Publications by authors named "Robin B Gasser"

487 Publications

Detection of sp. (Nematoda) in the Leadbeater's possum ().

Int J Parasitol Parasites Wildl 2021 Aug 24;15:249-254. Epub 2021 Jun 24.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.

The Leadbeater's possum () is a critically endangered marsupial in south-eastern Australia. Among other conservation efforts, free-ranging animals in the two remaining geographically separate populations (highland and lowland) have been extensively studied; however, little is known about their health and mortality. Although some wild populations are frequently monitored, cadavers are rarely recovered for examination. In June 2019, a recently deceased, wild, adult male lowland Leadbeater's possum was collected from a nest box and a comprehensive examination was conducted. Microfilariae of a filarioid nematode were observed in testes, liver, lung and skin samples in tissue impression smears and upon histopathological examination. No gross or histological changes were seen associated with the parasites, except for a focal area of tissue damage in the skin, suggesting that the possum is a natural host. Using a PCR-coupled sequencing method the filarioid was identified as a species of . Species of occur in other Australian marsupials and rodents.
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http://dx.doi.org/10.1016/j.ijppaw.2021.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8255185PMC
August 2021

Prospects of Using High-Throughput Proteomics to Underpin the Discovery of Animal Host-Nematode Interactions.

Pathogens 2021 Jun 30;10(7). Epub 2021 Jun 30.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.

Parasitic nematodes impose a significant public health burden, and cause major economic losses to agriculture worldwide. Due to the widespread of anthelmintic resistance and lack of effective vaccines for most nematode species, there is an urgent need to discover novel therapeutic and vaccine targets, informed through an understanding of host-parasite interactions. Proteomics, underpinned by genomics, enables the global characterisation proteins expressed in a particular cell type, tissue and organism, and provides a key to insights at the host-parasite interface using advanced high-throughput mass spectrometry-based proteomic technologies. Here, we (i) review current mass-spectrometry-based proteomic methods, with an emphasis on a high-throughput 'bottom-up' approach; (ii) summarise recent progress in the proteomics of parasitic nematodes of animals, with a focus on molecules inferred to be involved in host-parasite interactions; and (iii) discuss future research directions that could enhance our knowledge and understanding of the molecular interplay between nematodes and host animals, in order to work toward new, improved methods for the treatment, diagnosis and control of nematodiases.
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http://dx.doi.org/10.3390/pathogens10070825DOI Listing
June 2021

High-Throughput Phenotypic Assay to Screen for Anthelmintic Activity on .

Pharmaceuticals (Basel) 2021 Jun 26;14(7). Epub 2021 Jun 26.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.

Parasitic worms cause very significant diseases in animals and humans worldwide, and their control is critical to enhance health, well-being and productivity. Due to widespread drug resistance in many parasitic worms of animals globally, there is a major, continuing demand for the discovery and development of anthelmintic drugs for use to control these worms. Here, we established a practical, cost-effective and semi-automated high throughput screening (HTS) assay, which relies on the measurement of motility of larvae of the barber's pole worm () using infrared light-interference. Using this assay, we screened 80,500 small molecules and achieved a hit rate of 0.05%. We identified three small molecules that reproducibly inhibited larval motility and/or development (IC values of ~4 to 41 µM). Future work will critically assess the potential of selected hits as candidates for subsequent optimisation or repurposing against parasitic nematodes. This HTS assay has a major advantage over most previous assays in that it achieves a ≥ 10-times higher throughput (i.e., 10,000 compounds per week), and is thus suited to the screening of libraries of tens of thousands to hundreds of thousands of compounds for subsequent hit-to-lead optimisation or effective repurposing and development. The current assay should be adaptable to many socioeconomically important parasitic nematodes, including those that cause neglected tropical diseases (NTDs). This aspect is of relevance, given the goals of the World Health Organization (WHO) Roadmap for NTDs 2021-2030, to develop more effective drugs and drug combinations to improve patient outcomes and circumvent the ineffectiveness of some current anthelmintic drugs and possible drug resistance.
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http://dx.doi.org/10.3390/ph14070616DOI Listing
June 2021

Three Small Molecule Entities (MPK18, MPK334 and YAK308) with Activity against In Vitro.

Molecules 2021 May 10;26(9). Epub 2021 May 10.

Department of Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Victoria, Australia.

