Quack, quack – quack it out! Twelve years of flu research in Mallards!

A good day in the duck trap! Duck trapper Gabriel Norevik is herding the ducks. Photo by Ville Fagerström

A good day in the duck trap! Duck trapper Gabriel Norevik is herding the ducks. Photo by Ville Fagerström

By Jonas Waldenström

It is time to do a field season wrap-up. There are still a few weeks of fieldwork to do, but now it is mainly the everyday routine trapping of ducks that remains. And when I say routine, I mean it. We have run our Mallard disease-monitoring scheme at Ottenby Bird Observatory, Sweden, since 2002. A full dozen years with daily sampling during the field seasons! That is truly remarkable!

If you don’t think 12 years is a long time, then you are likely not a scientist, at least not one working with animals in the wild. The truth is that long time series are rare in biological systems. Very rare. The few that are still running (some for 50+ years) have produced fantastic data, such as the Darwin Finches at the Galapagos island Daphne Mayor, run by Peter and Rosemary Grant since 1973, the St Kilda Soay Sheep project in the UK, the Great Tit population in Wytham Woods outside Oxford, or the Collared Flycatchers of Southern Gotland, Sweden. For flu, there are the sampling schemes of shorebirds at Delaware Bay, and the long-running duck sampling in Alberta by St Jude’s Children Research Hospital – two programs that have shaped our view of flu. But why then, you may ask, are long time series rare? That my friend is an excellent question!

One failed grant application can put a grinding halt to a time series.

One failed grant application can put a grinding halt to a time series.

To start with, funding typically favors shorter projects, roughly 2-4 years long. No research body says ‘cool project, let’s fund it for the next 20 years’, unless it is mega-large projects like CERN (in France/Switzerland), the International Space Station (in orbit), or the Human Genome project (finished). For us mortal researchers, a long time series rely on successful applications in grant cycle, after grant cycle, after grant cycle. This is a major hurdle for long projects. For instance, the Swedish Research Council, one of the main funding bodies in Sweden, turned down 84 % of the proposals in 2013. Thus, it only takes one year with bad luck to put a grinding halt to a time series.

And even if it is the senior researcher(s) who fund the project, it is often the PhD and postdoctoral students that actually run it. The length of a PhD varies (in Sweden it is 4 years) but are fairly short, and postdocs even shorter. When the student has graduated, chances are that the continued fieldwork simply dies, especially if techniques/skills were not shared between staff, or that if no suitable replacement was found. Also, similar to old land-owning dynasties (where a drunken playboy lost the manor house and the estate playing dice), a wrong recruit may effectively spoil a time series.

The staff is always important in any project...

The staff is always important in any project…

Another pitfall is curiosity. Researchers are by and large driven by curiosity, and sometimes the allure of greener pastures elsewhere seems more compelling to pursue, than to dig where you stand yet another year. Consequently, there is a risk that the leading scientist leaves a project that could have grown into an important long-term data series because he/she started to grow bored and restless. Thus, funding is scarce, time changes, people move and priorities shift. And as a result few time series reach a decade.

So how come the Ottenby data series is still running after twelve years?

The project was started by professor Björn Olsen (birder, physician, and the chair of Infectious Diseases at Uppsala University) in 2002. Björn had worked with tick-borne infections, such as Lyme Disease, and gastrointestinal bacteria such as Salmonella and Campylobacter, and when a move to Kalmar Hospital brought him close to Ottenby Bird Observatory it was like pieces of the puzzle just came together. For what can be more of a perfect match for a physician interested in birds than the avian zoonotic pathogen influenza A virus? And to have a field site at the best birding spot in Sweden! Fabulous!

The dismantled duck trap from an earlier trapping period 1960s – 1980 was resurrected and hopes were high that ducks would start to appear. Which they did, but only after a few months of very low trapping numbers, which made everyone wondering whether we would have to cancel the whole thing. Furthermore, funding was initially modest. Agencies thought there were more pressing research fronts – one review of a proposal actually dismissed the value of birds as hosts for influenza at all, as he/she believed minks were the most important hosts… But the work was done, the publications started to come out and brick by brick the flu house was constructed. Funding came in more steadily, and in the last decade we have had grants from the regional councils (FORSS, Sparbanksstiftelsen Kronan), national councils (including the Swedish Research Councils VR and FORMAS), and international councils (EU-FP6, NIAID), plus authorities such as the Swedish Board of Agriculture and the European Commission. So far the grants have come when we needed them, and never too late. It has been close sometimes, but so far so good. Another reasons to why we still are in the business are great collaborations! Already from the start we collaborated closely with Albert D. M. E. Osterhaus and Ron Fouchier from Erasmus MC in Rotterdam – a collaboration that has continued ever since. Other long term research friends are Johan Elmberg in Kristianstad, Åke Lundqvist in Stockholm, Vladimir Grosbois and Nicolas Gaidet at CIRAD, France, and Martin Wikelski at Max Planck in Constance, Germany, as well as Calle Nyqvist and Kalmar Surveillance AB! And many, many more!

