Dr Joel Barratt is a Chancellor’s Postdoctoral researcher at the University of Technology Sydney. He holds a Bachelor of Biotechnology and first class Honours degree from UTS, and a PhD in molecular parasitology. He worked as a research assistant at St Vincent’s Hospital, Sydney for 3 years on a project involving the diagnosis of gastrointestinal protozoa and other potential pathogens. He has extensive experience working with gut protozoa, particularly Dientamoeba fragilis.
Joels PhD research involved a detailed study of the human gastrointestinal parasite, D. fragilis. His thesis was ranked among the top 6 submitted at UTS in 2013, qualifying it for inclusion on the 2013 Chancellor’s List. Joel was awarded the prestigious Chancellor’s Postdoctoral position at UTS in 2014 and currently holds this appointment. His project investigates the molecular biology of parasitic flagellates (trypanosomatids and trichomonads), particularly those associated with human disease.
Joel also presently holds an editorial position with the open access, peer reviewed journal Parasites & Vectors (Associate Editor: Protozoan biology and diseases).
Awards & Funding
Joel was awarded his Chancellor's Postdoctoral position in 2014 (salary and project costs incl.). In 2010, he obtained runners up in the competitive UniQuest Trailblazer competition, for presentation of a 5 minute pitch entitled "Development of a diagnostic test for D. fragilis" (prize of $2,500). In 2013, Joel was also awarded a Bio-Innovation prize (as part of a group of four scientists) from the Technion Israel Institute of Technology for the development of a novel commercial concept: “A new diagnostic tool for detecting metastatic cancer” (prize of $25,000).
- Australian Society for Parasitology
- Australian Society for Microbiology
General research interests:
- Parasitology (medical/veterinary)
- Molecular biology
Current Research Projects:
- Leishmania spp. and related organisms - taxonomy, genetics
- Dientamoeba fragilis – genetics, genomics, diagnostic development, transmission and life cycle
- Tissue-cyst forming coccidia – food (meat) safety, genetics
- Neospora caninum – genomics, transcriptomics
Joels work committments are currently 25% teaching and 75% research.
His primary teaching areas include:
- Molecular Biology
Second and third generation sequencing methods are crucial for population genetic studies, and variant detection is a popular approach for exploiting this sequence data. While mini- and microsatellites are historically useful markers for studying important Protozoa such as Toxoplasma and Plasmodium spp., detecting non-repetitive variants such as those found in genes can be fundamental to investigating a pathogen's biology. These variants, namely single nucleotide polymorphisms and insertions and deletions, can help elucidate the genetic basis of an organism's pathogenicity, identify selective pressures, and resolve phylogenetic relationships. They also have the added benefit of possessing a comparatively low mutation rate, which contributes to their stability. However, there is a plethora of variant analysis tools with nuanced pipelines and conflicting recommendations for best practise, which can be confounding. This lack of standardisation means that variant analysis requires careful parameter optimisation, an understanding of its limitations, and the availability of high quality data. This review explores the value of variant detection when applied to non-model organisms such as clinically important protozoan pathogens. The limitations of current methods are discussed, including special considerations that require the end-users' attention to ensure that the results generated are reproducible, and the biological conclusions drawn are valid.
Gough, R, Barratt, J, Stark, D & Ellis, J 2020, 'Diversity profiling of xenic cultures of Dientamoeba fragilis following systematic antibiotic treatment and prospects for genome sequencing.', Parasitology (Cambridge), vol. 147, no. 1, pp. 29-38.View/Download from: Publisher's site
The presence of bacterial DNA in Dientamoeba fragilis DNA extracts from culture poses a substantial challenge to sequencing the D. fragilis genome. However, elimination of bacteria from D. fragilis cultures has proven difficult in the past, presumably due to its dependence on some unknown prokaryote/s. This study explored options for removal of bacteria from D. fragilis cultures and for the generation of genome sequence data from D. fragilis. DNA was extracted from human faecal samples and xenic D. fragilis cultures. Extracts were subjected to 16S ribosomal DNA bacterial diversity profiling. Xenic D. fragilis cultures were then subject to antibiotic treatment regimens that systematically removed bacterial species depending on their membrane structure (Gram-positive or Gram-negative) and aerobic requirements. The impact of these treatments on cultures was assessed by 16S amplicon sequencing. Prior to antibiotic treatment, the cultures were dominated by Gram-negative bacteria. Addition of meropenem to cultures eliminated anaerobic Gram-negative bacteria, but it also led to protozoan death after 5 days incubation. The seeding of meropenem resistant Klebsiella pneumoniae strain KPC-2 into cultures before treatment by meropenem prevented death of D. fragilis cells beyond this 5 day period, suggesting that one or more species of Gram-negative bacteria may be an essential nutritional requirement for D. fragilis. Gram-positive cells were completely eliminated using vancomycin without affecting trophozoite growth. Finally, this study shows that genome sequencing of D. fragilis is feasible following bacterial elimination from cultures as the result of the major advances occurring in bioinformatics. We provide evidence on this fact by successfully sequencing the D. fragilis 28S large ribosomal DNA subunit gene using culture-derived DNA.