Due to widespread multi-drug resistance in parasitic nematodes of livestock animals, there is an urgent need to discover new anthelmintics with distinct mechanisms of action. Extending previous work, here we screened a panel of 245 chemically-diverse small molecules for anti-parasitic activity against -an economically important parasitic nematode of livestock. This panel was screened in vitro against exsheathed third-stage larvae (xL3) of using an established phenotypic assay, and the potency of select compounds to inhibit larval motility and development assessed in dose-response assays. Of the 245 compounds screened, three-designated MPK18, MPK334 and YAK308-induced non-wildtype larval phenotypes and repeatedly inhibited xL3-motility, with IC values of 45.2 µM, 17.1 µM and 52.7 µM, respectively; two also inhibited larval development, with IC values of 12.3 µM (MPK334) and 6.5 µM (YAK308), and none of the three was toxic to human liver cells (HepG2). These findings suggest that these compounds deserve further evaluation as nematocidal candidates. Future work should focus on structure-activity relationship (SAR) studies of these chemical scaffolds, and assess the in vitro and in vivo efficacies and safety of optimised compounds against adults of .
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http://dx.doi.org/10.3390/molecules26092819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8126080PMC
May 2021

How qPCR complements the WHO roadmap (2021-2030) for soil-transmitted helminths.

Trends Parasitol 2021 08 27;37(8):698-708. Epub 2021 Apr 27.

Department of Infectious Disease Epidemiology, St Mary's Campus, Imperial College London, London, UK; London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, UK.

Complementing the launch of the World Health Organization (WHO) roadmap (2021-2030) we explore key elements needing attention before recruitment of qPCR as the main diagnostics tool to confirm reduction or elimination of soil-transmitted helminth (STH) transmission in both control and elimination programmes. Given the performance limitations of conventional methods, a proposed harmonised qPCR will provide a diagnostic tool, with the sensitivity and specificity required to monitor low-intensity infections, following mass drug administration (MDA). Technical and logistical challenges associated with introducing qPCR as a stand-alone tool are highlighted, and a decision-making scheme on how qPCR can support surveillance, resistance detection, and elimination is presented. An accurate point-of-care (POC) diagnostic test needs to be developed to support STH control in the field, and STH biorepositories need to be established and maintained to ensure that reference materials are available for research and validation.
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http://dx.doi.org/10.1016/j.pt.2021.04.005DOI Listing
August 2021

Dipylidium caninum draft genome - a new resource for comparative genomic and genetic explorations of flatworms.

Genomics 2021 May 4;113(3):1272-1280. Epub 2021 Mar 4.

State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China. Electronic address:

Here, we present a draft genome of the tapeworm Dipylidium caninum (family Dipylidiidae) and compare it with other cestode genomes. This draft genome of D. caninum is 110 Mb in size, has a repeat content of ~13.4% and is predicted to encode ~10,000 protein-coding genes. We inferred excretory/secretory molecules (representing the secretome), other key groups of proteins (including peptidases, kinases, phosphatases, GTPases, receptors, transporters and ion-channels) and predicted potential intervention targets for future evaluation. Using 144 shared single-copy orthologous sequences, we investigated the genetic relationships of cestodes for which nuclear genomes are available. This study provides first insights into the molecular biology of D. caninum and a new resource for comparative genomic and genetic explorations of this and other flatworms.
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http://dx.doi.org/10.1016/j.ygeno.2021.02.019DOI Listing
May 2021

High-quality reference genome for Clonorchis sinensis.

Genomics 2021 May 4;113(3):1605-1615. Epub 2021 Mar 4.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.

The Chinese liver fluke, Clonorchis sinensis, causes the disease clonorchiasis, affecting ~35 million people in regions of China, Vietnam, Korea and the Russian Far East. Chronic clonorchiasis causes cholangitis and can induce a malignant cancer, called cholangiocarcinoma, in the biliary system. Control in endemic regions is challenging, and often relies largely on chemotherapy with one anthelmintic, called praziquantel. Routine treatment carries a significant risk of inducing resistance to this anthelmintic in the fluke, such that the discovery of new interventions is considered important. It is hoped that the use of molecular technologies will assist this endeavour by enabling the identification of drug or vaccine targets involved in crucial biological processes and/or pathways in the parasite. Although draft genomes of C. sinensis have been published, their assemblies are fragmented. In the present study, we tackle this genome fragmentation issue by utilising, in an integrated way, advanced (second- and third-generation) DNA sequencing and informatic approaches to build a high-quality reference genome for C. sinensis, with chromosome-level contiguity and curated gene models. This substantially-enhanced genome provides a resource that could accelerate fundamental and applied molecular investigations of C. sinensis, clonorchiasis and/or cholangiocarcinoma, and assist in the discovery of new interventions against what is a highly significant, but neglected disease-complex.
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http://dx.doi.org/10.1016/j.ygeno.2021.03.001DOI Listing
May 2021

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes.

Int J Mol Sci 2021 Feb 11;22(4). Epub 2021 Feb 11.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.

Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, , and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow.
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http://dx.doi.org/10.3390/ijms22041811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7918261PMC
February 2021

Phytochemical Profiling and Biological Activity of the Australian Carnivorous Plant, .

