Showing posts with label parasite. Show all posts
Showing posts with label parasite. Show all posts

Tuesday, September 1, 2015

This Month in Blastocystis Research (AUG 2015)

I would like to highlight a comment that we published in PLoS Pathogens, - a paper that is free for download here. It gained some attention on Twitter, and it was recently reviewed in the Faculty of 1000.

We basically highlight the tricky situation that we so often encounter in the field of clinical microbiology, namely the one in which all non-fungal organisms isolated from the human intestinal tract are being referred to collectively as 'parasites'. The word 'parasite' has a negative connotation, indicating that the organism exploits the host with detrimental effects on the host. While this is true for some ciliates, for instance Giardia, other ciliates may in fact be mutualists, which means that these organisms have adapted to a life within a host, providing the host with one or more advantages. One such example is seen in herbivores, where ciliates and flagallates break down cellulose.

In the clinical microbiology lab we face different types of organisms when dealing with stool samples: Giardia, Cryptosporidium and Entamoeba histolytica are considered true parasites, i.e. organisms benefitting from the environment of a host, at the expense of the host, and symptoms such as diarrhoea may develop, indicating host damage. Parasites such as Cryptospordium are usually infecting an individual for a short while, with immunity developing. Meanwhile, we also encounter eukaryotic organisms that are known to be able to colonise the intestine for a very long time, - decades, without being expelled by the host; Blastocystis belong to this group. For some reason it is as if the body 'tolerates' the presence of the organism. Maybe Blastocystis is good at evading local immune responses, or maybe the body wishes to 'keep' Blastocystis for some reason and so  developed a way to tolerate it... as I've hinted at before on this blog, maybe Blastocystis may assist us in one or more metabolic processes, for instance, either directly or indirectly, maybe by selecting for or influencing bacterial communities. Indeed, we recently found evidence of Blastocystis being specifically related to certain groups of bacteria, which, if confirmed, opens up for a whole new line of research, including the use of Blastocystis as a probiotic.

I know that this last sentence may sound harsh in some people's ears; nevertheless, most research involving Blastocystis so far has been quite static and unimaginative, and it's about time that food microbiologist and the like start taking an interest in the micro-eukaryotes that tend to be common and stable conolisers of our guts.

If YOU take an interest in this topic, I suggest you look up the articles cited below.

References and further reading:

Andersen LO, Bonde I, Nielsen HB, & Stensvold CR (2015). A retrospective metagenomics approach to studying Blastocystis. FEMS Microbiology Ecology, 91 (7) PMID: 26130823

Lukeš J, Stensvold CR, Jirků-Pomajbíková K, & Wegener Parfrey L (2015). Are Human Intestinal Eukaryotes Beneficial or Commensals? PLoS Pathogens, 11 (8) PMID: 26270819

Parfrey LW, Walters WA, & Knight R (2011). Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Frontiers in Microbiology, 2 PMID: 21808637

Scanlan PD, Stensvold CR, Rajilić-Stojanović M, Heilig HG, De Vos WM, O'Toole PW, & Cotter PD (2014). The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. FEMS Microbiology Ecology, 90 (1), 326-30 PMID: 25077936

Tuesday, March 31, 2015

This Month in Blastocystis Research - MAR 2015

"Show me your gut bacteria and I'll tell you if you're infected with Entamoeba"

One of my 'partners in crime', science reporter Jop de Vrieze, made me aware of a study just published now by Elise R Morton and colleagues. The study appeared in bioRxiv—The Preprint Server for Biology, operated by Cold Spring Harbor Laboratory. The study is totally in line with one of the research foci in our lab.

The paper is called 'Variation in rural African gut microbiomes is strongly shaped by parasitism and diet', and can be downloaded here. The backbone in this type of research is the recognition that studies revealing a large contrast between the microbiomes of populations in developing countries and those of populations in urban industrialised areas have shown that geography is an important factor associated with the gut microbiome, but that such studies yet have to disentangle the effects of factors such as climate, diet, host genetics, hygiene and parasitism.

It's very refreshing that for once, 'parasitism' is included in such considerations. As mentioned in one or more of my previous blog posts, we have metagenomics data stongly indicating that Blastocystis colonisation is associated with certain microbial communities. As of yet, we have no idea about cause and effet, but the idea alone is immensely intriguing.

