Category Archives: biosecurity

The Microbial Anthropocene


Over the last decade or so, geologists and ecologists have begun to talk about planet earth entering a new geologic period called the Anthropocene, defined as the period when humans became the driving force of change on planet Earth. Debates continue on when the Anthropocene begins; sometime in the late 18th century when the industrial age is underway with the first steam engines, new products appear like plastic that persist in geology, and in medicine, Jenner begins his work on vaccines in the 1790s, would make sense.  I suggest that this also marks the beginning of the microbial Anthropocene — when humans become a driving force in microbial evolution.

Microbiology of the Anthropocene (Gillings and Paulson, 2013). Note the logarithmic time scale.

The graphic above is eye-opening. The Anthropocene is apparent in every level of microbial ecology examined. It is a good reminder that human intervention in microbial evolution goes far beyond infectious disease.

Perhaps most stunning message this graphic brought to me is the logarithmic nature of change. It finally dawned on me looking at this graphic that it also reflects the periods of epidemiological transition theory (ETT). The hunter-gatherer period correlates with the Pleistocene, then the first transition to the farmer-urban period (of epidemics) correlates with the Holocene, and the second transition to the modern third epidemiological phase characterized by longer lifespans and chronic disease is the Anthropocene.  Finally, the time scale of the epidemiologic transitions makes some sense. The logarithmic scale may not bode well for the speed of future transitions.

The changes of the Anthropocene filter down through all living and non-living things. Among living things, there are winners and losers: species whose range and differentiation expands and others are driven to extinction. We can see this on a huge scale in the ocean where we have coral bleaching caused by loss of microbial symbionts, while there is an increasing incidence of toxic blooms and an enlarging dead zone in the Gulf of Mexico both caused by an overgrowth of some microbial species. With each transition, natural selection seems to go into overdrive until a new equilibrium is established (Gilling and Paulsen, 2).

Michael Gillings and Ian Paulsen identified several areas of microbial evolution and ecology impacted during the Anthropocene. The strong selective pressure antibiotics have exerted on infectious agents is the most commonly discussed risk in modern medical microbiology. Changes in the human microbiome are most closely related to diet changes (another feature of the Anthropocene), but our normal flora is also collateral damage of antimicrobial treatment. We often overlook that most antibiotics consumed by humans and livestock are washed through our bodies into the watershed where they alter the microbial ecology of entire ecosystems. Antimicrobial therapy began long before traditional modern antibiotics; mercury was used in medieval medicine to treat syphilis, leprosy and as a topical treatment for lice. Arsenic is still used to poison pests like rats. These early antimicrobials prompted the increase and spread of mercury and arsenic resistance in a wide variety of pathogens and environmental bacteria.

Industrial and agricultural practices have involved bacteria in changes to the global biogeochemistry and played a major role in climate change. The spread of industrialized agriculture has increased the methane production from (bacteria in) livestock, rice patties, and landfills. Crop rotations with legumes with their nitrogen-fixing symbionts increase the agricultural output of the land but in doing so the symbionts have altered the global nitrogen cycle. Gillings and Paulsen observed that the combined effect of burning fossil fuels, cultivating legumes, and industrial nitrogen fixation in fertilizer now accounts for about 45% of global nitrogen fixation. Agriculture on an industrial scale has impacted soil microbiology to the point where it has altered the carbon and nitrogen cycle of the entire planet. Elevated levels of methane and carbon dioxide do more than raise just the global temperature. While some have breathed a sigh of relief that the oceans have acted as a carbon sink, it has not been without cost. An acidic ocean is a price we pay for the carbon sink.  The drop in marine pH will affect all microbial communities down to the depths of the abyss. Coral bleaching due to a loss of their microbial symbionts is just one of the most obvious outcomes.