J Nat Prod 2021 04 25;84(4):964-971. Epub 2021 Feb 25.

School of Science (Applied Chemistry and Environmental Science), RMIT University, GPO Box 2476 Melbourne, Victoria 3001, Australia.

Phytochemical profiling was undertaken on the crude extracts of to determine the nature of the chemical constituents present. In total, three new flavonol diglycosides (-), one new flavan-3-ol glycoside (), and 12 previously reported compounds of the flavonol (, ), flavan-3-ol (), flavanone (), 1,4-napthoquinone (, , , ), 2,3-dehydroxynapthalene-1,4-dione (-), and phenolic acid () structure classes were isolated and identified. Compounds -, , , and were assessed for antimicrobial activity, with compounds , , , and showing significant activity. Compounds , , and were also evaluated for anthelmintic activity against larval forms of , with compound being active.
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http://dx.doi.org/10.1021/acs.jnatprod.0c00869DOI Listing
April 2021

Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome.

PLoS Negl Trop Dis 2021 02 24;15(2):e0009149. Epub 2021 Feb 24.

QIMR Berghofer Medical Research Institute, Brisbane, Australia.

Background: The suboptimal sensitivity and specificity of available diagnostic methods for scabies hampers clinical management, trials of new therapies and epidemiologic studies. Additionally, parasitologic diagnosis by microscopic examination of skin scrapings requires sample collection with a sharp scalpel blade, causing discomfort to patients and difficulty in children. Polymerase chain reaction (PCR)-based diagnostic assays, combined with non-invasive sampling methods, represent an attractive approach. In this study, we aimed to develop a real-time probe-based PCR test for scabies, test a non-invasive sampling method and evaluate its diagnostic performance in two clinical settings.

Methodology/principal Findings: High copy-number repetitive DNA elements were identified in draft Sarcoptes scabiei genome sequences and used as assay targets for diagnostic PCR. Two suitable repetitive DNA sequences, a 375 base pair microsatellite (SSR5) and a 606 base pair long tandem repeat (SSR6), were identified. Diagnostic sensitivity and specificity were tested using relevant positive and negative control materials and compared to a published assay targeting the mitochondrial cox1 gene. Both assays were positive at a 1:100 dilution of DNA from a single mite; no amplification was observed in DNA from samples from 19 patients with other skin conditions nor from house dust, sheep or dog mites, head and body lice or from six common skin bacterial and fungal species. Moderate sensitivity of the assays was achieved in a pilot study, detecting 5/7 (71.4% [95% CI: 29.0% - 96.3%]) of clinically diagnosed untreated scabies patients). Greater sensitivity was observed in samples collected by FLOQ swabs compared to skin scrapings.

Conclusions/significance: This newly developed qPCR assay, combined with the use of an alternative non-invasive swab sampling technique offers the possibility of enhanced diagnosis of scabies. Further studies will be required to better define the diagnostic performance of these tests.
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http://dx.doi.org/10.1371/journal.pntd.0009149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7939366PMC
February 2021

Combined use of feature engineering and machine-learning to predict essential genes in .

NAR Genom Bioinform 2020 Sep 22;2(3):lqaa051. Epub 2020 Jul 22.

Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.

Characterizing genes that are critical for the survival of an organism (i.e. essential) is important to gain a deep understanding of the fundamental cellular and molecular mechanisms that sustain life. Functional genomic investigations of the vinegar fly, , have unravelled the functions of numerous genes of this model species, but results from phenomic experiments can sometimes be ambiguous. Moreover, the features underlying gene essentiality are poorly understood, posing challenges for computational prediction. Here, we harnessed comprehensive genomic-phenomic datasets publicly available for and a machine-learning-based workflow to predict essential genes of this fly. We discovered strong predictors of such genes, paving the way for computational predictions of essentiality in less-studied arthropod pests and vectors of infectious diseases.
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http://dx.doi.org/10.1093/nargab/lqaa051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671374PMC
September 2020

Advances in the discovery and development of anthelmintics by harnessing natural product scaffolds.

Adv Parasitol 2021 8;111:203-251. Epub 2021 Jan 8.

Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia. Electronic address:

Widespread resistance to currently-used anthelmintics represents a major obstacle to controlling parasitic nematodes of livestock animals. Given the reliance on anthelmintics in many control regimens, there is a need for the continued discovery and development of new nematocides. Enabling such a focus are: (i) the major chemical diversity of natural products; (ii) the availability of curated, drug-like extract-, fraction- and/or compound-libraries from natural sources; (iii) the utility and practicality of well-established whole-worm bioassays for Haemonchus contortus-an important parasitic nematodes of livestock-to screen natural product libraries; and (iv) the availability of advanced chromatographic (HPLC), spectroscopic (NMR) and spectrometric (MS) techniques for bioassay-guided fractionation and structural elucidation. This context provides a sound basis for the identification and characterisation of anthelmintic candidates from natural sources. This chapter provides a background on the importance and impact of helminth infections/diseases, parasite control and aspects of drug discovery, and reviews recent work focused on (i) screening well-defined compound libraries to establish the methods needed for large-scale screening of natural extract libraries; (ii) discovering plant and marine extracts with nematocidal or nematostatic activity, and purifying bioactive compounds and assessing their potential for further development; and (iii) synthesising analogues of selected purified natural compounds for the identification of possible 'lead' candidates. The chapter describes some lessons learned from this work and proposes future areas of focus for drug discovery. Collectively, the findings from this recent work show potential for selected natural product scaffolds as candidates for future development. Developing such candidates via future chemical optimisation, efficacy and safety evaluations, broad spectrum activity assessments, and target identification represents an exciting prospect and, if successful, could pave the way to subsequent pre-clinical and clinical evaluations.
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http://dx.doi.org/10.1016/bs.apar.2020.10.002DOI Listing
January 2021

Enterocytozoon bieneusi of animals-With an 'Australian twist'.

Adv Parasitol 2021 8;111:1-73. Epub 2021 Jan 8.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia. Electronic address:

Enterocytozoon bieneusi is a microsporidian microorganism that causes intestinal disease in animals including humans. E. bieneusi is an obligate intracellular pathogen, typically causing severe or chronic diarrhoea, malabsorption and/or wasting. Currently, E. bieneusi is recognised as a fungus, although its exact classification remains contentious. The transmission of E. bieneusi can occur from person to person and/or animals to people. Transmission is usually via the faecal-oral route through E. bieneusi spore-contaminated water, environment or food, or direct contact with infected individuals. Enterocytozoon bieneusi genotypes are usually identified and classified by PCR-based sequencing of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA. To date, ~600 distinct genotypes of E. bieneusi have been recorded in ~170 species of animals, including various orders of mammals and reptiles as well as insects in >40 countries. Moreover, E. bieneusi has also been found in recreational water, irrigation water, and treated raw- and waste-waters. Although many studies have been conducted on the epidemiology of E. bieneusi, prevalence surveys of animals and humans are scant in some countries, such as Australia, and transmission routes of individual genotypes and related risk factors are poorly understood. This article/chapter reviews aspects of the taxonomy, biology and epidemiology of E. bieneusi; the diagnosis, treatment and prevention of microsporidiosis; critically appraises the naming system for E. bieneusi genotypes as well as the phylogenetic relationships of these genotypes; provides new insights into the prevalence and genetic composition of E. bieneusi populations in animals in parts of Australia using molecular epidemiological tools; and proposes some areas for future research in the E. bieneusi/microsporidiosis field.
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http://dx.doi.org/10.1016/bs.apar.2020.10.001DOI Listing
January 2021

Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions.

Microorganisms 2020 Dec 23;9(1). Epub 2020 Dec 23.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC 3030, Australia.

Protists of the genera and (piroplasms) cause some of the most prevalent and debilitating diseases for bovines worldwide. In this study, we established and used a next-generation sequencing-informatic approach to explore the composition of and populations in cattle and water buffalo in a country (Pakistan) endemic for these pathogens. We collected individual blood samples from cattle ( = 212) and water buffalo ( = 154), extracted genomic DNAs, PCR-amplified the V4 hypervariable region of 18S small subunit rRNA gene from piroplasms, sequenced amplicons using Illumina technology, and then analysed data using bioinformatic platforms. The results revealed piroplasms in 68.9% (252/366) samples, with overall occurrence being markedly higher in cattle (85.8%) than in water buffaloes (45.5%). () and () -like species were recorded for the first time in Pakistan, and, overall, was most commonly detected (65.8%) followed by (7.1%), (4.4%), and (0.5%), with the genetic variability within being pronounced. The occurrence and composition of piroplasm species varied markedly across different agro-ecological zones. The high detection of in asymptomatic animals suggested a relatively high level of endemic stability of tropical theileriosis in the bovine population.
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http://dx.doi.org/10.3390/microorganisms9010021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7822421PMC
December 2020

1-Methyl-1-pyrazole-5-carboxamide Derivatives Exhibit Unexpected Acute Mammalian Toxicity.

J Med Chem 2021 01 22;64(1):840-844. Epub 2020 Dec 22.

School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.

