Monday, July 29, 2013

Birds of America

Yesterday evening, I was watching another compelling BBC production, broadcast on Danish television: Earthflight, North America. In quite a unique way, the viewers got the rare opportunity to see through the eyes of birds such as eagles, geese, and pelicans and follow birds as they were migrating, escaping, hunting for prey, etc. It made me think of the 19th century masterpiece 'Birds of America' by John James Audubon, which can be viewed in the National History Museum in London. The book features 435 stunning hand-coloured plates that show birds life-size, in natural positions and in their natural habitat.

One of the things that I find interesting - and quite unexplored - is Blastocystis in birds. By 'unexplored' I mean that relatively little sampling has been done, and so the number of observations of Blastocystis in birds is still limited compared to other types of hosts. However, there is a brand new paper out in 'Infection, Genetics and Evolution' which includes observations on Blastocystis in birds (of America!).

You see, I was invited in on a study by colleagues in Colombia who had access to DNA from quite a few faecal samples from a number of host species, including feral birds, and what we found confirms the quite unambiguous trend seen so far: Birds - no matter where on this planet - appear to be colonised mainly by ST6 and ST7. As a matter of fact, in the present study only ST6 was seen in almost 50 Colombian passerine birds of varying species, most of which I believe are limited in geographical distribution to the Americas: Passer domesticus, Thraupis episcopus, Oryzoborus maximiliani, Sicalis flaveola, and Petrochelidon pyrrhonota. Moreover, only one allele of ST6, allele 122, was identified. Notably, the prevalence of Blastocystis in the sampled bird population was 90%. I believe that this is the first official report on Blastocystis in passeriformes. Other major groups of birds previously sampled include galliformes, anseriformes, and ratites (Stensvold et al., 2009; Alfellani et al., 2013).

Other subtypes have been reported in birds (Alfellani et al., 2013), but due to the very low number of samplings these subtypes may be more or less co-incidental/abberant findings. Of note, some samples from birds have been untypable. I have a slight recollection of detecting ST3 in Icelandic rock ptarmigans (in mixed ST infection) collected by Dr Karl Skírnission, but that certainly needs confirmation.

Bird contact/bird droppings - a significant source of Blastocystis in humans? Me feeding some 'Birds of Australia'. Photo by Dr Rebecca J Traub.

ST6 is very rarely seen in humans in Europe. In other parts of the world, for instance in Egypt and some Asian countries, ST6 appears relatively common, but we do not know much about 'bird subtypes' in those particular regions. Also, the situation in the US and Canada is more or less completely unknown (Blastocystis subtyping is something that appears not to attract research groups in North America apart from the one led by Dr Ron Fayer in Beltsville, Maryland).

ST7 is occasionally seen in humans in countries such as Sweden and Denmark. But in my - still limited - experience, individuals infected by these subtypes are not necessarily prone to 'suffer more' from intestinal symptoms than those who do not have these subtypes. While human cases of ST6 (and ST7) may represent cases of zoonotic transmission, it is far to early to draw any conclusions on this. It would be important to compare ST6 and ST7 18S alleles from humans and birds. MLST typing systems for these two subtypes are not yet available, but 18S analysis in itself may prove valuable for molecular epidemiological analyses as in the case of other subtypes (Stensvold et al., 2012).

Walton Ford: "Falling Bough" (Source). You will also see the now extinct Passenger Pigeon in 'Birds of America'.


Ramírez JD, Sánchez LV, Bautista DC, Corredor AF, Flórez AC, & Stensvold CR (2013). Blastocystis subtypes detected in humans and animals from Colombia. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases PMID: 23886615

Alfellani MA, Taner-Mulla D, Jacob AS, Imeede CA, Yoshikawa H, Stensvold CR, & Clark CG (2013). Genetic diversity of Blastocystis in livestock and zoo animals. Protist, 164 (4), 497-509 PMID: 23770574

Stensvold CR, Alfellani M, & Clark CG (2012). Levels of genetic diversity vary dramatically between Blastocystis subtypes. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 12 (2), 263-73 PMID: 22116021

Stensvold CR, Alfellani MA, Nørskov-Lauritsen S, Prip K, Victory EL, Maddox C, Nielsen HV, & Clark CG (2009). Subtype distribution of Blastocystis isolates from synanthropic and zoo animals and identification of a new subtype. International Journal for Parasitology, 39 (4), 473-9 PMID: 18755193

Monday, July 22, 2013

My 'Thoughts on Blastocystis' now as eBook in Amazon!