Barratt, JLN, Lane, M, Talundzic, E, Richins, T, Robertson, G, Formenti, F, Pritt, B, Verocai, G, De Souza, JN, Soares, NM, Traub, R, Buonfrate, D & Bradbury, RS 2019, 'A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing', PLoS Neglected Tropical Diseases, vol. 13, no. 9.View/Download from: UTS OPUS or Publisher's site
© 2019 This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Strongyloidiasis is a neglected tropical disease caused by the human infective nematodes Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. Previous large-scale studies exploring the genetic diversity of this important genus have focused on Southeast Asia, with a small number of isolates from the USA, Switzerland, Australia and several African countries having been genotyped. Consequently, little is known about the global distribution of geographic sub-variants of these nematodes and the genetic diversity that exists within the genus Strongyloides generally. We extracted DNA from human, dog and primate feces containing Strongyloides, collected from several countries representing all inhabited continents. Using a genotyping assay adapted for deep amplicon sequencing on the Illumina MiSeq platform, we sequenced the hyper-variable I and hyper-variable IV regions of the Strongyloides 18S rRNA gene and a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene from these specimens. We report several novel findings including unique S. stercoralis and S. fuelleborni genotypes, and the first identifications of a previously unknown S. fuelleborni infecting humans within Australia. We expand on an existing Strongyloides genotyping scheme to accommodate S. fuelleborni and these novel genotypes. In doing so, we compare our data to all 18S and cox1 sequences of S. fuelleborni and S. stercoralis available in GenBank (to our knowledge), that overlap with the sequences generated using our approach. As this analysis represents more than 1,000 sequences collected from diverse hosts and locations, representing all inhabited continents, it allow...
Barratt, JLN, Park, S, Nascimento, FS, Hofstetter, J, Plucinski, M, Casillas, S, Bradbury, RS, Arrowood, MJ, Qvarnstrom, Y & Talundzic, E 2019, 'Genotyping genetically heterogeneous Cyclospora cayetanensis infections to complement epidemiological case linkage', PARASITOLOGY, vol. 146, no. 10, pp. 1275-1283.View/Download from: Publisher's site
Beknazarova, M, Barratt, JLN, Bradbury, RS, Lane, M, Whiley, H & Ross, K 2019, 'Detection of classic and cryptic Strongyloides genotypes by deep amplicon sequencing: A preliminary survey of dog and human specimens collected from remote Australian communities.', PLoS neglected tropical diseases, vol. 13, no. 8.View/Download from: UTS OPUS or Publisher's site
Strongyloidiasis is caused by the human infective nematodes Strongyloides stercoralis, Strongyloides fuelleborni subsp. fuelleborni and Strongyloides fuelleborni subsp. kellyi. The zoonotic potential of S. stercoralis and the potential role of dogs in the maintenance of strongyloidiasis transmission has been a topic of interest and discussion for many years. In Australia, strongyloidiasis is prevalent in remote socioeconomically disadvantaged communities in the north of the continent. Being an isolated continent that has been separated from other regions for a long geological period, description of diversity of Australian Strongyloides genotypes adds to our understanding of the genetic diversity within the genus. Using PCR and amplicon sequencing (Illumina sequencing technology), we sequenced the Strongyloides SSU rDNA hyper-variable I and hyper-variable IV regions using Strongyloides-specific primers, and a fragment of the mtDNA cox1 gene using primers that are broadly specific for Strongyloides sp. and hookworms. These loci were amplified from DNA extracted from Australian human and dog faeces, and one human sputum sample. Using this approach, we confirm for the first time that potentially zoonotic S. stercoralis populations are present in Australia, suggesting that dogs represent a potential reservoir of human strongyloidiasis in remote Australian communities.
Nascimento, FS, Barta, JR, Whale, J, Hofstetter, JN, Casillas, S, Barratt, J, Talundzic, E, Arrowood, MJ & Qvarnstrom, Y 2019, 'Mitochondrial Junction Region as Genotyping Marker for Cyclospora cayetanensis.', Emerging infectious diseases, vol. 25, no. 7, pp. 1314-1319.View/Download from: UTS OPUS or Publisher's site
Cyclosporiasis is an infection caused by Cyclospora cayetanensis, which is acquired by consumption of contaminated fresh food or water. In the United States, cases of cyclosporiasis are often associated with foodborne outbreaks linked to imported fresh produce or travel to disease-endemic countries. Epidemiologic investigation has been the primary method for linking outbreak cases. A molecular typing marker that can identify genetically related samples would be helpful in tracking outbreaks. We evaluated the mitochondrial junction region as a potential genotyping marker. We tested stool samples from 134 laboratory-confirmed cases in the United States by using PCR and Sanger sequencing. All but 2 samples were successfully typed and divided into 14 sequence types. Typing results were identical among samples within each epidemiologically defined case cluster for 7 of 10 clusters. These findings suggest that this marker can distinguish between distinct case clusters and might be helpful during cyclosporiasis outbreak investigations.