A series of 1-methyl-1-pyrazole-5-carboxamides were synthesized as potent inhibitors of the parasitic nematode of sheep, . These compounds did not show overt cytotoxicity to a range of mammalian cell lines under standard in vitro culture conditions, had high selectivity indices, and were progressed to an acute toxicity study in a rodent model. Strikingly, acute toxicity was observed in mice. Experiments measuring cellular respiration showed a dose-dependent inhibition of mitochondrial respiration. Under these conditions, potent cytotoxicity was observed for these compounds in rat hepatocytes suggesting that the potent acute mammalian toxicity of this chemotype is most likely associated with respiratory inhibition. In contrast, parasite toxicity was not correlated to acute toxicity or cytotoxicity in respiring cells. This paper highlights the importance of identifying an appropriate in vitro predictor of in vivo toxicity early on in the drug discovery pipeline, in particular assessment for in vitro mitochondrial toxicity.
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http://dx.doi.org/10.1021/acs.jmedchem.0c01793DOI Listing
January 2021

Ocular Filariasis in Human Caused by Breinlia (Johnstonema) annulipapillata Nematode, Australia.

Emerg Infect Dis 2021 01;27(1):297-300

We report a human case of ocular filariasis, caused by a species of Breinlia nematode, from Queensland, Australia. Morphological and molecular evidence indicated that the nematode Breinlia (Johnstonema) annulipapillata, or a closely related taxon, likely transmitted from a macropodid marsupial host was involved, which might represent an accidental finding or an emerging zoonosis.
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http://dx.doi.org/10.3201/eid2701.203585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7774559PMC
January 2021

Phylogenetic Analysis of Mitogenomic Data Sets Resolves the Relationship of Seven Species from Australian Macropodid and Vombatid Marsupials.

Pathogens 2020 Dec 12;9(12). Epub 2020 Dec 12.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne 3030, Australia.

Nematodes of the genus inhabit the large intestines or stomachs of macropodid (kangaroos and wallabies) and vombatid (wombats) marsupials. This study established the relationships of seven species of using mitochondrial (mt) protein amino acid sequence data sets. Phylogenetic analyses revealed that species of (, , , , and ) from the large intestines of their hosts formed a monophyletic assemblage with strong nodal support to the exclusion of from the stomach of the swamp wallaby. Furthermore, the mitochondrial protein-coding genes provided greater insights into the diversity and phylogeny of the genus ; such data sets could potentially be used to elucidate the relationships among other parasitic nematodes of Australian marsupials.
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http://dx.doi.org/10.3390/pathogens9121042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7763074PMC
December 2020

Quantitative lipidomic analysis of Ascaris suum.

PLoS Negl Trop Dis 2020 12 2;14(12):e0008848. Epub 2020 Dec 2.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia.

Ascaris is a soil-transmitted nematode that causes ascariasis, a neglected tropical disease affecting predominantly children and adolescents in the tropics and subtropics. Approximately 0.8 billion people are affected worldwide, equating to 0.86 million disability-adjusted life-years (DALYs). Exploring the molecular biology of Ascaris is important to gain a better understanding of the host-parasite interactions and disease processes, and supports the development of novel interventions. Although advances have been made in the genomics, transcriptomics and proteomics of Ascaris, its lipidome has received very limited attention. Lipidomics is an important sub-discipline of systems biology, focused on exploring lipids profiles in tissues and cells, and elucidating their biological and metabolic roles. Here, we characterised the lipidomes of key developmental stages and organ systems of Ascaris of porcine origin via high throughput LC-MS/MS. In total, > 500 lipid species belonging to 18 lipid classes within three lipid categories were identified and quantified-in precise molar amounts in relation to the dry weight of worm material-in different developmental stages/sexes and organ systems. The results showed substantial differences in the composition and abundance of lipids with key roles in cellular processes and functions (e.g. energy storage regulation and membrane structure) among distinct stages and among organ systems, likely reflecting differing demands for lipids, depending on stage of growth and development as well as the need to adapt to constantly changing environments within and outside of the host animal. This work provides the first step toward understanding the biology of lipids in Ascaris, with possibilities to work toward designing new interventions against ascariasis.
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http://dx.doi.org/10.1371/journal.pntd.0008848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710092PMC
December 2020

Major SCP/TAPS protein expansion in Lucilia cuprina is associated with novel tandem array organisation and domain architecture.

Parasit Vectors 2020 Nov 27;13(1):598. Epub 2020 Nov 27.

Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, 3010, Australia.

Background: Larvae of the Australian sheep blowfly, Lucilia cuprina, parasitise sheep by feeding on skin excretions, dermal tissue and blood, causing severe damage known as flystrike or myiasis. Recent advances in -omic technologies and bioinformatic data analyses have led to a greater understanding of blowfly biology and should allow the identification of protein families involved in host-parasite interactions and disease. Current literature suggests that proteins of the SCP (Sperm-Coating Protein)/TAPS (Tpx-1/Ag5/PR-1/Sc7) (SCP/TAPS) superfamily play key roles in immune modulation, cross-talk between parasite and host as well as developmental and reproductive processes in parasites.