A large and a small cyst of Entamoeba coli. Courtesy of Dr Marianne Lebbad.
Now, Morton et al. have produced data that suggest that the presence of Entamoeba—another gut-associated eukaryotic genus comprising multiple species of varying pathogencitiy—is strongly correlated with microbial composition and diversity. They showed that an individual's liability to being infected by Entamoeba could be predicted with 79% accuracy based on gut microbiome composition.

The authors used 16S PCR and Illumina-based sequencing of 16S amplicons, and I could have wished that molecular assays, e.g., the 18S PCR that we have developed in our lab + associated software, had also been used to test the faecal samples from the 64 individuals enrolled in the study in order to obtain more precise data, not only on Entamoeba but also on other human-associated gut protists, such as Blastocystis.

While alpha (intra-host) diversity of Entamoeba-positive individuals was significantly higher than that of Entamoeba-negative individuals, analysis of the beta (inter-host) diversity revealed that gut communities across Entamoeba-positive individuals were more similar than across Entamoeba-negative individuals, suggesting that, as alpha diversity increases, there are fewer potential stable states for individual gut communities, or that infection by Entamoeba drives changes in the microbiome that are dominant over other factors.

Right—this is Entamoeba, I know, but in principle, the type of analyses that were performed in the present study could be applicable to Blastocystis, Dientamoeba, and other gut parasites, which may help us understand their role in health and disease. Are these parasites able to influence gut microbiota? Can they be used for gut microbiota manipulation? Or do they only infect people with certain microbiota profiles? Time will show... maybe.

For those of you who would like to read more about what is shaping our microbiomes and how the gut microbiota may impact on our gastrointestinal health, I recently did a couple of blog posts for United European Gastroenterology (UEG) Education that might be of some interest:

Are we finally saluting the fungal kingdom as a co-ruler of GI health and disease?

The intestinal microbiome—Rosetta Stone or Tower of Babel?


Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, Blekham R, Segurel L.
Variation in rural African gut microbiomes is strongly shaped by parasitism and diet. bioRxiv doi

Wednesday, February 4, 2015

This Month in Blastcystis Research - JAN 2015

I'm going to dedicate this blog post entirely to the upcoming 1st International Blastocystis Symposium.

I'm not sure how much advertising there is for this congress (our budgets are limited), but the fact that we are already receiving abstracts is a good sign! Abstacts may be submitted until April 1st, 2015. Please note that the 'early bird' registration discount expires at the 15th of February.

You will find the online abstract submission form here.

If you think about going but have not paid a visit to the official conference website, I recommend you to do so, clicking this link. You'll hopefully find most if not all the information that you'd be looking for, and there's a lot to be learned. Please also make sure to browse the social programme in order to be able to make appropriate arrangments.

It's a two-day symposium, running from the 28th to the 29th of May, 2015. Moreover, on the 27th, there will be an all-day workshop on various diagnostic and molecular epidemiological aspects, including a barcoding (subtyping) course. There will be more info on that very soon, - please keep an eye on the website.

We are doing all we can to attract scientists with vast experience in Blastocystis research to cover the floor with exciting and stimulating talks, and I think we're doing more than OK. Some of the speakers will be writing up reviews on their respective topics, and these reviews will appear in a special themed issue in Parasitology International.

There will be a quite a few prizes for best talks and posters, etc., thanks to ELSEVIER among others.

It will be one-track symposium, and the first day will focus mostly on some fundamental topics, such as genomics and biochemistry, while the next day will include talks on clinical and diagnostic data.

It's my clear impression that main organiser Dr Funda Dogruman-Al is working 25 hours a day to make everything come together, and Dr Hisao Yoshikawa has also already invested a lot of energy.

Again: please note that early registration will close at the 15th of February, and abstract submission deadline has been extended to April 1st, 2015.

Looking very much forward to seeing you there!

Saturday, May 10, 2014

Parasite-Microbiota-Host Interactions

One of the current mantras in microbiology is that 'bacterial cells in the human body outnumber human cells 10 to one'. This has been known for a long time, but I guess that the main reason why this is being hyped nowadays is due to the fact that current technologies now enable us to look at entire microbial communities in a given ecological niche at any time point and how for instance they relate to health and disease.

Casadevall and Pirofski already made this point clear back in 2000 in their great minireview in the journal Infection and Immunity on 'Host-Pathogen Interactions: Basic Concepts of Microbial Commensalism, Colonization, Infection, and Disease'. This is a great paper that helps us understand and distinguish between the many ways microbes impact on our body. First and foremost, it allows us to understand that microbes can be commensals in some hosts but cause disease in other hosts, and that very few microbes are obligate pathogens.

