what killed indigenous peoples at European contact certainly Salmonella enterica is not the only disease but we have been completely hamstrung in trying to identify this and have as Johanna said only the records written be fifty to a hundred and fifty years after the fact in order to please the king that are of little value today the second point I'd like to make is if you're going to get into this work try to find a nice location this is Tabasco Lula it's in the highlands of Mexico which not only do you want a nice location now that you've heard yo.hannes you realize that this doesn't take a village it takes several cities across many countries to pull off and so when you're starting it's probably good to start with a really good excavation of well-preserved materials and as Johannes has pointed out try to find a really excellent archaeologist which we did in the form of Nellie Robles Garcia so temos was excavated by Nelly and a very large team of people and these are this is one of the graves from tempos and I want you to notice two things one this was carved into a flooring a plaster flooring which probably percolated down through a few hundred years and buffered the pH of the skeletons and so they were magnificently preserved the other thing you'll notice is there are three people in this burial this was true of many of the burials in tempos people were dying so fast that they couldn't give them individual burials this is sad but when you find this it's a very good indication of an infectious epidemic the indigenous people were brought to the top of this mountain by the Dominicans to help build a church and the epidemic ensued and the deaths were so fast that as Johanna said the top of the mountain was abandoned and today and the last comment I'd like to make is that the other reason Tepes Antipas kahlúa is really important is that it's the gift that's going to keep on giving this collection is available in large amounts in my laboratory it was taken at excavation my gloved hands and put immediately in a freezer and taken to the United States the rest of the collection is in this building which one the Dominicans left the mountain they came down to the village and built this church in what is now the village of to Posca Lula and what you're looking at is at the outside Chapel which has been restored by the Mexican government it's an outdoor Chapel because the indigenous people were although they were welcomed into the Catholic faith by the Dominicans were not allowed inside the building and so they had to stand on the lawn in order to receive Communion and so the indigenous people that helped build this we're never actually allowed to go inside however the remains of their ancestors are now stored inside the building something I take great pleasure in telling you we continue to work on this site and I would just stress how important it is to be able to go back to material and keep reanalyzing it because there are people in this room who will have new ideas and if we can build on collections and information this is going to be transformative I think a lot of credit to Johannes and his group and to Alexander Herbig and the development of malt thank you Hannes thank you for a wonderful wonderful talk and mica very much thank you very much for the invitation so I have about a thousand things and maybe we can flow over into the reception but I guess a couple of things a parrot IPC is a strange bug right so there's there's all different sound Mandela's and Salmonella is there's over 2,000 serovars and and they have most of them are zoonotic there's only four there's only actually three that are human restricted that's parrot IV a parrot type you'd be in tyfa itself sea is even an outlier in that it's a cause of typhoid fever you know the person can get a typhoid alil 'no so can cause abscesses and sepsis and it can persist in the body for a very long time Perth there's multiple reports of people with parts IPC who have an abscess drained and a liver their spleen and 30 years later they have another abscess and their liver and spleen and they've moved from wherever they came from and they then have the exact same bug 30 years later so it can persist the way that tuberculosis can I guess is one thing number two the patients go much more Sept ID which means they get sicker most salmonella is we break into two categories it either causes a gastroenteritis or it goes deep it has immune stealth mechanism manipulates the immune system and it actually doesn't cause a major diarrhea problem and goes deep in the body and the question is why do they do that evolutionary don't you want a lot of diarrhea so I can contaminate the water source or something and we think what it is and we're not sure is that as we move out as migrations Out of Africa we actually moved in small relatively smaller bands and we didn't have the ability to keep infecting and keep the organism going the typhoid 'el ones tend to hide long-term inside your body inside of your gall bladder and you about one or two percent of people who survive Salmonella typhi at least is where our best data are from and we think it's the equivalent with the others one or two percent those people get infected in the gallbladder and they intermittently shed it through their biliary system back down through their stool and that's the typhoid oh mary that johannes mentioned and we think that that's that allowed it to then travel with our hunter-gatherer teams as they spread out and to introduce them to new environments etc and parasite PC though it doesn't really it's a strange bug in that regard you can get that chronic colonization that and that chronic sort of shedding but you have this more sep tide features as well which is a bit atypical now we don't see you know I guess what's strange here also