Methods: Here, we employed a bioinformatics workflow to curate the SCP/TAPS protein gene family in L. cuprina. Protein sequence, the presence and number of conserved CAP-domains and phylogeny were used to group identified SCP/TAPS proteins; these were compared to those found in Drosophila melanogaster to make functional predictions. In addition, transcription levels of SCP/TAPS protein-encoding genes were explored in different developmental stages.

Results: A total of 27 genes were identified as belonging to the SCP/TAPS gene family: encoding 26 single-domain proteins each with a single CAP domain and a solitary double-domain protein containing two conserved cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domains. Surprisingly, 16 SCP/TAPS predicted proteins formed an extended tandem array spanning a 53 kb region of one genomic region, which was confirmed by MinION long-read sequencing. RNA-seq data indicated that these 16 genes are highly transcribed in all developmental stages (excluding the embryo).

Conclusions: Future work should assess the potential of selected SCP/TAPS proteins as novel targets for the control of L. cuprina and related parasitic flies of major socioeconomic importance.
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http://dx.doi.org/10.1186/s13071-020-04476-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7694928PMC
November 2020

SARS-CoV-2 seroprevalence worldwide: a systematic review and meta-analysis.

Clin Microbiol Infect 2021 Mar 24;27(3):331-340. Epub 2020 Oct 24.

Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia. Electronic address:

Objectives: COVID-19 has been arguably the most important public health concern worldwide in 2020, and efforts are now escalating to suppress or eliminate its spread. In this study we undertook a meta-analysis to estimate the global and regional seroprevalence rates in humans of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to assess whether seroprevalence is associated with geographical, climatic and/or sociodemographic factors.

Methods: We systematically reviewed PubMed, Scopus, Embase, medRxiv and bioRxiv databases for preprints or peer-reviewed articles (up to 14 August 2020). Study eligibility criteria were population-based studies describing the prevalence of anti-SARS-CoV-2 (IgG and/or IgM) serum antibodies. Participants were people from different socioeconomic and ethnic backgrounds (from the general population), whose prior COVID-19 status was unknown and who were tested for the presence of anti-SARS-CoV-2 serum antibodies. We used a random-effects model to estimate pooled seroprevalence, and then extrapolated the findings to the global population (for 2020). Subgroup and meta-regression analyses explored potential sources of heterogeneity in the data, and relationships between seroprevalence and sociodemographic, geographical and/or climatic factors.

Results: In total, 47 studies involving 399 265 people from 23 countries met the inclusion criteria. Heterogeneity (I = 99.4%, p < 0.001) was seen among studies; SARS-CoV-2 seroprevalence in the general population varied from 0.37% to 22.1%, with a pooled estimate of 3.38% (95%CI 3.05-3.72%; 15 879/399 265). On a regional level, seroprevalence varied from 1.45% (0.95-1.94%, South America) to 5.27% (3.97-6.57%, Northern Europe), although some variation appeared to relate to the serological assay used. The findings suggested an association of seroprevalence with income levels, human development indices, geographic latitudes and/or climate. Extrapolating to the 2020 world population, we estimated that 263.5 million individuals had been exposed or infected at the time of this study.

Conclusions: This study showed that SARS-CoV-2 seroprevalence varied markedly among geographic regions, as might be expected early in a pandemic. Longitudinal surveys to continually monitor seroprevalence around the globe will be critical to support prevention and control efforts, and might indicate levels of endemic stability or instability in particular countries and regions.
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http://dx.doi.org/10.1016/j.cmi.2020.10.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7584920PMC
March 2021

"Begging the Question"-Does Infection/Exposure Associate with Multiple Sclerosis-Risk?

Pathogens 2020 Nov 11;9(11). Epub 2020 Nov 11.

Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville 3010, VIC, Australia.

Although the cause of multiple sclerosis (MS) is unclear, infectious agents, including some parasitic roundworms (nematodes), have been proposed as possible risk factors or contributors. Here, we conducted a systematic review and meta-analysis of published observational studies to evaluate whether there is a possible association between infection with, or exposure to, one or more members of the genus (phylum Nematoda; superfamily Ascaridoidea) and MS. We undertook a search of public literature databases to identify relevant studies and then used a random-effects meta-analysis model to generate the pooled odds ratio (OR) and 95% confidence intervals (CIs). This search identified six of a total of 1371 articles that were relevant to the topic; these published studies involved totals of 473 MS patients and 647 control subjects. Anti- IgG serum antibodies were detected in 62 MS patients and 37 controls, resulting in respective seroprevalences of 13.1% (95% CI: 8.2-20.3) and 4.8% (95% CI: 2.5-9.2), indicating an association (pooled OR, 3.01; 95% CI: 1.46-6.21). Because of the publication bias identified (six eligible studies), well-designed and -controlled studies are required in the future to rigorously test the hypothesis that infection/exposure has an association with MS.
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http://dx.doi.org/10.3390/pathogens9110938DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7696196PMC
November 2020

cf. in an inland-bearded dragon () - A case report and review of the literature.