Barratt, JL & Ellis, J 2019, 'Angiostrongylus cantonensis: a review of its distribution, molecular biology and clinical significance as a human pathogen - CORRIGENDUM.', Parasitology, pp. 1-1.View/Download from: UTS OPUS or Publisher's site
Kaufer, A, Barratt, J, Stark, D & Ellis, J 2019, 'The complete coding region of the maxicircle as a superior phylogenetic marker for exploring evolutionary relationships between members of the Leishmaniinae.', Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, vol. 70, pp. 90-100.View/Download from: UTS OPUS or Publisher's site
The mitochondrial DNA (mtDNA) is a potentially valuable phylogenetic marker given its presence across all eukaryotic taxa and its relative conservation in structure and sequence. In trypanosomatids, a homologue of the mtDNA referred to as the maxicircle DNA, is located within a specialised structure in the single mitochondrion of the trypanosomatids called the kinetoplast; a high molecular weight network of DNA composed of thousands of catenated minicircles and a smaller number of larger maxicircles. Unique to the kinetoplastid protists, the maxicircle component of this complex network could represent a desirable target for taxonomic inquiry that may also facilitate exploration of the evolutionary history of this important group of parasites. The aim of this study was to investigate the phylogenetic value of the trypanosomatid maxicircle for these applications. Maxicircle sequences were obtained either by assembling raw sequence data publicly accessible in online databases (i.e., NCBI), or by amplification of novel maxicircle sequences from trypanosomatid DNA using long-range (LR) PCR with subsequent Illumina sequencing. This procedure facilitated the generation of nearly complete maxicircle sequences (i.e., excluding the divergent region) for numerous dixenous and monoxenous trypanosomatid species. Annotation of each maxicircle sequence confirmed that their structure was conserved across all taxa examined. Phylogenetic analyses confirmed that Z. australiensis showed a greater genetic relatedness with the dixenous trypanosomatids of the genera Leishmania and Endotrypanum, as opposed to members of the monoxenous genera Crithidia and Leptomonas. Additionally, molecular clock analysis supported that the dixenous Leishmaniinae appeared approximately 75 million years ago during the breakup of Gondwana. In line with previous studies, our results support the Supercontinents hypothesis regarding the origin of dixenous Leishmaniinae. Ultimately, we demonstrate that the ma...
Flaherty, BR, Talundzic, E, Barratt, J, Kines, KJ, Olsen, C, Lane, M, Sheth, M & Bradbury, RS 2018, 'Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing', MICROBIOME, vol. 6.View/Download from: Publisher's site
Calarco, L, Barratt, J & Ellis, J 2018, 'Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence', GENOME BIOLOGY AND EVOLUTION, vol. 10, no. 9, pp. 2417-2431.View/Download from: UTS OPUS or Publisher's site
Barratt, J, Kaufer, A, Peters, B, Craig, D, Lawrence, A, Roberts, T, Lee, R, McAuliffe, G, Stark, D & Ellis, J 2017, 'Isolation of Novel Trypanosomatid, Zelonia australiensis sp. nov. (Kinetoplastida: Trypanosomatidae) Provides Support for a Gondwanan Origin of Dixenous Parasitism in the Leishmaniinae.', PLoS Neglected Tropical Diseases, vol. 11, no. 1, pp. 1-26.View/Download from: UTS OPUS or Publisher's site
The genus Leishmania includes approximately 53 species, 20 of which cause human leishmaniais; a significant albeit neglected tropical disease. Leishmaniasis has afflicted humans for millennia, but how ancient is Leishmania and where did it arise? These questions have been hotly debated for decades and several theories have been proposed. One theory suggests Leishmania originated in the Palearctic, and dispersed to the New World via the Bering land bridge. Others propose that Leishmania evolved in the Neotropics. The Multiple Origins theory suggests that separation of certain Old World and New World species occurred due to the opening of the Atlantic Ocean. Some suggest that the ancestor of the dixenous genera Leishmania, Endotrypanum and Porcisia evolved on Gondwana between 90 and 140 million years ago. In the present study a detailed molecular and morphological characterisation was performed on a novel Australian trypanosomatid following its isolation in Australia's tropics from the native black fly, Simulium (Morops) dycei Colbo, 1976. Phylogenetic analyses were conducted and confirmed this parasite as a sibling to Zelonia costaricensis, a close relative of Leishmania previously isolated from a reduviid bug in Costa Rica. Consequently, this parasite was assigned the name Zelonia australiensis sp. nov. Assuming Z. costaricensis and Z. australiensis diverged when Australia and South America became completely separated, their divergence occurred between 36 and 41 million years ago at least. Using this vicariance event as a calibration point for a phylogenetic time tree, the common ancestor of the dixenous genera Leishmania, Endotrypanum and Porcisia appeared in Gondwana approximately 91 million years ago. Ultimately, this study contributes to our understanding of trypanosomatid diversity, and of Leishmania origins by providing support for a Gondwanan origin of dixenous parasitism in the Leishmaniinae.
Trypanosomatids are protozoan parasites of the class Kinetoplastida predominately restricted to invertebrate hosts (i.e. possess a monoxenous life-cycle). However, several genera are pathogenic to humans, animals and plants, and have an invertebrate vector that facilitates their transmission (i.e. possess a dixenous life-cycle). Phytomonas is one dixenous genus that includes several plant pathogens transmitted by phytophagous insects. Trypanosoma and Leishmania are dixenous genera that infect vertebrates, including humans, and are transmitted by hematophagous invertebrates. Traditionally, monoxenous trypanosomatids such as Leptomonas were distinguished from morphologically similar dixenous species based on their restriction to an invertebrate host. Nonetheless, this criterion is somewhat flawed as exemplified by Leptomonas seymouri which reportedly infects vertebrates opportunistically. Similarly, Novymonas and Zelonia are presumably monoxenous genera yet sit comfortably in the dixenous clade occupied by Leishmania. The isolation of Leishmania macropodum from a biting midge (Forcipomyia spp.) rather than a phlebotomine sand fly calls into question the exclusivity of the Leishmania-sand fly relationship, and its suitability for defining the Leishmania genus. It is now accepted that classic genus-defining characteristics based on parasite morphology and host range are insufficient to form the sole basis of trypanosomatid taxonomy as this has led to several instances of paraphyly. While improvements have been made, resolution of evolutionary relationships within the Trypanosomatidae is confounded by our incomplete knowledge of its true diversity. The known trypanosomatids probably represent a fraction of those that exist and isolation of new species will help resolve relationships in this group with greater accuracy. This review incites a dialogue on how our understanding of the relationships between certain trypanosomatids has shifted, and discusses new knowledge t...
