Do wild birds give you campylobacteriosis?

Blackbird, Turdus merula. Photo from Flickr under a CC BY-NC-ND 2.0 license.

Blackbird, Turdus merula. Photo from Flickr under a CC BY-NC-ND 2.0 license.

There is magic in large numbers. Most often we scientist – regardless if we are field scientists or lab rats – struggle with acquiring sufficiently large sample sizes for the statistical tests we have set out to do. There are ways to deal with sparse data, but nothing beats a good-looking huge dataset if you want to test your hypothesis with confidence. Moreover, given that every biological system we measure has a degree of uncertainty, so called noise, means that if we are to find effects that are small we need to collect a lot of data.

Earlier this year, I co-authored a publication on Campylobacter epidemiology that really took advantage of large numbers. In this case, Cody et al. investigated if people get campylobacters from wild birds. This is something that has been suspected given the huge impact domestic poultry has – the single largest source of human campylobacteriosis – but not really proven. Over the years, the lab in Oxford has collected an enormous  dataset on the occurrence of Campylobacter jejuni in patients in Oxfordshire, UK. Not only is there a lot of data, each and every clinical case is associated with a genotyped bacterial isolate. That is an awesome treasure trove to investigate.

In this study, 5628 genotyped clinical isolates from Oxfordshire were run in a STRUCTURE analysis to try to associate each isolate with a putative source. The rationale here is that there are distinct sets of C. jejuni genotypes in different types of animals, especially in different species of birds. And as campylobacteriosis is a zoonotic infection with little to non human-to-human transmission such an analysis can indicate the degree of relevance of different sources for human epidemiology.

Did that sound awfully advanced? Perhaps. It really is quite simple. Consider you make a row of bins. Each bin gets a name, such as ‘chicken’, ‘cattle’, ‘goose’, ‘blackbird’ etc. Then you take each bacterial isolate in your hand, scrutinize it and put in a bin that you think it fits best in. A little bit like a sorting box for children. Starshaped objects go into the starshape hole, square objects in the square hole, etc. Except that it in this case it is the degree of resemblance at the genetic level that decides whether an isolate should be grouped with a particular source. The second thing is that you let the computer rerun this procedure over and over again until you get a probabilistic assignment to each bin.

STRUCTURE

The principle of STRUCTURE analysis.

In this paper, it was shown that the proportion of clinical isolates from Oxfordshire attributed to wild birds was 2.1%-3.5% each year. That is way lower than the values for chicken products, but given the very high incidence of campylobacteriosis in the human population it still means a large number of actual infections caused by bacteria that normally are found in wild birds. Which wild birds, you may ask. Primarily thrushes, is the answer – at least in Oxfordshire. The blackbird and the song thrush are two common garden birds that like to live close to us humans. Looking at the seasonal variation, the analysis showed that wild bird associated campylobacteriosis cases was more common during the warmer months of the year. This makes sense, as it is in summer when we loiter around in our gardens, and in nature, eating fruits and vegetables potentially contaminated with bird feces.

There is magic in large numbers, for sure.

Link to the paper:

Cody, A.J., McCarthy, N.D., Bray, J.E., Wimalarathna, H.M.L., Colles, F.C., Jansen van Rensburg, M.J., Dingle, K.E., Waldenström, J. & Maiden, M.C.J. 2015. Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom. Environmental Microbiology Reports 7: 782-788.

What are the effects of influenza virus sampling on ducks?

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In our research we capture and sample birds. Many, many birds – as in several thousands of birds over the years (2002 up to now). The reason we do this is to be able to connect individual birds with a test result. Is this duck infected or not with influenza? If, so what was its age, sex, and body condition at the time of sampling? This information helps us understand the disease dynamics in the mallard – virus system; how viruses affect the birds, and how birds affect virus evolution through their immune system.

We like to think that our meddling with the ducks is rather mild. The normal procedure includes the actual capture in the duck trap, the ringing and measuring of the bird, and the biological sampling procedure – normally a fecal or cloacal sample, but also feather samples or blood samples are sometimes taken. At times we have also used different loggers to collect data on movements, ranging from local stopover to migratory flights.

Given the questions we address in our research, we of course want the effects to be as small as possible. We haven’t formally investigated this ourselves. Fortunately, a recent publication, in the journal Ibis, used data from a similar influenza A virus surveillance scheme in France to investigate whether sampling incurs a cost or not. The authors focused on blood and cloacal swab sampling, and primarily analyzed survival and re-encounter rates.

They investigated four different duck species: Tufted duck, Pochard, Mallard and Teal. By comparing sets of ducks that only differed in which sampling type that had be taken (no sampling, cloacal sampling, blood sampling) the authors could use capture-mark-recapture analysis and logistic regression to test the hypothesis that sampling affected survival and re-encounter rates. To cut a long story short, they did not find any support for a negative effect on survival for any of the duck species tested due to sampling. Furthermore, re-encounter rates did not differ for three of the species, but did so for Teals (suggesting trap avoidance in this species).

This is a very good initiative, and I hope more researchers follow up their analysis. In my group, we have a lot of capture-mark-recapture data plus data on ring recoveries and we should be in a good position to look at these types of questions in the future, too. The results from the French paper corroborate my general gut feeling and some early preliminary analyses we conducted years ago. But it is good to get reliable, peer-reviewed data on this. Not the least given that surveillance schemes in Europe and North America have included sampling of hundred thousands of birds in the search for highly pathogenic H5N1 and H5N8.

Link to the article:

Guillemain, M., Champagnon, J., Gourlay-Larour, M-L., Cavallo, F., Brochet, A-L., Hars, J., Massez, G., George, T., Perroi, P-Y., Jestin, V. & Caizergues, A. 2015. Blood and cloacal swab sampling for avian influenza monitoring has no effect on survival rates of free-ranging ducks. Ibis 157: 743-753.