Int J Parasitol Parasites Wildl 2020 Dec 2;13:150-159. Epub 2020 Oct 2.

Faculty of Veterinary and Agricultural Sciences,The University of Melbourne, Parkville, Victoria 3010,Australia.

Here, we report the first case of cf. from an inland bearded dragon () from a wildlife sanctuary in Victoria, Australia. Molecular characterisation was conducted by PCR-coupled sequencing of regions in the small subunit of nuclear RNA (), and large subunit of nuclear RNA () genes. The sequences obtained grouped with those of . and other genotypes/variants originating from reptiles or birds. We discuss this case in relation to the current state of knowledge of of birds and reptiles, considering provenance and environment (agricultural, pet industry, wildlife, zoo or wildlife park) as well as clinical context, and pathological changes associated with cryptosporidiosis in these host animals.
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http://dx.doi.org/10.1016/j.ijppaw.2020.09.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7560628PMC
December 2020

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines.

Nucleic Acids Res 2021 01;49(D1):D998-D1003

Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China.

OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality. We tagged conditionally essential genes that show variable essentiality statuses across datasets to highlight complex interplays between gene functions and environmental/experimental perturbations. OGEE v3 contains gene essentiality datasets for 91 species; almost doubled from 48 species in previous version. To accommodate recent advances on human cancer essential genes (as known as tumor dependency genes) that could serve as targets for cancer treatment and/or drug development, we expanded the collection of human essential genes from 16 cell lines in previous to 581. These human cancer cell lines were tested with high-throughput experiments such as CRISPR-Cas9 and RNAi; in total, 150 of which were tested by both techniques. We also included factors known to contribute to gene essentiality for these cell lines, such as genomic mutation, methylation and gene expression, along with extensive graphical visualizations for ease of understanding of these factors. OGEE v3 can be accessible freely at https://v3.ogee.info.
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http://dx.doi.org/10.1093/nar/gkaa884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779042PMC
January 2021

High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite.

PLoS Negl Trop Dis 2020 10 1;14(10):e0008720. Epub 2020 Oct 1.

Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.

The parasitic mite Sarcoptes scabiei is an economically highly significant parasite of the skin of humans and animals worldwide. In humans, this mite causes a neglected tropical disease (NTD), called scabies. This disease results in major morbidity, disability, stigma and poverty globally and is often associated with secondary bacterial infections. Currently, anti-scabies treatments are not sufficiently effective, resistance to them is emerging and no vaccine is available. Here, we report the first high-quality genome and transcriptomic data for S. scabiei. The genome is 56.6 Mb in size, has a a repeat content of 10.6% and codes for 9,174 proteins. We explored key molecules involved in development, reproduction, host-parasite interactions, immunity and disease. The enhanced 'omic data sets for S. scabiei represent comprehensive and critical resources for genetic, functional genomic, metabolomic, phylogenetic, ecological and/or epidemiological investigations, and will underpin the design and development of new treatments, vaccines and/or diagnostic tests.
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http://dx.doi.org/10.1371/journal.pntd.0008720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591027PMC
October 2020

Case Report: Neurocysticercosis Acquired in Australia.

Am J Trop Med Hyg 2020 12 17;103(6):2318-2322. Epub 2020 Sep 17.

The Peter Doherty Institute for Infection and Immunity, University of Melbourne and the Royal Melbourne Hospital, Parkville, Australia.

Neurocysticercosis (NCC) is a disease caused by infection of the central nervous system with the larval stage of the tapeworm This disease is endemic in many parts of the world, including Africa, Asia, and Latin America, where animal husbandry practices are common such that pigs reared for human consumption ingest feces from humans infected with . Neurocysticercosis is rarely acquired in economically affluent regions, including North America, Central Europe, Japan, and Australasia, and in countries where pork consumption is discouraged by religious or social practices. In these countries, NCC is usually diagnosed in immigrants or returning travelers who have spent time in endemic regions. Here, we report a case of NCC in a 25-year-old woman presenting with worsening visual symptoms in association with headache, diagnosed previously as a migraine with visual aura. This person had always lived in Australia and had never traveled overseas to a country endemic for . The unusual features of the clinical presentation and epidemiology are highlighted to raise physicians' awareness that attention needs to be paid to the risk of autochthonous infection occurring in non-endemic countries.
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http://dx.doi.org/10.4269/ajtmh.20-0839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7695046PMC
December 2020

An Assessment of the Molecular Diversity of Ticks and Tick-Borne Microorganisms of Small Ruminants in Pakistan.