Barratt, J, Chan, D, Sandaradura, I, Malik, R, Spielman, D, Lee, R, Marriott, D, Harkness, J, Ellis, J & Stark, D 2016, 'Angiostrongylus cantonensis: a review of its distribution, molecular biology and clinical significance as a human pathogen', PARASITOLOGY, vol. 143, no. 9, pp. 1087-1118.View/Download from: Publisher's site
Barratt, J, Gough, R, Stark, D & Ellis, J 2016, 'Bulky Trichomonad Genomes: Encoding a Swiss Army Knife', TRENDS IN PARASITOLOGY, vol. 32, no. 10, pp. 783-797.View/Download from: UTS OPUS or Publisher's site
Chan, D, Barratt, J, Roberts, T, Phillips, O, Slapeta, J, Ryan, U, Marriott, D, Harkness, J, Ellis, J & Stark, D 2016, 'Detection of Dientamoeba fragilis in animal faeces using species specific real time PCR assay', VETERINARY PARASITOLOGY, vol. 227, pp. 42-47.View/Download from: UTS OPUS or Publisher's site
Stark, D, Barratt, J, Chan, D & Ellis, JT 2016, 'Dientamoeba fragilis, the Neglected Trichomonad of the Human Bowel', CLINICAL MICROBIOLOGY REVIEWS, vol. 29, no. 3, pp. 553-580.View/Download from: UTS OPUS or Publisher's site
Barratt, JLN, Cao, M, Stark, DJ & Ellis, JT 2015, 'The Transcriptome Sequence of Dientamoeba fragilis Offers New Biological Insights on its Metabolism, Kinome, Degradome and Potential Mechanisms of Pathogenicity', PROTIST, vol. 166, no. 4, pp. 389-408.View/Download from: Publisher's site
Chan, D, Barratt, J, Roberts, T, Lee, R, Shea, M, Marriott, D, Harkness, J, Malik, R, Jones, M, Aghazadeh, M, Ellis, J & Stark, D 2015, 'The Prevalence of Angiostrongylus cantonensis/mackerrasae Complex in Molluscs from the Sydney Region', PLOS ONE, vol. 10, no. 5.View/Download from: UTS OPUS or Publisher's site
Goodswen, SJ, Barratt, JLN, Kennedy, PJ & Ellis, JT 2015, 'Improving the gene structure annotation of the apicomplexan parasite Neospora caninum fulfils a vital requirement towards an in silico-derived vaccine', International Journal for Parasitology, pp. 305-318.View/Download from: UTS OPUS or Publisher's site
Neospora caninum is an apicomplexan parasite which can cause abortion in cattle, instigating major economic burden. Vaccination has been proposed as the most cost-effective control measure to alleviate this burden. Consequently the overriding aspiration for N. caninum research is the identification and subsequent evaluation of vaccine candidates in animal models. To save time, cost and effort, it is now feasible to use an in silico approach for vaccine candidate prediction. Precise protein sequences, derived from the correct open reading frame, are paramount and arguably the most important factor determining the success or failure of this approach. The challenge is that publicly available N. caninum sequences are mostly derived from gene predictions. Annotated inaccuracies can lead to erroneously predicted vaccine candidates by bioinformatics programs. This study evaluates the current N. caninum annotation for potential inaccuracies. Comparisons with annotation from a closely related pathogen, Toxoplasma gondii, are also made to distinguish patterns of inconsistency. More importantly, a mRNA sequencing (RNA-Seq) experiment is used to validate the annotation. Potential discrepancies originating from a questionable start codon context and exon boundaries were identified in 1943 protein coding sequences. We conclude, where experimental data were available, that the majority of N. caninum gene sequences were reliably predicted. Nevertheless, almost 28% of genes were identified as questionable. Given the limitations of RNA-Seq, the intention of this study was not to replace the existing annotation but to support or oppose particular aspects of it. Ideally, many studies aimed at improving the annotation are required to build a consensus. We believe this study, in providing a new resource on gene structure and annotation, is a worthy contributor to this endeavour.