Anatomical drawing of abdomen, ca. 1900 (Elisa Schorn). Source.

Commensalism is defined by these authors as 'a state of infection that results in either no damage or clinically inapparent damage to the host, though it can elicit an immune response'. And a commensal is a 'microbe that induces either no damage or clinically inapparent damage after primary infection; a state that is thought to be established early in life'. In terms of the antibody response, 'it is not known whether these immune responses reflect the occurrence of an unidentified form of damage to the host'. Importantly, 'commensals also synthesise metabolites that are essential nutrients for the host'.

According to Casadevall and Pirofski, colonisation is 'a state of infection that results in a continuum of damage from none to great, with the latter leading to the induction of host responses that could eliminate or retain the microbe, or progress to chronicity or disease; for organisms that induce no damage during infection this state is indistinguishable from commensalism'.

I guess that to this end comes the concept of tolerance...Some single-celled parasites are common in young mammals such as calves and lambs (for instance Cryptosporidium and - it appears - microsporidia (unpublished data)), but appear to be cleared by host immune response mechanisms, while other parasites are establishing chronic colonisation, - parasites such as Entamoeba and Blastocystis. The latter parasites may also colonise humans for years on end... So why do we not eliminate these parasites? Blaser writes back in 1997: 'Failure to eliminate the parasite implies that the cost to the host is greater than the benefit. This may be due to high costs (e.g., loss of vital (...) functions), or significant benefits (e.g., protection against lethal diseases), or that both cost and benefit are relatively low'.

In Blastocystis research most scientists appear to be preoccupied by identifying a role for Blastocystis in disease, driven by the black and white concept that either it's pathogenic or not... or at least that if it can cause disease, it's by definition a pathogen! I think the paper by Casadevall and Pirofski shows with great clarity why we should try and take a much more differentiated view on Blastocystis and it's role in health and disease.

As mentioned in a previous blog post, Blastocystis is practically an obligate finding in some societies, while more rare in others. In some communities it may be common to contract it in very early childhood (infants/toddlers), while in other communities you may not be infected or infected only in adulthood. In Denmark, the prevalence in the healthy adult population is about 30%, and there may be countries where the prevalence is even lower - typically in regions, where the general population has been 'intestinally defaunated' (presumably due to excessive hygiene combined with a Westernised diet). And so, in some places this parasite is getting so uncommon that it may at some point become a cause of disease, a so-called 'emerging pathogen'... Conjectural maybe, but still not far fetched.

Simultaneously, evidence is emerging that intestinal microbial eukaryotes (Blastocystis and Dientamoeba fragilis) are significantly more common in healthy individuals than in patients with gastrointestinal disease such as IBS and - especially - IBD, suggesting that these parasites are protective of functional and organic bowel disease. Do they prime our immune system in a beneficial way? Do they select for beneficial bacteria? Do they keep potential harmful microbial intruders at bay? Could they be synthesising metabolites beneficial to the host just like ciliates involved in fermentation processes in the large intestine of various herbivorous mammals?

This is why the exploration of the structure and function of intestinal pro- and eukaryotic communities is so important. For instance, can we link Blastocystis to any intestinal microbial patterns? At our lab, we think we can, and it's something that we will try and explore further (if funding can be obtained). Our null hypotheses include the following:

1) The distribution of pro- and eukaryotes is random (for instance: Blastocystis is not statistically associated with the presence of particular bacteria or other eukaryotes (fungi, parasites)).

2) The introduction of a Blastocystis strain into an intestinal microbial niche does not cause alteration of the composition of the pro- and eukaryotic flora. This can be studied using an animal model, and it is tempting to try and study host immunological parameters during and after challenge with Blastocystis. Also gene expression in both host and microbial communities could be studied.

Take home message is that we should be cautious with regard to deeming a parasite as being either 'pathogenic' or 'non-pathogenic'... parasites may have a multitude of functions and may impact their hosts in a variety of ways that together with all other types of impact from and interactions with other microorganisms (microbiota) results in a health/disease matrix in every single individual.

Finally: Here's to pageview # 200,000! See you in Boston on Sunday morning at the #ASM2014 conference: Passion for Parasites !