Disease emergence and dispersal has been more of a mixed bag. New diseases get a great deal of attention but with the exception of HIV, they are not worse than the “age of epidemics”  (plague, typhoid fever, yellow fever, etc.).   Vaccines have still amounted to an overall decrease in infectious disease deaths. The three worst diseases to emerge during the Anthropocene are cholera, influenza, and HIV/AIDS. The greatest concerns today are the speed of dispersal for antibiotic resistant strains of old foes and development of new vaccines. Still, though, there are possibly more infectious organisms than ever.  We have driven only two viruses to extinction — smallpox and rinderpest — while new zoonotic diseases emerge at a steady clip.

Completely synthetic microbes created in a laboratory may well eventually be the primary hallmark of the Anthropocene. We are on the verge of being there now and there are an uncountable number of engineered microbes that produce a variety of products from biofuels to drugs. It will be up to us to manage the use of a technology capable of resurrecting a long-extinct bacterial strain or virus.

Do we really think we are smart enough to manage the tsunami of change occurring the microbial world?



Gillings, M. R., & Paulsen, I. T. (2013). Microbiology of the Anthropocene. Anthropocene, 5, 1-8.

War as a Driver in Tuberculosis Evolution

by Michelle Ziegler

Russia has been all over the news lately. Beyond our recent election, increased Russian activity on the world stage has public health consequences for Europe and farther afield. It has been known for a long time that post-Soviet Russia had and continues to have serious public health problems. One of their particular problems that they have shared with the world is their alarmingly high rate of antibiotic resistant tuberculosis. There is no mystery over the root cause of their antibiotic resistance woes — poor antibiotic stewardship (Garrett, 2000; Bernard et al 2013).

A study by Vegard Eldholm and colleagues that came out this fall sheds light on the origins of particularly virulent tuberculosis strains with high rates of antibiotic resistance that recently entered Europe.  A large outbreak among Afghan refugees and Norwegians in Oslo, Norway, provided a core set of 26 specimens for this study that could be compared with results generated elsewhere in Europe (Eldholm et al, 2010). The Oslo outbreak clearly fits within the Russian clade A group that is concentrated to the east of the Volga River in countries of the former Soviet Union. They name this cluster the Central Asian Clade, noting that it co-localizes with region of origin of migrants carrying the MDR strains of tuberculosis reported in Europe.

Figure 5. Phylogeny of the Afghan Strain Family (ASF). Colored boxes represent the country of origin: Afghanistan is orange; other countries are gray. (Eldholm et al, 2016)

When the Oslo samples are added to the family tree, phylogeny, of recent tuberculosis isolates from elsewhere in Europe a distinctive pattern emerges. The branches on the family tree are short and dense, suggesting that this is recent diversity, that they calculate to have occurred within approximately the last twenty years (Eldholm et al, 2016).

The Central Asian Clade spread into Afghanistan before drug resistance began to develop, probably during the Soviet-Afghan war (1979-1989) producing the Afghan Strain Diversity clade. Slightly later, the Central Asian Clade still in the former Soviet states begins to accumulate antibiotic resistance as the public health infrastructure crumbles in the wake of the dissolution of the USSR. The invasion of Afghanistan by the US and its allies in 2002 toppled the Afghan state, crippling infrastructure and spurring refugee movements within and out of Afghanistan. The lack of modern public health standards in Afghanistan since their war with the introduction of these strains by the Soviets in the 1980s provided fertile ground for the establishment and diversity of tuberculosis in the country. Instability has been pervasive throughout the entire region sending refugees and economic migrants from both Afghanistan and the former Soviet states into Europe.

Movements of the Central Asian Clade (CAC) since c. 1960 and the subsequent Afghan Strain Family (ASF). (Eldholm et al, 2016)

Their dating of the last common ancestor for the Central Asian Clade to c. 1961 is significantly younger than the previous dating of 4,415 years before present for the Russian clade A (CC1) of the Beijing lineage of Mycobacteria tuberculosis. They account for this difference by noting differences in their methods of assessing sequence differences and note that their method is in line with other recent evolutionary rates for other tuberculosis clades.  The diagnosis dates and length of the arms on their reconstructed phylogeny suggests that there were multiple, independent introductions of the cases from Afghanistan and the former Soviet republics. This is consistent with a repeated periods of refugee movements from central Asia into Europe.