Roberts, T, Barratt, J, Sandaradura, I, Lee, R, Harkness, J, Marriott, D, Ellis, J & Stark, D 2015, 'Molecular Epidemiology of Imported Cases of Leishmaniasis in Australia from 2008 to 2014', PLOS ONE, vol. 10, no. 3.View/Download from: UTS OPUS or Publisher's site
Stark, DJ, Barratt, JL, Roberts, TJ, Marriott, DJ, Harkness, JL & Ellis, JT 2014, 'Activity of benzimidazoles against Dientamoeba fragilis (Trichomonadida, Monocercomonadidae) in vitro and correlation of beta-tubulin sequences as an indicator of resistance', Parasite, vol. 21.View/Download from: UTS OPUS or Publisher's site
Stark, DJ, Garcia, L, Barratt, JL, Phillips, O, Roberts, TJ, Marriott, DJ, Harkness, JL & Ellis, JT 2014, 'Description of Dientamoeba fragilis cyst and precystic forms from human samples', Journal Of Clinical Microbiology, vol. 52, no. 7, pp. 2680-2683.View/Download from: UTS OPUS or Publisher's site
Banik, G, Barratt, JL, Marriott, DJ, Harkness, JL, Ellis, JT & Stark, DJ 2011, 'A case-controlled study of Dientamoeba fragilis infections in children', Parasitology, vol. 138, no. 7, pp. 819-823.View/Download from: UTS OPUS or Publisher's site
Dientamoeba fragilis is a pathogenic protozoan parasite that is implicated as a cause of human diarrhoea. A case-controlled study was conducted to determine the clinical signs associated with D. fragilis infection in children presenting to a Sydney Hospital. Treatment options are also discussed. Stool specimens were collected from children aged 15 years or younger and analysed for the presence of D. fragilis. In total, 41 children were included in the study along with a control group. Laboratory diagnosis was performed by microscopy of permanently stained, fixed faecal smears and by real-time PCR. Gastrointestinal symptoms were present in 40/41 (98%) of these children with dientamoebiasis, with diarrhoea (71%) and abdominal pain (29%) the most common clinical signs. Chronic gastrointestinal symptoms were present in 2% of cases. The most common anti-microbial used for treatment was metronidazole (n=41), with complete resolution of symptoms and clearance of parasite occurring in 85% of cases. A treatment failure rate occurred in 15% of those treated with metronidazole. Follow-up treatment comprised of an additional course of metronidazole or iodoquinol was needed in order to achieve complete resolution of infection and symptoms in this group. This study demonstrates the pathogenic potential of D. fragilis in children and as such it is recommended that all laboratories must routinely test for this organism and treat if detected.
Barratt, JL, Harkness, JL, Marriott, DJ, Ellis, JT & Stark, DJ 2011, 'A review of Dientamoeba fragilis carriage in man: Several reasons why this organism should be considered in the diagnosis of gastrointestinal illness', Gut Microbes, vol. 23, no. 1, pp. 1-10.View/Download from: UTS OPUS or Publisher's site
Dientamoeba fragilis is a protozoan that inhabits the human gut. It is approximately 100 years since Dientamoebas discovery and first description when it was described as a rare and harmless commensal. Since then it has struggled to gain recognition as a pathogen despite the evidence supporting its pathogenicity. Dientamoeba remains neglected, probably due to the misconceptions that it is uncommon and non-pathogenic. Usually, carriage of Dientamoeba is associated with symptoms such as abdominal pain and diarrhea. Moreover, antimicrobial therapy followed by resolution of symptoms coincides with the eradication of Dientamoeba. This manuscript reviews the scientific literature relating to Dientamoebas prevalence and pathogenicity. While much of the evidence supporting its pathogenicity is only circumstantial, it is apparent that most researchers agree that Dientamoeba is pathogenic. Therefore, in symptomatic patients who harbor Dientamoeba and no other pathogen, Dientamoeba should be considered as the etiological agent and treated as such.
Barratt, JL, Harkness, JL, Marriott, DJ, Ellis, JT & Stark, DJ 2011, 'The ambiguous life of Dientamoeba fragilis: the need to investigate current hypotheses on transmission?', Parasitology, vol. 138, no. 5, pp. 557-572.View/Download from: UTS OPUS or Publisher's site
Dientamoeba fragilis is an inhabitant of the human bowel and is associated with gastrointestinal illness. Despite its discovery over a century ago, the details of Dientamoebas life cycle are unclear and its mode of transmission is unknown. Several theories exist which attempt to explain how Dientamoeba may be transmitted. One theory suggests that animals are responsible for the transmission of Dientamoeba. However, reports of Dientamoeba in animals are sporadic and most are not supported by molecular evidence. Another theory suggests that Dientamoeba may be transmitted via the ova of a helminth. Given that the closest relative of Dientamoeba is transmitted via the ova of a helminth, this theory seems plausible. It has also been suggested that Dientamoeba could be transmitted directly between humans. This theory also seems plausible given that other relatives of Dientamoeba are transmitted in this way. Despite numerous investigations, Dientamoebas mode of transmission remains unknown. This review discusses the strengths and weaknesses of theories relating to Dientamoebas mode of transmission and, by doing so, indicates where gaps in current knowledge exist. Where information is lacking, suggestions are made as to how future research could improve our knowledge on the life cycle of Dientamoeba.