Blaser, M. (1997). Ecology of Helicobacter pylori in the human stomach. Journal of Clinical Investigation, 100 (4), 759-762 DOI: 10.1172/JCI119588  

Casadevall, A., & Pirofski, L. (2000). Host-Pathogen Interactions: Basic Concepts of Microbial Commensalism, Colonization, Infection, and Disease. Infection and Immunity, 68 (12), 6511-6518 DOI: 10.1128/IAI.68.12.6511-6518.2000

Sunday, March 16, 2014

What's In A Name?

When people have had their stools examined and are told that they have Blastocystis, most of them will not have a clue about what that is. And eventually they'll be told that it's a parasite. A parasite? As in tapeworm? Ok it's not. But then what? As in malaria? Oh... ok, I see... So it's....? Huh? As in ... what???

Now, which are those parasites in and on your body, and what in fact makes a parasite? Depends on who you ask. For parasitologists and public health/clinical microbiologists, a parasite means something along the lines of a eukaryotic organism (i.e. not a bacterium and not a virus) that is not a fungus and that is capable of living and maybe even multiplying on or inside another organism. Some organisms are considered somewhere in between parasites and fungi, such as microsporidia and Pneumocystis. But whether an organism is a fungus or a parasite is not important in most cases. You will also sometimes see that 'parasite' is used as a term meant to cover living organisms causing disease, and in this sense the term may include for instance bacteria and viruses; for instance. A lot of research deals with 'host-parasite' relationships, evolution of virulence and tolerance in parasites and hosts, respectively; also here, bacteria may be referred to as parasites.

 Mosquitos are practically parasites that may transmit other parasites. Source (eyeweed on Flickr).

The word 'parasite' stems from Greek, and means something like 'eating beside' or 'eating at someone else's table'. Parasitism is a non-mutual symbiotic relationship where one organism (the parasite) benefits at the expense of another (the host).

People like me usually divide parasites (sensu stricto) into protozoa (single-celled) and helminths (multi-cellular; worms). Effectively, this should be protists and helminths, since not all single-celled parasitic eukaryotes are protozoa. Please note that most protists and helminths (the nematode fraction) are free-living, - but some have adapted a parasitic life style and very effectively so.

So, when we're told by doctors that we are in fact hosting parasites, - how do we react? I guess  some of us will be quite alarmed: Creatures eating defenseless hosts from within, castrating them and turning them into zombies come to our minds, for instance Sacculina, Dicrocoelium, and Leucochloridium, just to mention a few ones (if you're not familiar with these ones, I suggest you look them up - you will hardly believe what they are capable of doing, and despite the horrifying subtlety and cold-bloodedness with which these creatures operate, one can hardly help marveling on how cunningly evolution makes way for some organisms' ability to exploit others). Other parasites are known to cause less spectacular phenotypic changes while having huge consequences for human health and disease: Malaria continues to be a significant cause of morbidity and mortality in many larger regions, and recently, diarrhoea caused by species of Cryptospordium was recognised as one of the most significant health issues in infants and toddlers in select sentinel areas sub-Saharan Africa and South Asia.

Some parasites, however, are commensals (ie. they just sit there with a more or less neutral outcome) or even beneficial to the host; for instance, there's evidence of ciliates assisting herbivores in metabolising cellulose. So while, these organisms from one point of view are parasites, the hole symbiotic relationship between these protozoa and herbivores may be seen as mutualistic. Maybe this particular relationship started out as 'parasitsm' but developed into 'mutualism'? There may be a lot more examples of this. Animals usually host various types of parasites, and humans probably used to host a much larger zoo of parasites than many of us do today; what is the public health significance of the recent and rapid 'defaunation' of humans in certain parts of the world?

At least technically, Blastocystis is also a parasite: Sitting in the colon, it lives on food delivered by its host, and thereby it certainly eats at someone else's table. Moreover, the parasite is probably not capable of completing its life cycle without a host. But what does it do apart from eating? Does it do us any good just like the ciliates in the herbivores? Blastocystis has co-evolved with humans (and other host species) and maybe humans have learned to exploit Blastocystis so that it's not only Blastocystis exploiting us? Does Blastocystis compete with other organisms in the gut? Does it secrete substances that impact other organisms including the host, and if so, in what way? What's its impact on the immune system? Etc.

I guess the take-home message here is that 'parasite' is just a word, - a name for something, and there are examples of parasitism turning into mutualism. Not all parasites induce disease, and parasites are not always organisms that should be sought eradicated.


