23Blastocystis is a common unicellular anaerobic eukaryote that inhabits the large intestine of 24 many animals worldwide, including humans. The finding of Blastocystis in faeces in 25 mammals and birds has led to proposals of zoonotic potential and that these hosts may be the 26 source of many human infections. Blastocystis is, however, a genetically diverse complex of 27 many distinct organisms (termed subtypes; STs), and sampling to date has been limited, both 28 geographically and in the range of hosts studied. In order to expand our understanding of host 29 specificity of Blastocystis STs, 557 samples were examined from various non-primate animal 30 hosts and from a variety of different countries in Africa, Asia and Europe. STs were 31 identified using 'barcoding' of the small subunit rRNA gene using DNA extracted either 32 from culture or directly from faeces. The host and geographic range of several STs has 33 thereby been greatly expanded and the evidence suggests that livestock is not a major 34 contributor to human infection. Two new STs were detected among the barcode sequences 35 obtained; for these, and for three others where the data were incomplete, the corresponding 36 genes were fully sequenced and phylogenetic analysis was undertaken. 37 38

Blastocystis is a common intestinal micro-eukaryote found in both humans and non-human hosts and known to be genetically very diverse. It has been divided into numerous subtypes (STs), nine of which have been identified in humans to date. Surveys of ST prevalence have started to emerge over the past few years but to date no data are available for any African country except Egypt and Tanzania. In this study, we determined the prevalence of Blastocystis STs in populations from Libya, Liberia and Nigeria, as well as expanding the dataset available for the UK. A total of 356 Blastocystis STs were identified in this study, 271 from the UK, 38 from Libya, 25 from Liberia and 22 from Nigeria. SSU rRNA gene sequences revealed the presence of eight of the nine STs known from humans but at varying frequencies between countries. ST1 was the most common ST in Libya and Nigeria whereas ST3 showed the highest frequency in the other two countries, as indeed is the case in most populations around the world. ST4 was absent in Libya and ST2 in Nigeria, while no ST5, ST6, ST8 or ST9 infections were detected in any of the three African populations. The picture emerging from this and other surveys suggests that there is significant variation in ST prevalence between populations. Some of the possible reasons for and implications of this diversity are discussed.

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Abstract:Blastocystis is a common parasite of the human large intestine but has an uncertain role in disease. In this review, we appraise the published evidence addressing this and its weaknesses. Genetic diversity studies have led to the identification of numerous subtypes within the genus Blastocystis and, recently, methods for studying variation within subtypes have been developed, with implications for our understanding of host specificity. The geographic distribution of subtypes is summarised and the impact this may have on investigations into the role of the organism in disease is discussed. Finally, we describe the organelle and nuclear genome characteristics and look to future developments in the field.

Based on current data we propose that the uninucleated-cyst-producing Entamoeba infecting 36 humans is called Entamoeba polecki and divided into four subtypes (ST1-ST4) and that 37Entamoeba coli is divided into two subtypes (ST1-ST2). New hosts for several species were 38 detected and while host specificity and genetic diversity of several species remain to be 39 clarified, it is clear that previous reliance on cultivated material has given us a misleading and 40 incomplete picture of variation within the genus Entamoeba.

Blastocystis is a common single-celled parasite of humans and other animals comprising at least 13 genetically distinct small subunit ribosomal RNA lineages (subtypes (STs)). In this study we investigated intra-subtype genetic diversity and host specificity of two of the most common subtypes in humans, namely ST3 and ST4, by analysing and comparing over 400 complete and partial nuclear SSU-rDNAs and data from multilocus sequence typing (MLST) of the mitochondrion-like organelle (MLO) genome of 132 samples. Inferences from phylogenetic analyses of nuclear SSU-rDNA and concatenated MLST sequences were compatible. Human ST3 infections were restricted to one of four identified MLO clades except where exposure to non-human primates had occurred. This suggests relatively high host specificity within ST3, that human ST3 infections are caused predominantly by human-to-human transmission, and that human strains falling into other clades are almost certainly the result of zoonotic transmission. ST4 from humans belonged almost exclusively to one of two SSU-rDNA clades, and only five MLST sequence types were found among 50 ST4s belonging to Clade 1 (discriminatory index: 0.41) compared to 58 MLST sequence types among 81 ST3s (discriminatory index: 0.99). The remarkable differences in intra-subtype genetic variability suggest that ST4 has a more recent history of colonising humans than ST3. This is congruent with the apparently restricted geographical distribution of ST4 relative to ST3. The implications of this observation are unclear, however, and the population structure and distribution of ST4 should be subject to further scrutiny in view of the fact ST4 is being increasingly linked with intestinal disease.

Blastocystis SSU-rDNA sequence data from 317 captive and free-living non-human primates (NHPs) representing 30 genera of apes, Old and New World (OW and NW) monkeys and prosimians were analysed to investigate subtype (ST) and allele distribution among hosts. Excluding 20 mixed ST infections, 27% of the sequences belonged to ST1, 22% to ST2, 34% to ST3, 1% to ST4, 4% to ST5, 11% to ST8, <1% to ST13 and 1% to ST15. The study confirmed cryptic host specificity of ST1 and ST3; conversely, considerable overlap in ST2 alleles exists among humans and NHPs. Subtype distribution in humans and NHPs differs mainly in that ST4 is rarely reported in NHPs while ST5 and ST8 are both unusual in humans. This may be due to host specificity and/or the apparent geographically restricted range of some subtypes. While the distribution of ST1, ST2 and ST3 was independent of NHP group or geographical association, ST5 was seen only in apes and OW monkeys and ST8 primarily in arboreal NHPs and only in species native to Asia or South America.

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