A tipping point was when the highly pathogenic avian influenza H5N1 crossed Eurasia and hit Europe with force in the winter 2005/2006. This was almost like a deus ex machina moment, and suddenly the things we did were what everyone wanted. We were at the center – the eye of a hurricane – and delivered data to national and European authorities, helped with risk assessments, answered billions of news reporters, and through out it all continued to do good science and publish quality papers. In those days, Björn could be seen in three, four major newspapers, and national TV in the same day! Crazy times!

Throughout there has been a great team that made it all possible. The Ottenby project has so far directly involved seven PhD students:

  • Anders Wallensten (now at the Swedish Institute for Communicable Disease Control)
  • Neus Latorre-Margalef (now at University of Georgia, USA)
  • John Wahlgren (now at Qiagene in Denmark)
  • Josef Järhult (rising star at Uppsala University)
  • Goran Orozovic
  • Michelle Wille (still in the lab trenches)
  • Daniel Bengtsson (still in the field trenches)

And five postdocs:

  • Elsa Jourdain (now at INRA, France)
  • Gunnar Gunnarsson (now at Kristianstad University, Sweden)
  • Conny Tolf (longstanding king in the lab)
  • Alexis Avril (battling the computer with CMR epidemiology models)
  • Joanne Chapman (defending the innate immune system of ducks)

Lab work has been immense and a large number of hands have helped out during longer and shorter times. Among others: Abbtesaim Jawad, Sara Larsson, Maria Blomqvist, Diana Axelsson-Olsson, Lovisa Svensson, Petra Griekspoor, Jenny Olofsson, Jorge Hernandez, Oskar Gunnarsson, Lorena Grubovic, Anna Schager, and many, many more.

And in the field we talk about more than 40 duck trappers and >33,000 duck trap/retrap occasions! The two most frequent are Stina Andersson and Frida Johnsson that have made several seasons in the duck trap! The list is too long to post here – but I promise to return soon with a ‘best of’ post with statistics of duck trapping and trappers! Simply, without the trappers no science – incredibly important people!

Who knows what the future may bring? Painting by French artist in 1910 imagining what life would be in 2000.

Who knows what the future may bring? Painting by French artist in 1910 imagining what life would be in 2000.

To sum up a long post: we have done well because of fortunate timing, a good study site, great staff in the field and in the lab, good collaborators, and lastly great science! A few weeks ago we learned that we have funding for another three years – hopefully we can get this virus-host time series through adolescence and into adulthood! Time will tell.

In the mean time – shout it out for the ducks! Quack, quack, quack!

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Travel the world – can antibiotic resistant bacteria hitchhike with migratory birds?

By Jonas Waldenström

800px-Seasons1.svgThe beauty of a planet rotating around a slightly tilted axis (23.5 % to the orbital plane, to be exact) is the variation this brings to the intensity of the sunlight that hits the ground. It gives rise to predictable seasonal changes, at our high latitudes equal to a blooming spring, a warm summer, a foggy and mild autumn, and a frosty winter. The tilted axis also means that when it is dark and cold Sweden, it is sunny and lovely on the other side of the globe. Or in other words: when my kids make snow angels in the yard, the penguins rear their chicks under the austral sun.

A large number of animals, in particular birds, but also bats, antelopes, and even insects, utilize the shifts in climate and migrate to make most of the boom of ephemeral resources made available during the warmer seasons. Go to the food, reproduce, raise the offspring, and then pull back to chill-out at lower latitudes during the non-breeding season. A related phenomenon has evolved in some human populations – it is now common that British, German and Swedish people undertake annual migratory movements to Spain. Unlike the other animals mention above, the human movements mainly involve the post-reproductive life-stages. Hordes of well-off elderly now bask in the sun and marinate their livers in cheap red wine. Senescence in the sun.

Basking in the sun

Basking in the sun

A reason why our elderly go to Spain, and not onwards to Morocco, or east to Turkey is the apparent similarities to home. It is different in Spain, yes, but still rather similar to Bavaria, Sussex or Jönköping – just warmer and more vibrant. But not too dangerous, or too vibrant. You can trust the water to be (moderately) clean, and you can eat the food without worrying too much about infections. A prophylactic intake of wine and a diet consisting of 50% canned foodstuffs from home and you are unlikely to succumb to nasty disease.