Kotloff KL, Nataro JP, Blackwelder WC, Nasrin D, Farag TH, Panchalingam S, Wu Y, Sow SO, Sur D, Breiman RF, Faruque AS, Zaidi AK, Saha D, Alonso PL, Tamboura B, Sanogo D, Onwuchekwa U, Manna B, Ramamurthy T, Kanungo S, Ochieng JB, Omore R, Oundo JO, Hossain A, Das SK, Ahmed S, Qureshi S, Quadri F, Adegbola RA, Antonio M, Hossain MJ, Akinsola A, Mandomando I, Nhampossa T, Acácio S, Biswas K, O'Reilly CE, Mintz ED, Berkeley LY, Muhsen K, Sommerfelt H, Robins-Browne RM, & Levine MM (2013). Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet, 382 (9888), 209-22 PMID: 23680352

Veira DM (1986). The role of ciliate protozoa in nutrition of the ruminant. Journal of Animal Science, 63 (5), 1547-60 PMID: 3098727

Sunday, September 8, 2013

Fellowships in Blastocystis Research

We are continually looking into the opportunity for funding for research in Blastocystis and we are on the lookout for young researchers with a MSc or PhD degree who want to spend at least a couple of years in Blastocystis research. Right now, taking an omics approach to studying the clinical significance of Blastocystis is extremely relevant of course, given the amount of genetic diversity of the parasite, its apparent association to groups of bacteria/bacterial richness, its varied distribution across different cohorts, and the general availability of ngs technology and data pipelines.

I'm going to focus my next funding application on the integration of metagenomics, metabolomics, comparative genomics, and transcriptomics, and I'm hoping to find one or two persons with track records documenting extensive experience with one or more of these disciplines and who take an interest in parasites/parasitic protists in general and/or in Blastocystis in particular.

Please note that this is NOT a job offer, but merely an invitation to get into some sort of a dialogue. What we can offer is access to samples, strains, technology, and a Blastocystis-centred network.

Please do not answer in the comments section, but contact me directly (mail/phone) for further info + expression of interest. You'll find a link to my contact details in the previous blog post. Thanks.

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

Sunday, May 5, 2013

More on 'Bugs as Drugs'

This morning, I was doing a lazy ramble through my favourite blogs and found a post by Carl Zimmer on 'Bugs as Drugs' - primarily on probiotics. And I just came to realise that there is a very interesting tendency these years of using bugs as drugs in a variety of fields.

We are all very much aware of the worries about the increase in antibiotic resistance in bacterial and other pathogens. Moreover, it appears that sometimes antibiotic treatment leads to imbalance in the intestinal microbiota (dysbiosis); a well-known example is intractable Clostridium difficile infections which can potentially lead to pseudomembranous colitis.

C. difficile infection can lead to pseudomembranous colitis
Earlier this year, an article appeared in the renowned The New England Journal of Medicine on a randomised, controlled treatment study on duodenal infusion of donor faeces for recurrent C. difficile. The researchers found that the infusion of donor faeces was significantly more effective for the treatment of recurrent C. difficile infection than the use of vancomycin, the drug usually recommended in this situation. In fact 15/16 patients had resolution of C. difficile-associated diarrhoea upon first or second infusion; however, it might be worthwhile 'shopping around' for the right donor.

And so, how are these faecal transplants developed and administered? Well, it appears that donors are volunteers who have been through a selection process based on a questionnaire on risk factors of infectious diseases. Then donor faeces is screened for parasites (including Blastocystis and Dientamoeba - yes, it warms my heart to see this so explicitly spelled out in the paper... but I wonder which methods were used - it doesn't say!) and enteropathogenic bacteria. Moreover, blood samples from donors are screened for e.g. HIV, hepatitis and antibodies against e.g. Entamoeba histolytica and Strongyloides. Next, a donor pool is created with repeated screening every 4 months. On the day of infusion, faeces is collected by the donor and immediately brought to the hospital, where it is diluted with 500 mL of sterile saline. The solution is stirred, and the supernatant strained and poured in a sterile bottle. Within 6 h after collection of the faecal sample by the donor, the solution is infused through a nasoduodenal tube (2 to 3 mintues per 50 mL). Patients are subsequently monitored for 2 h. Apparently, this is how it works!