Roberts, TJ, Barratt, JL, Harkness, JL, Ellis, JT & Stark, DJ 2011, 'Comparison of Microscopy, Culture, and Conventional Polymerase Chain Reaction for Detection of Blastocystis sp. in Clinical Stool Samples.', American Journal of Tropical Medicine and Hygiene, vol. 84, no. 2S, pp. 308-312.View/Download from: UTS OPUS or Publisher's site
We tested 513 stool samples from patients in Sydney, Australia for Blastocystis by using five diagnostic techniques: microscopy of a permanently stained smear using a modified iron-hematoxylin stain, two xenic culture systems (a modified Boeck and Drbohlav's medium and tryptone, yeast extract, glucose, methionine-9 medium), and two published conventional polymerase chain reaction methods specific for the small subunit ribosomal DNA. Ninety-eight (19%) samples were positive for Blastocystis in one or more of the diagnostic techniques. The PCR 2 method was the most sensitive at detecting Blastocystis with a sensitivity of 94%, and the least sensitive was microscopy of the permanent stain (48%). Subtype 3 was the most predominant subtype (present in 43% of samples assigned to this group). This study highlights the low sensitivity of microscopy when used as the sole diagnostic modality for detection of Blastocystis sp
Stark, DJ, Al-Qassab, SE, Barratt, JL, Stanley, K, Roberts, TJ, Marriott, DJ, Harkness, JL & Ellis, JT 2011, 'Evaluation of Multiplex Tandem Real-Time PCR for Detection of Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis in Clinical Stool Samples', Journal Of Clinical Microbiology, vol. 49, no. 1, pp. 257-262.View/Download from: UTS OPUS or Publisher's site
The aim of this study was to describe the first development and evaluation of a multiplex tandem PCR (MT-PCR) assay for the detection and identification of 4 common pathogenic protozoan parasites; Cryptosporidium spp., Dientamoeba fragilis, Entamoeba histolytica, and Giardia intestinalis from human clinical samples. A total of 472 faecal samples submitted to the Department of Microbiology at St. Vincent's Hospital were included in the study. The MT-PCR assay was compared to four real-time PCR assays (RT-PCR) and microscopy by a traditional modified iron haematoxylin stain. The MT-PCR detected 28 G. intestinalis, 26 D. fragilis, 11 E. histolytica, and 9 Cryptosporidium spp. isolates. Detection and identification of the faecal protozoa by MT-PCR demonstrated 100% correlation with the RT-PCR results and when compared to RT-PCR the MT-PCR exhibited 100% sensitivity and specificity, while traditional microscopy of stained fixed faecal smears exhibited sensitivities and specificities of 56% and 100% for Cryptosporidium ssp., 38% and 99% for D. fragilis, 47% and 97% for E. histolytica and 50% and 100% for G. intestinalis respectively. No cross reactivity was detected in 100 stool samples containing various other bacterial, viral and protozoan species. The MT-PCR assay was able to provide rapid, sensitive and specific simultaneous detection and identification of the four most important diarrhoea causing protozoan parasites that infect humans. This study also highlights the lack of sensitivity demonstrated by microscopy and as such molecular methods such as MT-PCR must be considered the diagnostic method of choice for enteric protozoan parasites.
Barratt, JL, Harkness, JL, Marriott, DJ, Ellis, JT & Stark, DJ 2010, 'Importance of Nonenteric Protozoan Infections in Immunocompromised People', Clinical Microbiology Reviews, vol. 23, no. 4, pp. 795-836.View/Download from: UTS OPUS or Publisher's site
There are many neglected nonenteric protozoa able to cause serious morbidity and mortality in humans, particularly in the developing world. Diseases caused by certain protozoa are often more severe in the presence of HIV. While information regarding neglected tropical diseases caused by trypanosomatids and Plasmodium is abundant, these protozoa are often not a first consideration in Western countries where they are not endemic.
James, R, Barratt, J, Marriott, D, Harkness, J & Stark, D 2010, 'Short Report: Seroprevalence of Entamoeba histolytica Infection among Men Who Have Sex with Men in Sydney, Australia', AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, vol. 83, no. 4, pp. 914-916.View/Download from: Publisher's site
Barratt, JL, Banik, G, Harkness, JL, Marriott, DJ, Ellis, JT & Stark, DJ 2010, 'Newly defined conditions for the in vitro cultivation and cryopreservation of Dientamoeba fragilis: new techniques set to fast track molecular studies on this organism', Parasitology, vol. 137, no. 13, pp. 1867-1878.View/Download from: UTS OPUS or Publisher's site
Dientamoeba fragilis is a pathogen of the human gastrointestinal tract that is a common cause of diarrhoea. A paucity of knowledge on the in vitro cultivation and cryopreservation of Dientamoeba has meant that few studies have been conducted to investigate its biology. The objective of this study was to define, for the first time, in vitro culture conditions able to support the long-term in vitro growth of Dientamoeba. Also, we aimed to define a suitable method for cryopreserving viable Dientamoeba trophozoites. A modified BD medium, TYGM-9, Loeffler's slope medium, Robinson's medium, Medium 199, Trichosel and a Tritrichomonas fetus medium were compared, using cell counts, for their ability to support the growth of D. fragilis at various temperatures and atmospheric conditions. Loeffler's slope medium supported significantly better growth compared to other media. A temperature of 42°C and a microaerophilic atmosphere were also optimum for Dientamoeba growth. To our knowledge, this is the first study to describe and compare different culture media and conditions for the growth of clinical isolates of D. fragilis. This new technology will aid the development of diagnostics for dientamoebiasis as well as facilitate large-scale sequencing projects that will fast track molecular studies on D. fragilis.