In epidemiology, we know for certain that travel brings you in contact with disease-causing organisms. When we travel we expose ourselves to pathogens to which our immune systems lack experience, and therefore fail to take swift actions. This is nothing new – this was the fait of the native Indians in South America facing the import of pathogens such as smallpox and whooping cough from invading conquistadores. And in tropical Africa, the Yellow Fever took a large toll of the missionaries sent to christen the heathens; and those fortunate to survive had to endure repeated spells of malaria fevers, and gastrointestinal unpleasantness. Today, prophylaxis and vaccines make us more prepared, but disease risks are a constant worry for the traveller even in our time. And when we get back from our travels we may carry bugs with us and cause secondary cases back at home. In the last weeks we have seen cases of MERS coronavirus associated with haji in Mecca in Arabic countries and Europe. In many gastrointestinal bacterial infections we see a higher degree of antibiotic resistance in travel-associated cases than in domestic cases. Simply, what goes around comes around – and travelling stirs the pot to a boil.

Furthermore, what we put in the pot – the meat and the apples – is highly important. Very little on your dinner plate was grown in your backyard, in fact the ingredients that make up the dish may have travelled half around the globe before being eaten by you. Our food animals are amplifying hosts for many pathogens that cause human infections. The shear numbers of animal involved, the transportation of animals and products, and the frequent use of antibiotics in the food production industry make an additional potent driving force for antibiotic resistance evolution.

On top of this, in the last decade a question whether wild birds can act as flying intercontinental carriers of resistant bacteria has emerged, again and again. The idea can be summarized as follows: If a bird picks up a resistant bug during the non-breeding period, and that bacterium becomes established in the gut, there is a chance that the bacterium could be disseminated along the migratory route all the way to the breeding grounds. Given the state of the world, where for instance there is a marked south-to-north gradient in bacterial resistance problems in Europe, and likewise between South and North America, bird migration can be associated with words like ‘risk’ and ‘threats’. Birds as flying missiles, or pathogen arks.

Did the pathogens fit on the Ark?

Did the pathogens fit on the Ark?

Seemingly elegant, this hypothesis suffers from a number of limitations. First, birds need to be colonized by the nasty bacteria in the first place. Then the bacteria need to be maintained in the gut of the bird for a considerable time, allowing the bird and the bug to move during migration. Once migrated, the bacteria need to be shed in such a manner that they find their way to humans, or more likely our domestic food animals, and then end up on our plate. A long way to go for a microorganism.

Our research group is addressing such questions. The first step is to thoroughly survey the occurrence of antibiotic resistant bacteria in wild birds. This process has going on for a few years, and although there is room for many, many more studies we do know something by now. First, antibiotic resistant bacteria are everywhere, literally everywhere – from the Arctic tundra to the vicinity of the Antarctic research bases. Wildlife is exposed to resistant bacteria and some birds, such as gulls and crows, tend to often carry resistant bugs. Second, we know from genotyping studies that the same types of resistance markers occur in bacteria both from human/food animals and in wild birds. Thus, there is an exchange between sources, likely heavily tilted towards a dissemination from anthropogenic sources to wildlife (rather than the opposite) and it seems most strongly occurring in specific bird species that are in close proximity to humans and food animals.

The most recent study from our group on this subject was published a few weeks ago. The study focused on a bird species that qualify for all of the check points that make a species a possible resistance disseminator culprit: the Franklin’s gull Leucophaeus pipixan. This species breeds in North America, in shallow lakes on the prairies between USA and Canada, but spend the non-breeding season all the way down in southern South America. In Peru and Chile it is common to see thousands of Franklin’s gulls at river mouths on the Pacific coast. And in these rivers the collected wastewater from millions of people are discharged. Thus the gulls find themselves in a habitat that potentially is full of unwanted antibiotic resistant microbes.

Gaviotas de Franclin at Con-con. Photo Jonas Bonnedahl

Gaviotas de Franclin at Con-con. Photo Jonas Bonnedahl

The team visited the Aconcagua and the Bio-Bio rivers in central Chile, where the water met the sea at Concón and Talcahuano, respectively. At these gorgeous sand beaches they sampled Franklin’s gulls. Samples were also collected from 49 healthy human volunteers from the city of San Antonio. Back in Sweden, the samples were cultivated for the presence of Escherichia coli, the most commonly used indicator bacterium in antibiotic research. Randomly collected isolates were then tested against a panel of 10 different antibiotics to measure the degree of acquired resistance. The original samples were also screened for a specific class of resistance mechanisms called extended spectrum beta-lactamases. Bacteria that produce these ESBL enzymes are resistant to a range of lactam antibiotics. ESBL resistance is an emerging problem all over the world, causing suffering and premature deaths.