is we don't see mortality to this level to parrot IPC you know where did this bug go if you know there's this it was first report in the modern era in a Serbian soldier in World War one and it was and it was reported and then they started looking at these title malaria cases and a subset of them but she's not big outbreaks the biggest outbreak that I'm aware of that was reported was in South Africa that maybe I had a hundred ashore so over a three-year time period in the Transvaal and there was another outbreak in British Guiana back in the 1920s or so that had maybe forty five patients etc but even those large outbreaks were relative that logs different than what might have happened here so I mean there's questions here of you know of and this is the other atypical thing about this is is very closely related to cholera suus and Collar Suez as Johannes mentioned is a pig porcine pathogen and DeSoto introduced pigs to the new world in 1915 39 in in Tampa I don't know when it made it down to Omaha but I guess a question is you know what what what allowed this to circulate among the people was it person-to-person would be really high attack rate was it through the pigs were the pigs where they're pigs there at this time I don't know if you can mention about if you know if there's any pink Esmond tree during this error I don't know if you can talk about you know could the pigs have even that with ancient DNA could pigs from the 1540s have routed up the bodies and defecated into those areas so yes it might still be ancient DNA but did they introduce it from their GI tract which creates big color suus means the collar of pigs they don't get cholera in our sense but it was a bad diarrhea illness of pigs and they died it's a veterinary problem etc so it's fascinating questions here and I guess the question is with your reads that identify this is parrot IP see if this is parrots I see see that cause Coco literally either the bug has changed or it was the people are different in that they the group there had a very specific HLA type etc that really that they just didn't do well with the bug and we can't really necessarily answer that latter one but the first one is whatever reads you hit for parrot type we see it would be very interesting to see how they match up with modern-day parrot IPC's because something something is different about this bug and 500 years ago is not that long ago so it would be really interesting to say so so lots lots of thoughts and lots of questions that we can have a chance to chat with that debris [Applause] so just to come in the on the on the last part we have actually looked at many more samples now which are not part of this t-post collection but actually through the three thousand genomes that are genome-wide data sets that we have throughout human history basically from all continents and we have founded in Eurasia to be present over 8,000 years and quite a number of individuals places there are no pigs for sure because they are from the step from the in Neolithic that was you know even before domestication of pigs and we also find that that is very exciting I think for me at least that if you look at the big diversity of Salmonella those two thousand eight hundred several Wars or gene gene and white data is available they all cluster with our part ofyou see we find nothing that falls anywhere else they all clusters prioritize you see that I'm really puzzled by that because it really seems to suggest that it has been quite prevalent in the past we find it as much as we find the senior pastors which we've also identified them and many individuals but they're all clustering together so they seem to have something in common that causes some sort of enteric state that seems to kill people because if we find in large amounts in those people I mean it could be that a pic just defecated on top of it but they are also falling in different places not just as cholera sues but actually were in different places in this whole branch of parrot IPC branch basically also there's different close relatives there are a presence which are actually today found in in Wales for example and turtles in all kind of like chicken for example and other animals so I don't really think that this is I think there's a high chance finding it in such a high amount that it must have been present in that person we also don't find DNA of other animals I mean correctly I'm not sure if we look for pig DNA in those samples is actually good idea we could yeah I mean we were comparing it to the whole genbank now so the pig genome would also be in there so I think we would have seen it but I can ask the people that did work again that actually happened so I do think it is it is some sort of disease from the past but it's a very intriguing and good question if it then changed somehow and we have looked over this eight thousand year period now at virulence factors and actually the the strains from from T pause as well as other strains going back to the Roman Empire they have all the kind of virulence factors that we find in modern Part IV C so there's most of them are there the cassettes are there and it's quite complex is kind of different different cassettes with basically pathogenicity islands but then if you move further back in time some are missing some more gained it's quite complicated because a lot of recombination actually happening through time but yeah we're currently kind of looking if there's something that they all have in common which differentiates them from typhi and from basically all the other Salmonella because they seem to have something that allows them maybe to to enter become some sort of enteric state or whatever that would be into quite interested to talk more about that if you have some insights on that because it's really something