Barratt, JL, Harkness, JL, Marriott, DJ, Ellis, JT & Stark, DJ 2010, 'The Importance of Non-enteric Protozoan Infections in Immunocompromised Patients', Clinical Microbiology Reviews, vol. 23, no. 4, pp. 795-836.View/Download from: UTS OPUS or Publisher's site
There are many neglected nonenteric protozoa able to cause serious morbidity and mortality in humans, particularly in the developing world. Diseases caused by certain protozoa are often more severe in the presence of HIV. While information regarding neglected tropical diseases caused by trypanosomatids and Plasmodium is abundant, these protozoa are often not a first consideration in Western countries where they are not endemic. As such, diagnostics may not be available in these regions. Due to global travel and immigration, this has become an increasing problem. Inversely, in certain parts of the world (particularly sub-Saharan Africa), the HIV problem is so severe that diseases like microsporidiosis and toxoplasmosis are common. In Western countries, due to the availability of highly active antiretroviral therapy (HAART), these diseases are infrequently encountered. While free-living amoebae are rarely encountered in a clinical setting, when infections do occur, they are often fatal. Rapid diagnosis and treatment are essential to the survival of patients infected with these organisms. This paper reviews information on the diagnosis and treatment of nonenteric protozoal diseases in immunocompromised people, with a focus on patients infected with HIV. The nonenteric microsporidia, some trypanosomatids, Toxoplasma spp., Neospora spp., some free-living amoebae, Plasmodium spp., and Babesia spp. are discussed.
Stark, DJ, Barratt, JL, Roberts, TJ, Marriott, DJ, Harkness, JL & Ellis, JT 2010, 'A review of the clinical presentation of dientamoebiasis', American Journal Of Tropical Medicine And Hygiene, vol. 82, no. 4, pp. 614-619.View/Download from: UTS OPUS or Publisher's site
Among 750 symptomatic and asymptomatic patients, Dientamoeba fragilis was detected at a prevalence of 5.2% and more common than Giardia intestinalis. Most infected patients presented with diarrhea and abdominal pain with symptoms greater than 2 weeks duration being common. Bacterial and viral causes of infection were excluded by routine microbiological techniques. Treatment of D. fragilis infection with either iodoquinol, paromomycin, or combination therapy resulted in the eradication of the parasite and complete resolution of symptoms. Treatment failure/relapses were associated only with the use of metronidazole. Nineteen patients were examined for pin worm, no Enterobius vermicularis, a proposed vector of transmission, were detected. Intermittent shedding of D. fragilis was found to be highly variable. These studies confirm the pathogenic nature of D. fragilis and we recommend laboratories routinely test for the organism.
Stark, DJ, Barratt, JL, Roberts, TJ, Marriott, DJ, Harkness, JL & Ellis, JT 2010, 'Comparison of microscopy, two xenic culture techniques, conventional and real-time PCR for the detection of Dientamoeba fragilis in clinical stool samples.', European Journal of Clinical Microbiology & Infectious Diseases, vol. 29, no. 4, pp. 411-416.View/Download from: UTS OPUS or Publisher's site
Dientamoeba fragilis is a pathogenic protozoan parasite that is notoriously difficult to diagnose. The aim of this study was to detennine the gold standard for laboratory detection of D. fragilis. A total of 650 human faecal samples were included in the study. All specimens underwent the following: microscopy using a pennanent stain (modified iron-haematoxylin), culture using a modified Boeck and Drbohlav's medium (MBD) and TYGM-9, a conventional polymerase chain reaction (peR) and a realtime PCR (RT-PCR). The overall prevalence of D. fragilis in the study population was 5.4% (35/650). RT-PCR detected 35 isolates, conventional PCR detected 15 isolates, MBD culture detected 14 isolates, TYGM-9 detected ten isolates, while microscopy' detected 12 isolates. RT-PCR detected an additional 15 positive samples compared to the other diagnostic methods, all of which were confinned by sequencing. When all methods were compared to each other, RT-PCR showed a sensitivity and specificity of 100 and 100%, conventional POR 42.9 and 100%, MBD culture 40 and 100%, TYGM-9 culture 28.6 and 100%, and microscopy 34.3 and 99%, respectively. These results show that RT-PCR is the diagnostic method of choice for the detection of D. fragilis in clinical samples and, as such, should be considered as the gold standard for diagnosis.
Miyakis, S, van Hal, SJ, Barratt, J, Stark, D, Marriott, D & Harkness, J 2009, 'Absence of human Bocavirus in bronchoalveolar lavage fluid of lung transplant patients', JOURNAL OF CLINICAL VIROLOGY, vol. 44, no. 2, pp. 179-180.View/Download from: Publisher's site
van Hal, SJ, Gilgado, F, Doyle, T, Barratt, J, Stark, D, Meyer, W & Harkness, J 2009, 'Clinical Significance and Phylogenetic Relationship of Novel Australian Pneumocystis jirovecii Genotypes', JOURNAL OF CLINICAL MICROBIOLOGY, vol. 47, no. 6, pp. 1818-1823.View/Download from: Publisher's site
Stark, DJ, Barratt, JL, Ellis, JT, Harkness, JL & Marriott, DJ 2009, 'Repeated Dientamoeba fragilis infections: a case report of two families from Sydney, Australia', Infectious Disease Reports, vol. 1, no. e4, pp. 7-9.View/Download from: UTS OPUS or Publisher's site
We report cases of two unrelated families who both presented with recurrent Dientamoeba fragilis infections. Subsequent antimicrobial therapy resulted in the clearance of D. fragilis and total resolution of gastrointestinal symptoms in both families. This report highlights the potentially recurrent nature of D. fragilis infections and the need for laboratories to routinely test for this organism.