The rapid proliferation and diversification of the Afghan Strain Family may be explained by a known syndemic between tuberculosis and war (Ostrach & Singer, 2013). Conditions of war everywhere disrupt food systems, destroy critical infrastructures such as electricity and water systems, interrupts medical supplies, and the human public health infrastructure of the country. Malnutrition and stress are known contributors to immune suppression. Many pathogens flourish simultaneously in these conditions increasing the infectious challenges the population must fend off. Diarrheal diseases are the most acute and demanding of rapid attention, allowing longer-term diseases like tuberculosis to slip through the overburdened healthcare system. Afghanistan has experienced nearly forty years of war, political instability, and repeated infrastructure destruction. Thus, they were primed for both the establishment of new tuberculosis strains during the Afghan-Soviet war in the 1980s along with the proliferation and diversification of tuberculosis during the Afghan-American war of the last sixteen years.

Established syndemics between tuberculosis and war have been made retrospectively following the Vietnam war and the Persian Gulf war of 1991 (Ostrach & Singer, 2013). In Vietnam, prolonged malnutrition caused an eruption of tuberculosis along with malaria, leprosy, typhoid, cholera, plague, and parasitic diseases.  A WHO survey in 1976 found that Vietnam had twice the incidence of tuberculosis over all of its neighboring countries (Ostrach & Singer, 2013). When the military intentionally targets water infrastructure as it did in Vietnam and Iraq, the production of civilian infectious disease is a tactic of war. In both Vietnam and post-Gulf war Iraq, more civilians died of malnutrition and infectious disease than enemy soldiers died of all causes (Ostrach & Singler, 2013).

It seems likely that this is just one of the first studies to establish a link between serious infectious disease developments and the Afghan wars. The current war zones throughout central Asia and the Middle East already have ramifications for the public health of the entire world that walls along borders will not be able to stop. Most of the cases in the Oslo outbreak were Norwegians, not Afghan immigrants. Diseases will spread beyond the migrants so country of origin screening will be of little use before long.


Eldholm, V., Pettersson, J. H. O., Brynildsrud, O. B., Kitchen, A., Rasmussen, E. M., Lillebaek, T., et al. (2016). Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America, 201611283–16.

Ostrach, B., & Singer, M. C. (2013). Syndemics of War: Malnutrition-Infectious Disease Interactions and the Unintended Health Consequences of Intentional War Policies. Annals of Anthropological Practice, 36(2), 257–273.

Bernard, C., Brossier, F., Sougakoff, W., Veziris, N., Frechet-Jachym, M., Metivier, N., et al. (2013). A surge of MDR and XDR tuberculosis in France among patients born in the Former Soviet Union. Euro Surveillance: Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 18(33), 20555.

An Anniversary year for Natural Disasters: 1815, 1665, and 1315

There are major natural disasters every year. In the last year alone we have had the major earthquake in Nepal just in the last couple days and a historic epidemic of Ebola. It’s too soon to tell how these latest disasters will seen by history and effect historical interpretations. This year there are three natural disaster anniversaries that stand out from the rest not just due to their mortality but also because of their impact on how we interpret the past.

Tambora, 1815

Mount Tambora Volcano, Sumbawa Island, Indonesia
Mount Tambora Volcano, NASA image (public domain)
Just a few weeks ago there was a minor splash in the news to mark the 200th anniversary of the eruption of Tambora on April 5, 1815. The photo to the right is the caldera of Tambora taken from space. As tragic as the thousands of deaths directly related to the eruption are, 1815 is best known as the ‘year without a summer’, a volcanic winter. It is impossible to know how many deaths resulted from crop failures and unseasonable weather. As the most recent volcanic winter, 1815 is an important because we have the most reliable scientific data, economic data, and descriptions of the effects on health and culture from people in all walks of life all over the globe. I don’t know as much about Tambora and its after effects as I would like, so I’m planning on reading The Year Without a Summer by historian William Klingman and meteorologist Nicholas Klingman (2013). If I like it, maybe you will hear more about it later this year.