we just discovered this is unpublished just a couple of weeks all those results and it's very very exciting they were just preparing a manuscript on that it was just curious how if there were new very I guess new isn't the right word variance factors that are no longer found in the current strains to what extent would you be able to find them given the hybrid capture of for the hybrid selection approach if there was just an entirely new cassette I guess you might have found it from the original another way to ask this is how big are the fragments that you're pulling out might they have been attached to something you pulled down yeah it's an excellent question if there could be things for example present that we don't have today in the genetic diversity we would have a hard time to find them and if they would all fall into this one branch and they would all be closely related to each other I would kind of agree with you the thing is that and I should have brought it the tree I think I don't have one here I could pull it up or it would take me a few minutes and they're actually falling throughout the tree of the parrot IV kind of like a serovars so I fall in many different branches so then basically what would have had to happen is that this cassette or whatever was introduced in many different branches but then lost in many different branches and that's so put some sort of convergent loss and gain and that's kind of unlikely to happen so I don't think that this is a scenario that is possible but of course it could well be that we haven't understood all the pathogenicity I know all the different virulence factors and that could be something that we just don't know and of course there's recombination also which makes that type of analysis also quite difficult because you have lateral gene or gene transfer between different severa was basically that could have given some cassettes all of them are a bit simple question but I didn't hear and I'm not I'm not a Salmonella medic the drawings from that you showed yes versus the epidemiology of somebody who has this disease that's in Africa or Asia today do they look the same so the question is basically if you look at those codices and you see those kind of pictures of people kind of having some sort of bloody liquid coming out of their noses or or face or something like that this is something that usually is not so common with the type of Salmonella but there's certainly bloody dairy diarrhea which is quite common now the problem is again that's what what marine mentioned where I also said earlier on that the historical accounts that we have are usually coming from the end of the sixteenth century during the kind of the the second coalition third cocolate slea this is when when busy people then wrote about what happened 3040 years even one or two generations before and it might just be that they used whatever happened in the late 16th century to and for what happened then people getting sick and there's also some cases in the literature you can actually find where people also have some sort of hemorrhagic fever like symptoms having this pirate IPC and the kind of some septic stage where you also have some blood coming out of basically your mouth and not just blood Ria's but it can also happen in later stages of sepsis or the rash the body rash is a very typical symptom of salmonella so this is something that that would fit quite well so the only yeah I should have said that before they the only thing that doesn't really fit is the kind of basically blood coming out of your mouth that is that would be a bit untypical but all the other symptoms the fever the body rash this is something that you find in power typhoid fever commonly hi thank you for your talk I I'm an archaeologist in new world context and so I'm really excited to see these kinds of very innovative methodology is coming over to here at and doing have new things I have a little bit of a different kind of question for you today I read one of maybe these like publication that came out of this work and in listening to your talk today I'm a little bit curious about the way that this work on disease is being contextualized within the broader literature on colonialism in the new world for example in your talk today you refer to this sort of standard estimation of 95 percent depopulation that comes sort of from disease in the paper you know whoever wrote the paper themselves notes that disease is an underappreciated factor in depopulation in my opinion I feel like it's somewhat over appreciate and it allows us to sort of look past the violence there's done of these people for example in this context that seems like potentially the answer to one of the questions of like why is it so different here could be that well these people are being coerced into labor to build churches or something so I guess I was just wondering if you could speak a little bit to how this work its contextualized within the archaeological side of things I mean the I mean you're absolutely right and it's often used as an excuse to say if 95 percent of the native population was killed by disease then all the poor people died because they got sick so what can we do right but we don't talk about all the murder and all the mistreatment that those people actually suffered from so I agree with you I guess in that regard and I can just say that I mean we're kind of relying on the historians and archaeologists that have been working on this topic in the past and I think our research doesn't really contribute to much on kind of those estimates if it's 95 percent it's 50 percent is 20 percent we can't really say that we have a large cemetery with a lot of people that died likely of this disease that and talked about today and doesn't really tell us about the numbers and how you then