I edited and assembled quite a few blog posts and published them as the eBook Thoughts on Blastocystis in Amazon! 

Buying it will set you back only about one pound, and even if you're completely broke, you may be able to borrow it through the Kindle Owners' Lending Library service. How cool is that?!

Anyway, the book summarises a lot of facts, thoughts, hypotheses and new research data on Blastocystis with a personal take here and there and also with parallels to other areas of clinical microbiology, gastroenterology and microbiomology. I hope you'll enjoy it!

Please also note that our review 'Recent Developments in Blastocystis Research' published in Advances in Parasitology Vol. 82 is also available for purchase in Amazon.


Clark CG, van der Giezen M, Alfellani MA, & Stensvold CR (2013). Recent developments in Blastocystis research. Advances in Parasitology, 82, 1-32 PMID: 23548084

Wednesday, July 17, 2013

ICOP XIV in Vancouver 28 July to 2 August 2013

The International Congress of Protistology (ICOP) takes place every four years, and so the 14th ICOP takes place from the 28th of July to the 2nd of August in Vancouver, Canada.

Most single-celled parasites infecting humans are known as 'protozoa', but Blastocystis does not belong to this group of organisms; meanwhile, protists comprise both protozoa along with a multitude of other very diverse species, including the Stramenopiles, to which Blastocystis belong. Protists include both uni- and multi-cellular eukaryotic organisms and are distinguished from animals, fungi and plants by a simpler cellular organisation.

The conference abstract book can be downloaded here, and presents a perplexing multitude of very interesting and diverse abstracts. There are four abstracts on Blastocystis alone, and two of them are presented by Dr Roger's group in Halifax, Canada + their international colleagues.

Phylogenomic analyses of large-scale alignments enable the outlining  of evolutionary relationship among major eukaryotic lineages and are highly facilitated by recent technological advances; several abstracts deal with such analyses. Eme et al. (Roger's group) present additional observations from an important phylogenomic study of Blastocystis sp. ST1 reiterating the importance of lateral gene transfer in enabling Blastocystis to adapt to a parasitic life style. Gentekaki et al. (Roger's group) present data on the draft genome of Blastocystis sp. ST1. Until recently, only one Blastocystis genome was available, namely that of ST7. The present data show remarkable differences between the ST1 draft genome and the ST7 genome. While the genome of ST7 comprises 18.8 MB, the genome of ST1 is only 14.0 MB long, and apparently there's  virtually no synteny among the two genomes! Almost 30% of the 5,637 predicted ST1 genes had no homologues in ST7. What is more: 'Orthologous proteins shared by the two genomes are only 51% identical on average. The predicted secreted protein repertoire also differs significantly; ST7 possesses ~300 whereas ST1-NandII has only 129.' Indeed, it appears that Blastocystis comprises some extremely diverse organisms! We are still trying to explore the clinical implications of this...

Alison Jacob, Graham Clark, and I contribute with an abstract on comparative analyses of 8 mitochondrion-like organelle (MLO) genomes from 5 subtypes. Contrary to the nuclear genomes, there is complete synteny and homology between the subtypes at MLO level, although the sequences diverge by up to 25%.

Tamalee Roberts and colleagues present data from analysis of 438 samples from a staggering 38 species in Australia. They found Blastocystis in 18 species, including kangaroos, wallaroos, snow leopard, and ostrich, and obtained subtype data from a total 80 samples.

The genetic universe of  Entamoeba is expanding quickly in these years. Silberman and colleagues (Arkansas, USA) provide data from analysis of Entamoeba from insects such as honeybees, cranefly larvae and multiple cockroach and beetle species. There is no information on any pathogenic properties of insect-infecting Entamoeba however.

The abstract book is also a place to learn that marine diatoms are responsible for about one-fifth of global photosynthesis (Armbrust, Seattle, USA) and that photosynthetic marine algae are responsible for 50% of global CO2 uptake (Worden, Moss Landing, USA).

There is quite a few abstracts on protist diversity and how NGS tools allow us to study this in a more comprehensive and exhaustive way and the need for taxonomic standardisation. Protist-barcoding includes metabarcoding (de Vargas, Roscoff, France) and some of the taxonomic challenges related to this are presented by Dr Pawlowski, Geneva, Switzerland.