Great Plague of London, 1665

This year is also the 350th anniversary of the Great London Plague that was followed closely by the Great London fire. Despite its reputation, the great plague of London was not the last major plague of Europe by a long shot.

17th century London
17th century London

The 1665 plague of London claimed up to 100,000 lives, about as many as died in the Marseille plague of 1720-3. Fifty years later, a similar size plague struck Moscow under Empress Catherine the Great. Yet, the London Plague is the one that gets the most attention.

A great deal of the notoriety of the Great Plague of London comes from the amount and quality of resources available in English.  Daniel Dafoe immortalized the plague in his novel, Journal of a Plague Year written in 1722. A savvy author, Dafoe timed it to take advantage of plague fears in southern Europe, concurrent with the plague in Marseille. It is testament to the Dafoe’s skill as a writer than his novel is often taken as historical evidence. I think I’ll mark the anniversary by reading Defoe’s classic.

The London plague has also been magnified by it linkage with the great fire of London in 1666. The relationship between the fire and the plague has been controversial. It has been sometimes assumed that the fire ended the plague, but the plague was winding down before the fire began. However, it is likely that the fire removed the environment that had supported the plague preventing its return; over 80% of the citizens of London were left homeless. Restoration of the capital city after the great fire also immortalized 1665-6 in the history of London.

Great European Famine, 1315

A less combustible but perhaps equally deadly anniversary this year is that of the Great Famine of 1315 that effected most of continental Europe. Seven hundred years ago the famine began and, while its hard to estimate famine mortality over three to seven years, perhaps up to 15% of Northern Europeans died. It began with soaking and then flooding rains that destroyed winter crops for two years with yields of wheat and rye in England and Wales 60% below normal in 1316, and again in 1321 with similar drops in yield. Also beginning in 1315 the great bovine pestilence, possibly rinderpest,  begins in Central Europe and spread across the continent: France and Germany, the Low Countries,  Denmark and England by 1319. In just one year, England and Wales lost approximately 62% of all bovines (Slavin 2012). The loss of dairy and beef was compounded by the fact that oxen provided the vast majority of traction and fertilizer. With similar losses across Europe, it took nearly 25 years to return cattle numbers to the pre-epizootic levels.

There was no respite for the 14th century. The childhood survivors of the famine and food shortage were the adults who were cut down by the Black Death in the 1340s. What effect malnutrition had on their developing immune system is a line of inquiry being explored by anthropologists Sharon DeWitte and historian Philip Slavin (2013). Let us not forget, it still got worse, between the crop failures and panzootic of 1315 and the Black Death in 1346 , the Hundred Years’ War begins in 1337.


Devaux, C. A. (2013). Small Oversights That Led to the Great Plague of Marseille (1720-1723) Lessons From the Past. Infection, Genetics and Evolution, 14(C), 169–185. doi:10.1016/j.meegid.2012.11.016 (for comparisons to other epidemics)

Slavin, P. (2010). The Crisis of the Fourteenth Century Reassessed: Between Ecology and Institutions — Evidence from England (1310-1350). EHA Paper, 1–14.

Slavin, P. (2012). The Great Bovine Pestilence and its economic and environmental consequences in England and Wales, 1318–501. The Economic History Review, 1–28.

Dewitte, S., & Slavin, P. (2013). Between Famine and Death: England on the Eve of the Black Death—Evidence from Paleoepidemiology and Manorial Accounts. Journal of Interdisciplinary History, 1–25.