kind of put that into the larger context of what happened in the 16th century I think is probably kind of giving it back to to us archaeologists or historians to kind of use that type of data and maybe to see I mean I think as we discussed before we need to explain why it's not so much of a kind of cause of death today and it's not so much of a pathogen that's present today but maybe in the past it had as you said higher mortality because of other reasons which come from the social context and not so much from the from the biology of the pathogen itself and one could probably explore that even further could even be quite interesting to see under what circumstances can power tie for if you're kind of be so high in its mortality and maybe if we kind of look at historical accounts from the 19th or 20th century we might actually find that there are cases in certain parts of the world where people were under certain conditions in prison for example or outbreaks or in other context that could then be applied to kind of the historical context of the 16th century in the new world that might be a possibility so it's a good idea about preserving the skeletal remains look for signs of acting work and trauma to see if this population was undergoing abuse physical abuse in order to the nutritional status to see what they had the kind of very low nutritional status is typical though still having access to the individuals allows for the possibility of looking at this particular population for macroscopic or microscopic evidence actualize the population up to explain a very high I have two questions first on the pathogen evolution you've got for some pathogens you have some data extending over 5000 years what evolution did you see in those pathogens and the second question is more technical one when you present the data from 1520 on of the population in Mexico you had a decreasing from 23 million to 15 million in one epidemic where did those numbers come from what's the evidence for them there and what are their uncertainty yeah I mean there's high uncertainties and as we just discussed this is something that's been debated and there as much yeah much debate on that as busy coming from historical accounts there wasn't real census until the 1570s in in mexico and then basically they tried to reconstruct what was there before and then comes from archeology comes from the view of historical texts that we have from this time period and then it could be seen as probably the highest estimate in 95% and some people might actually say it's more 50% or 10% there's all kind of opinions and we do have historical accounts that that of course cover the sixteenth century from Dominicans and other explorers and of course those are kind of historical documents so they should be treated carefully because they're subjective they're not objective so people might have actually used them in their favor so this is of course a lot of uncertainty around those numbers so it will be hard to come up with the exact numbers I think even kind of bio archeology will not be able to quantify exactly how many people was what we do have in terms of genetic kind of data is that people have actually looked at human DNA to see if we find any signal of this decrease in the sixteenth century and we do find that for example mitochondrial DNA there's quite a decrease of effective population size so the genetic diversity is actually shrinking quite a bit so we see a strong signal from the genetics that the population size have plummeted in the sixteenth century but we can't really use that for a census we can just see that there is a signal that the effect of population size and have to has decrease by a factor of four if that kind of can be directly calculated into census I don't think so but we do see a little strong decrease and also in the genetic data then your first question if we look at long time evolution of pathogens so the one where we probably have the best understanding which I mentioned before is yes senior pestis which we kind of trace back know to about six thousand five thousand five hundred years before present where it's actually quite interesting and we had a whole workshop dedicated to this this morning here where we talked about some of the research that we have been doing some of the findings that we have in this it's quite fascinating we have something like a hundred or so genomes from the past from five thousand five hundred to basically the eighteenth century and then compared to the modern genomes from all over the world that we have and some really interesting patterns one kind of first thing that we notice is that the early form that we find in the late Neolithic early Bronze Age just present actually spreading with humans from the so called Pontic steppe north of the Black Sea it goes into the outliers but who goes into Europe this form is lacking some of the virulence factors which are needed for the effective transmission through rodents and fleas so it seems that this early form was actually not transmitted by fleas which then suggests it was not banach plague but it was some sort of other form we have been debating it could be some gastric form that enters somehow into some sort of sepsis State or it's some sort of pneumonic form that gets transmitted by droplet and faction we're not quite sure even how it got transmitted but it was not in this bubonic stage and then from about three thousand eight hundred years ago we see the emergence of the bubonic form we really see suddenly we have those virulence factors all in place and the whole apparatus or for flea transmission via kind of road and fleas into human problem would be their present from two thousand eight hundred years so from the middle Bronze Age on which is quite interesting but that only in the dressed