Thursday, March 21, 2013

LUMINEX xMAP Technology in Parasite Diagnostics

Over the past few years nucleic acid based methods have revolutionised parasite diagnostics in modern clinical microbiology (CM) labs. Real-time PCR is really gaining a foothold in CM labs, but despite the opportunity for plexing, mostly only up to 6 DNA targets can be included in each assay (due to the number of available channels).

LUMINEX xMAP technology used for detection of specific nucleic acids (Dunbar, 2006) bypasses this limit, and up to 100 DNA targets can be included in one single assay in a 96-well plate format. You can read about the technology here.

Monday, January 14, 2013

A Penny For Your Thoughts

So, what should we do about Blastocystis? What do we want to know?

I believe the imminent answer to the latter question is easy: We want to know whether it’s pathogenic, whether we should treat it and how. But I also think that there are many other interesting aspects of Blastocystis which are also of broad interest to the general public, namely: How about the many cases of asymptomatic Blastocystis carriage? What does Blastocystis do in our guts? Could it have any potentially beneficial impact on our health?

Given the fact that Blastocystis has not been implicated in any outbreaks (admittedly: I guess that no one actually ever looked for Blastocystis in outbreak investigations... except for me!), I reckon that the chance of it being involved in acute diarrhoea is small. So, in that respect it's very different from the other intestinal protists such as Giardia, Cryptosporidium, Cyclospora, microsporidia, even Entamoeba histolytica. It's actually more reminiscent of helminth infections, which are are often chronic, and when light hardly give rise to symptoms (depending on species that is!).So I'm more thinking along the lines of co-evolution, adaptation, etc.

Maybe future research will call for a shift in paradigm, but until then I think that we should do what we already can, just at a larger scale and see where it takes us, namely:

Thursday, April 26, 2012

What is Blastocystis?

Intestinal parasites of humans can be divided into mainly helminths ('worms' including cestodes, nematodes and trematodes), and single-celled eukaryotic organisms. Most single-celled intestinal parasites belong to one of four main groups:
  • Archamoebae or Amoeboids (e.g. Entamoba, Iodamoeba, Endolimax)
  • Ciliates (e.g. Balantidium)
  • Sporozoa (e.g. Cryptosporidium, Cyclospora, Cystoisospora; even microsporidia)
  • Flagellates (e.g. Giardia, Chilomastix, Enteromonas, Pentatrichomonas, Retortamonas, Dientamoeba (unflagellated flagellate!))
Traditionally, these four groups have been referred to as protozoa.

However, the most common, single-celled intestinal parasitic eukaryote, Blastocystis, does not belong in any of these four categories. Taxonomically, Blastocystis belongs to the heterogeneous group of Stramenopiles, which includes slime nets, diatoms, water moulds and brown algae. Most stramenopiles are free-living organisms. Blastocystis is an atypical stramenopile not only as this group is named for the straw-like tubular hairs on the flagella and sometimes the cell body - Blastocystis has no flagella and lacks any tubular hairs - but also due to its parasitic nature.

Often, Blastocystis is referred to as a 'protozoon', although 'protist' is more appropriate. Protists can be defined basically as any eukaryote that is not a plant, an animal or a fungus.

One of the closest relatives of Blastocystis identified to date is Proteromonas lacertae, a parasite of reptiles.

Interestingly, Proteromonas does have flagella and hairs on the cell body. For comparison, the image below shows Blastocystis (culture) - appearing almost amoeboid, only with very limited morphological hallmarks (note examples of binary fission and the eccentrically located nuclei and mitochondrion-like organelles).

Blastocystis is one of two Stramenopiles known to infect humans, the other being Pythium insidiosum, which has been associated with keratitis and dermatological lesions mainly in SE Asia.

Other organisms with close relation to Blastocystis include Karotomorpha, Cepedea, Protoopalina and Opalina.

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Silberman, J., Sogin, M., Leipe, D., & Clark, C. (1996). Human parasite finds taxonomic home Nature, 380 (6573), 398-398 DOI: 10.1038/380398a0  

HOEVERS, J., & SNOWDEN, K. (2005). Analysis of the ITS region and partial ssu and lsu rRNA genes of Blastocystis and Proteromonas lacertae Parasitology, 131 (2), 187-196 DOI: 10.1017/S0031182005007596  

Kostka, M., Cepicka, I., Hampl, V., & Flegr, J. (2007). Phylogenetic position of Karotomorpha and paraphyly of Proteromonadidae Molecular Phylogenetics and Evolution, 43 (3), 1167-1170 DOI: 10.1016/j.ympev.2006.11.002