Similar to Blastocystis, the trypanosomatids (Trypanosoma and Leishmania) cannot be classified according to morphology and host range, hence, molecular markers are warranted, and there's an abstract by Maslov (California, USA) on the general applicability of 'alternative barcoding', namely the use of Spliced Leader (SL) RNA gene repeats.

There is quite a few abstracts on 'rare ciliates' in harsh environments, and I bring your attention also to a previous blog post on extremophilic eukaryotes.

We also learn that free-living protozoa can tell us more about the origins of anaerobic parasites (Simpson, Halifax, Canada). And there is a group setting up a Plasmodium life cycle to study the metabolic steps critical to the malaria life cycle (McFadden, Melbourne, Australia).

There's a really teasing abstract on analysis of surface water samples from Italy, where Angelici et al. have developed a barcoding-like analysis based on ITS 2 and SSU rRNA genes to enable detection of parasites of clinical and epidemiological interest, but there is no information on how exactly the method was designed, and the authors do not list the parasites that they found... I'm not attending the congress myself, so here's hoping for some twitter updates on this...

One could go on and on, - why don't you have a look inside the abstract book yourself?!

Incidentally, Dr Tai from Vancouver, Canada, promts us to help protists getting into pop culture by wearing t-shirts silkscreened by hand using Ernst Haeckel's diagrams of phytoplankton and light micrographs of parabasalids! Don't know exactly how to get hold of these, but googling 'Ernst Haeckel' and 'phytoplankton' might get you started (go for Google images).

For those interested in protists (and art!), I recommend the blog 'The Ocelloid'. 

Suggested reading:

Denoeud F, Roussel M, Noel B, Wawrzyniak I, Da Silva C, Diogon M, Viscogliosi E, Brochier-Armanet C, Couloux A, Poulain J, Segurens B, Anthouard V, Texier C, Blot N, Poirier P, Ng GC, Tan KS, Artiguenave F, Jaillon O, Aury JM, Delbac F, Wincker P, Vivarès CP, & El Alaoui H (2011). Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. Genome Biology, 12 (3) PMID: 21439036

Stensvold CR, Lebbad M, Victory EL, Verweij JJ, Tannich E, Alfellani M, Legarraga P, & Clark CG (2011). Increased sampling reveals novel lineages of Entamoeba: consequences of genetic diversity and host specificity for taxonomy and molecular detection. Protist, 162 (3), 525-41 PMID: 21295520

Wednesday, July 10, 2013

This Month In Blastocystis Research (JUL 2013)

The open access journal 'Tropical Parasitology' (published by the Indian Academy of Tropical Parasitology) has included a symposium on Blastocystis in their January-June (Vol. 3) issue (available here). The symposium comprises three papers; one is on "taxonomy, biology and virulence", the next is on genetic diversity and molecular methods for diagnosis and epidemiology, and the last one is on treatment controversies. I believe that it may take quite a while before these papers will appear in PubMed.

The first paper written by Drs Parija and Jeremiah sums up a few of the aspects related to (especially historical) taxonomic issues and very little on the actual biology of Blastocystis. Meanwhile, there is quite a substantial section on Blastocystis morphology. Regarding virulence, the authors mention the possibility that differences in virulence may be due to differences in subtypes, but that subtyping alone does not predict pathogenicity which in part may be due to varying levels of intra-subtype genetic variation. The authors also briefly mention some of the morphological and phenotypical observations that have been associated with 'pathogenic Blastocystis', such as the amoeboid stage, large cells, rough surface, slow growth rate, and increased binding to lectins. It is always interesting to speculate on such associations, but it must be kept in mind that results from in-vitro experiments may not necessarily reflect in-vivo situations.

One topic that keeps popping up in the literature - and also in two of the papers here in this symposium - is the possibility of 'amoebic forms' of Blastocystis being associated with symptomatic infection. This hypothesis was introduced in 2006 by Tan and Suresh, I believe; Scanlan (2013) speculated that amoeboid forms might be the nutrient acquiring form potentially selecting for bacterial virulence or certain bacterial communities through grazing; please go here for more thoughts from a previous blog post.