in any plague we actually pick it up in large-scale pandemics so that's also something we debated this morning why it took two thousand years before it kind of causes major outbreaks within the pneuma population then there's all kind of questions why it kind of disappears in Europe again and then comes back and the Black Death in the 14th century but it's interesting to see those virulence factors emerging but from three thousand eight hundred years ago we have them all in place so we see the early evolution from something that was not bubonic likely to something that was bubonic so we really see evolution in see to enact the strains that were not not bubonic that kind of had not this genes they're getting extinct we lose them in the mid Bronze Age and the other ones pop up so there's some interesting kind of patterns there so it's really fascinating to see this evolution happening and see - and this is the one that we started about eight years ago to do research on hopefully this kind of Salmonella and kind of other pathogens that we're studying like leprosy for example we are now able to do similar things with then some things like that also for Treponema pallidum pallidum so what causes syphilis and pallidum apathy no way that causes yours which we also now have from the past actually also from Mexico from the seventeenth century and they are we also see kind of that there's actually antibiotic resistance popping up but later in the in the in the 20th century with strains that are then developing this antibiotic resistance which are spreading or they're actually kind of emerging right now all over the world and which we also see happening so it is so something that we can reconstruct with those ancient genomes oh I could probably go on with some other pathogens but not have time for that yes thank you Johannes you mentioned two other pandemics in 15-20 in 1576 and presumably there were a host of other epidemics of one kind or another if and when we are able to get samples from the other pandemics and epidemics do you expect Salmonella to be the pathogen in that case in the same way that you Sania pestis I think we still understand was the pathogen that returned regularly from 1348 onwards in Europe or would you expect perhaps to find different pathogens in those other cases and in either case why why would you expect one of the other that is a very good question what cost Google its lead to three not having a strong expectation I do think if you look at the kind of codices that were written later on would show a lot of this kind of hemorrhagic type of fever that that we see with the kind of blood coming out of the the mouth which we see in many distinction from that time period I would not expect that to be someone at all necessarily so I do think that looks more like a hemorrhagic fever which would be caused by some sort of file of the virus or something like that but and again it could be just kind of a missive presentation and just kind of extreme cases or people had a certain relationship to blood that they kind of depicted it in this way but in that case it would be an RNA virus which would give us a hard time to identify it because RNA viruses don't preserve because RNA is not stable enough so we would have a hard time to actually find that and general viruses are quite difficult because they have quite some similarity to mammalian genomes in many places which mammalians actually incorporate a lot of viruses into their genome so they are easily misidentified but that will be very difficult to look at those RNA viruses but we might find other things smallpox of course which is a DNA virus which we could potentially find so far we haven't been able to find we have actually screened more material from that time period on the late 16th century we haven't found anything else also not has salmonella but yeah I would hope that by screening more material we one day will find also material from this time period one should also say that there's not a whole lot of mass graves from the 16th century so this goes back to this question about was it infectious diseases that diminish the human population or whether it was maybe violence or something else and we don't have mass graves like we have to in the black death in Europe all over the place that Tebow's is actually the only mass grave we have from the great cook of Italy and this was also some like one of the reviewers actually pointed out what can we say from one man's grave about kind of larger pandemic it's the only one if we can't say anything from that one and we can't never say anything because it's the only one that is actually known and I think also from kind of the late 16th century we don't have a lot of massacres in general in the whole new world we don't really have mass graves left we have to end up like that so if 95% of the population has diminished the question is where are they right we have to be buried and we probably have to find those bodies before we can look at those pathogens [Applause]

Channel: Science of the Human Past

Views: 18,733

Rating: 4.7345972 out of 5

Keywords: SoHP, MHAAM, Johannes Krause, Ancient Pathogens, Ancient DNA, Epidemics, Epidemics in Early Mexico

Id: YhTL6Y4vhuA

Length: 97min 23sec (5843 seconds)

Published: Fri May 04 2018

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MHAAM Lecture: Johannes Krause on "Death by Contact: Ancient Pathogen Genomes from Epidemics in Early Mexico"

studying ancient pathogen genomics is like studying the fossilised skeletons of ancient pathogens. It allows us to study the ways in which ancient pathogens were adapted to infect their hosts, which pathogens were present, and make predictions abut future epidemics. In this lecture johannes krause describes his work on a mysterious ancient mexican epidemic.