The resistance profiles from the 267 avian E. coli were similar to that of human samples, with moderate resistance to ampicillin (10.1 %), tetracycline (8.2 %), and streptomycin (6.0 %). Only nitrofurantoin displayed full susceptibility in all samples; all others were in the range of 0.5 – 5 %. However, looking at ESBL in the samples, the gull sample had a prevalence of 30 %, compared to 12 % in the human sample. Not only were there loads of ESBL-positive birds, the ESBL variants were dominated by blaCTX-M-1 and blaCTX-M -15 genotypes that has been extensively described in E. coli causing human infections. Also a multilocus sequence typing of the bacteria showed connections to bacterial genotypes common in infections.

Thus, on the warm sands of Chile sits Franklin’s gulls and enjoy the austral summer. In their intestines they carry resistant bugs with the same genotypes that can cause  infections in humans. Remains to show if the birds can carry these bacteria to the US, or whether carriage is short-lived and more a product of the local environment.

Link to the article here:

Hernandez J, Johansson A, Stedt J, Bengtsson S, Porczak A, et al. (2013) Characterization and Comparison of Extended-Spectrum β-Lactamase (ESBL) Resistance Genotypes and Population Structure of Escherichia coli Isolated from Franklin’s Gulls (Leucophaeus pipixcan) and Humans in Chile. PLoS ONE 8(9): e76150. doi:10.1371/journal.pone.0076150

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Lost (and found) in translation

By Jonas Waldenström

We aim for the stars

We aim for the stars

Your mum likely told you not to brag, but I will do it anyway: we have such an awesome research group, and we are on a roll! A rare collection of individuals that fits surprisingly well together. It is like if you randomly twisted Rubik’s cube with your feet in the darkness and it came out all solved. Yes, we are great scientists (and humble), but more importantly we are witty, intelligent, friendly and caring. Good human beings.

Stewing in our pot at the moment we have ingredients from Iraq, Canada, New Zeeland, France, Catalonia, and Sweden (including the God’s forgotten little city of Västervik and the forested no-man’s-land Värmland). This makes for interesting conversations and different perspective on things. And good food. Especially if you like moose.

Some see 'the grandness of nature' in this picture - others see the 500+ kg of meat! (Photo from Wikimedia Commons, Oliver Abels)

Some see ‘the grandness of nature’ in this picture – others see the 500+ kg of meat! (Photo from Wikimedia Commons, Oliver Abels)

I enjoy the coffee discussions, which regularly include parasite life histories, the more gory the better, the weirdness of Swedish people in general, and the faiblesse for putting things in tubes in particular, all untranslatable words and silly signs. And, of course, the ever ongoing friendly bickering between the Kiwi and the Frenchman.

How Swedish can it get? This is smoked raindeer cheese in a tube! (Photo Jo Chapman)

How Swedish can it get? This is smoked raindeer cheese in a tube! (Photo Jo Chapman)

Language is both a barrier and bridge. Even though English is the language we us for communication, our various accents, proficiency and speed create misunderstandings. For instance, a ‘smiling’ and a ‘smelling’ face are two different things. And we do not sample ‘girls’ we sample ‘gulls’. And – very importantly – we put ‘candles’ not ‘condoms’ on cakes.

It is, as we often say in our group ‘largely sufficient’.

What the duck says

By Jonas Waldenström

Unlike the recent controversy regarding fox sounds, everyone knows that the duck says ‘quack’. And when I say everybody, I mean everybody – from the smallest toddler to the toothless elder. The ‘quack’ seems cosmopolitan as well, albeit with some variation in spelling – similar to the fact that dogs say ‘voff’, ‘viff’, or ‘vaff’ depending on where in Europe you are.

Okay, no controversies there. But actually, ‘quack’ isn’t all ducks say. You have teals that say ‘crecc’, garganeys that gives croaking sounds, and you have whistling ducks that (surprise, surprise) whistle. But the good old fat (and tasty) Mallard says ‘quack’. At least most of the time.Screen Shot 2013-11-03 at 9.07.32 PM

They can also whistle, at least the males do when they want to find a mate. And that is of course a great signal to use against them, for hunting purposes. Here is a video where a bearded man shows how to use the Duck Commander . (And why are they always equipped with beards??). A sweet tune, anyway.

If you are more up for the real thing, here is a link to the Xeno-Canto where over 40 minutes of Mallard quacking is stored. Music for the masses!

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