My own experience on Blastocystis morphology mainly stems from looking at cultures, and since we practically only get isolates from patients with gastrointestinal disease, I don't know what Blastocystis cultures from asymptomatic individuals look like. A dear colleague of mine - Marianne Lebbad, a brilliant Swedish parasitologist with many years in business - sent me the picture below (light microscopy of a faecal concentrate) and speculates that Blastocystis might be able to form groups/clusters of cells, maybe even with the ability to form a mono-layer on the surface of the gut mucosa? I've never observed the cluster formation in cultures, but then again, we have no idea of whether the stages seen in in vitro cultures (microaerophilic environment) are identical to the in vivo stages (strictly anaerobic), and exactly how Blastocystis lives and multiplies in the colon... Anyway, the idea of biofilm comes into mind. It would be nice to learn more from colleagues with a similar experience.

Light microscopy of Blastocystis apparently forming a cluster of cells; we wonder whether the cells are in fact 'glued' together and if so, how? Courtesy of Dr Marianne Lebbad.

Moving on to the next paper, this one was written by me and deals mostly with issues and developments within the field of diagnostics, molecular characterisation, and molecular epidemiology. The target audience comprises clinical microbiologists and those involved in Blastocystis epidemiology and genetic diversity research. Included is a table, which is basically a reproduction of the one included in the recent paper by Alfellani et al. (2013) displaying the distribution of subtypes in humans across different geographical regions. I hope that the open access feature of this paper will prompt even more researcher into Blastocystis epidemiology! At least it is currently listed on the site as 'popular'!

The third paper in the string is written by Drs Sekar and Shanthi. These authors put emphasis on the conspicuous lack of data on the metabolic processes of Blastocystis, making it difficult to establish how to best approach antibiotic intervention; we must anticipate that with more genomic and transcriptomic data analyses arriving within a foreseeable future we will soon know much more about this. They also reiterate what has been put forth by many, namely that differences in eradication may boil down to differences in drug susceptibility, which again may be due to a variety of reasons, including genetic diversity, which is extreme in Blastocystis.

According to these authors, 'therapy should be limited to patients with persistent symptoms subsequent to a complete work up for alternative etiologies'; at the present stage this appears sensible, although clinicians would probably appreciate a clearer definition of 'symptoms'!

The review goes through some of the drugs most commonly used for treating Blastocystis, including metronidazole, paromomycin and co-trimoxazole, but also includes a few data on the use of the probiotic Saccharomyces boulardii in attempts to eradicate Blastocystis. There is not very much on the mechanisms of drug action, - it's more like a summary of data coming out from different studies, including the few placebo-controlled ones.
Regarding co-trimoxazole (which is also known as 'Bactrim' or 'Septra') this drug combo is often administered to HIV-patients prophylactically against Pneumocystis. In a study of parasites in Danish HIV patients, only 6/96 patients were given co-trimoxazole (unpublished data); two of these patients had Blastocystis. Hence, one 'alternative' way of finding out about the efficacy of co-trimoxazole on Blatocystis is to test the stools from patients undergoing long-term Pneumocystis prophylaxis comparing these patients to a cohort not receiving Pneumocystis prophylaxis but otherwise similar.

I find it a bit peculiar though to go through a review on treatment data that does not at one single point mention the need for sensitive diagnostics when evaluating courses of treatment and the identification of carriers and non-carriers. Also, there are some passages which are quite difficult for me to follow, for instance p. 36, second column, bottom section.

I hope that this symposium will inspire some of our colleagues and contribute to an increased understanding of Blastocystis.



Parija SC & Jeremiah SS (2013). Blastocystis: Taxonomy, biology and virulence Tropical Parasitology DOI: 10.4103/2229-5070.113894
Stensvold CR (2013). Blastocystis: Genetic diversity and molecular methods for diagnosis and epidemiology Tropical Parasitology DOI: 10.4103/2229-5070.113896  

Sekar U & Shanthi M (2013). Blastocystis: Consensus of treatment and controversies Tropical Parasitology DOI: 10.4103/2229-5070.113901


Scanlan PD (2012). Blastocystis: past pitfalls and future perspectives. Trends in parasitology, 28 (8), 327-34 PMID: 22738855

Stensvold CR, Nielsen SD, Badsberg JH, Engberg J, Friis-Møller N, Nielsen SS, Nielsen HV, & Friis-Møller A (2011). The prevalence and clinical significance of intestinal parasites in HIV-infected patients in Denmark. Scandinavian Journal of Infectious Diseases, 43 (2), 129-35 PMID: 20936912  

Tan TC & Suresh KG (2006). Predominance of amoeboid forms of Blastocystis hominis in isolates from symptomatic patients. Parasitology Research, 98 (3), 189-93 PMID: 16323025