Stark, DJ, Barratt, JL, Van Hal, SJ, Marriott, DJ, Harkness, JL & Ellis, JT 2009, 'Clinical significance of enteric protozoa in the immunosuppressed human population', Clinical Microbiology Reviews, vol. 22, no. 4, pp. 634-650.View/Download from: UTS OPUS or Publisher's site
Globally, the number of immunosuppressed people increases each year, with the human immunodeficiency virus (HIV) pandemic continuing to spread unabated in many parts of the world. Immunosuppression may also occur in malnourished persons, patients undergoing chemotherapy for malignancy, and those receiving immunosuppressive therapy. Components of the immune system can be functionally or genetically abnormal as a result of acquired (e.g., caused by HIV infection, lymphoma, or high-dose steroids or other immunosuppressive medications) or congenital illnesses, with more than 120 congenital immunodeficiencies described to date that either affect humoral immunity or compromise T-cell function. All individuals affected by immunosuppression are at risk of infection by opportunistic parasites (such as the microsporidia) as well as those more commonly associated with gastrointestinal disease (such as Giardia). The outcome of infection by enteric protozoan parasites is dependent on absolute CD4+ cell counts, with lower counts being associated with more severe disease, more atypical disease, and a greater risk of disseminated disease. This review summarizes our current state of knowledge on the significance of enteric parasitic protozoa as a cause of disease in immunosuppressed persons and also provides guidance on recent advances in diagnosis and therapy for the control of these important parasites.
Stark, DJ, Van Hal, SJ, Barratt, JL, Ellis, JT, Marriott, DJ & Harkness, JL 2009, 'Limited genetic diversity among genotypes of Enterocytozoon bieneusi strains Isolated from HIV-Infected patients from Sydney, Australia', Journal of Medical Microbiology, vol. 58, no. 3, pp. 355-357.View/Download from: UTS OPUS or Publisher's site
Microsporidia are intracellular parasites, with over 1200 species belonging to 143 genera described to date. They are opportunistic pathogens in humans and can cause chronic diarrhoea in immunosuppressed patients. Both Enterocytozoon bieneusi and Encephalitozoon intestinalis cause intestinal disease, with Enterocytozoon bieneusi more commonly identified in patients with human immunodeficiency virus (HIV) infection. In this study, intestinal microsporidial clinical isolates from patients in Sydney, Australia, were genotyped. All specimens were from HIV-infected men with low CD4(+) T-cell counts (<100 cells mm(-3)). Genotyping of the internal transcribed spacer regions of the rRNA gene showed the presence of only one genotype, the anthroponotic Enterocytozoon bieneusi genotype B strain. This study thus highlighted the limited genetic diversity among Australian Enterocytozoon bieneusi isolates, and it is hypothesized that, due to the reduced incidence of microsporidia. and the subsequent reduction in the human reservoir of the anthroponotic genotype B, locally acquired intestinal microsporidiosis will rarely be seen in HIV-infected persons undergoing highly active antiretroviral therapy in the future in Australia.
Barratt, JL, Al-Qassab, SE, Reichel, MP & Ellis, JT 2008, 'The development and evaluation of a nested PCR assay for detection of Neospora caninum and Hammondia heydorni in feral mouse tissues', Molecular & Cellular Probes, vol. 22, no. 4, pp. 228-233.View/Download from: UTS OPUS or Publisher's site
The development of a novel nested polymerase chain reaction is desribed and used for detecting the presence of Neospora caninum and Hammondai heydorni DNA in DNA extracted from feral rodent tissues.
Barratt, J, Stark, D & Ellis, J 2012, 'Cytotoxic and Proteolytic Molecules of the Human Parasite Dientamoeba fragilis, Identified by RNA seq. Provide Support for its Pathogenic Capacity', TOXICON, 17th World Congress of the International-Society-on-Toxinology (IST)/Venom Week/4th International Scientific Symposium on All Things Venomous, PERGAMON-ELSEVIER SCIENCE LTD, Honolulu, HI, pp. 163-164.View/Download from: Publisher's site
Barratt, J, Stark, D, Roberts, T, Marriott, D, Harkness, J & Ellis, J 2010, 'Evaluation of diagnostic techniques for the detection of Dientamoeba fragilis in clinical stool specimens', 12th International Congress of Parasitology, Melbourne, Australia.
Ellis, J, Barratt, J, Harkness, J, Marriott, D & Stark, D 2010, 'Dientamoeba fragilis: Evidence for its role as a cause of human gastrointestinal disease', 12th International Congress of Parasitology, Melbourne, Australia.
Barratt, J, Al-Qassab, S, Reichel, M & Ellis, J 2008, 'The development and evaluation of a nested PCR assay for detection of Neospora caninum and Hammondia heydorni in feral mouse tissues', ASP & ARC/NHMRC Research Network for Parasitology Annual Conference, Adelaide, Australia.
Barratt, JOEL, Stark, D, Van Hal, S, Ellis, JOHN, Marriott, D & Harkness, J 2008, 'Limited genetic diversity among genotypes of Entercytozoon bieneusi strains isolated from HIV-infected patients from Sydney, Australia', ASP & ARC/NHMRC Research Network for Parasitology Annual Conference, Adelaide, Australia.
Roberts, T, Barratt, J, Stark, D, van hal, S, Ellis, J, Marriott, D & Harkness, J 2008, 'Limited genetic diversity among genotypes of Entercytozoon bieneusi strains isolated from HIV-infected patients from Sydney, Australia', The Australian Society for Microbiology scientific meeting & exhibition, Sydney, Australia.
Joel is currently involved in long term collaborations with researchers at St Vincent's Hospital and ICPMR, Westmead.