Microorganisms 2020 Sep 17;8(9). Epub 2020 Sep 17.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee 3030, Victoria, Australia.

This study investigated ticks and tick-borne microorganisms of small ruminants from five districts of the Federally Administered Tribal Area (FATA) of Pakistan. Morphological ( = 104) and molecular ( = 54) characterization of the ticks revealed the presence of six ixodid ticks: (.) , , , (.) , and . Phylogenetic analyses of nucleotide sequence data for two mitochondrial (16S and cytochrome oxidase 1) and one nuclear (second internal transcribed spacer) DNA regions provided strong support for the grouping of the six tick species identified in this study. Microfluidic real-time PCR, employing multiple pre-validated nuclear and mitochondrial genetic markers, detected 11 potential pathogens and endosymbionts in 72.2% of the ticks ( = 54) tested. () was the most common pathogen found (42.6% of ticks) followed by spp. (33.3%), () and (25.9% each). , , spp., , and endosymbionts (- and -like) were detected at much lower rates (1.9-22.2%) in ticks. Ticks from goats (83.9%) carried significantly higher microorganisms than those from sheep (56.5%). This study demonstrates that ticks of small ruminants from the FATA are carrying multiple microorganisms of veterinary and medical health significance and provides the basis for future investigations of ticks and tick-borne diseases of animals and humans in this and neighboring regions.
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http://dx.doi.org/10.3390/microorganisms8091428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7563897PMC
September 2020

Diversity in the intrinsic apoptosis pathway of nematodes.

Commun Biol 2020 08 28;3(1):478. Epub 2020 Aug 28.

Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.

Early studies of the free-living nematode C. elegans informed us how BCL-2-regulated apoptosis in humans is regulated. However, subsequent studies showed C. elegans apoptosis has several unique features compared with human apoptosis. To date, there has been no detailed analysis of apoptosis regulators in nematodes other than C. elegans. Here, we discovered BCL-2 orthologues in 89 free-living and parasitic nematode taxa representing four evolutionary clades (I, III, IV and V). Unlike in C. elegans, 15 species possess multiple (two to five) BCL-2-like proteins, and some do not have any recognisable BCL-2 sequences. Functional studies provided no evidence that BAX/BAK proteins have evolved in nematodes, and structural studies of a BCL-2 protein from the basal clade I revealed it lacks a functionally important feature of the C. elegans orthologue. Clade I CED-4/APAF-1 proteins also possess WD40-repeat sequences associated with apoptosome assembly, not present in C. elegans, or other nematode taxa studied.
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http://dx.doi.org/10.1038/s42003-020-01208-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456325PMC
August 2020

First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach.

PLoS Negl Trop Dis 2020 08 26;14(8):e0008552. Epub 2020 Aug 26.

Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia.

Background: Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them are incomplete relating to an inability of conventional techniques to reliably sequence non-coding (repetitive) regions. In the present study, we characterise the complete mitochondrial genome-including the long, non-coding region-of the carcinogenic Chinese liver fluke, Clonorchis sinensis, using long-read sequencing.

Methods: The mitochondrial genome was sequenced from total high molecular-weight genomic DNA isolated from a pool of 100 adult worms of C. sinensis using the MinION sequencing platform (Oxford Nanopore Technologies), and assembled and annotated using an informatic approach.

Results: From > 93,500 long-reads, we assembled a 18,304 bp-mitochondrial genome for C. sinensis. Within this genome we identified a novel non-coding region of 4,549 bp containing six tandem-repetitive units of 719-809 bp each. Given that genomic DNA from pooled worms was used for sequencing, some variability in length/sequence in this tandem-repetitive region was detectable, reflecting population variation.

Conclusions: For C. sinensis, we report the complete mitochondrial genome, which includes a long (> 4.5 kb) tandem-repetitive region. The discovery of this non-coding region using a nanopore-sequencing/informatic approach now paves the way to investigating the nature and extent of length/sequence variation in this region within and among individual worms, both within and among C. sinensis populations, and to exploring whether this region has a functional role in the regulation of replication and transcription, akin to the mitochondrial control region in mammals. Although applied to C. sinensis, the technological approach established here should be broadly applicable to characterise complex tandem-repetitive or homo-polymeric regions in the mitochondrial genomes of a wide range of taxa.
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http://dx.doi.org/10.1371/journal.pntd.0008552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449408PMC
August 2020

The oligomeric assembly of galectin-11 is critical for anti-parasitic activity in sheep (Ovis aries).

Commun Biol 2020 08 21;3(1):464. Epub 2020 Aug 21.

Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.

Galectins are a family of glycan-binding molecules with a characteristic affinity for ß-D-glycosides that mediate a variety of important cellular functions, including immune and inflammatory responses. Galectin-11 (LGALS-11) has been recently identified as a mediator induced specifically in animals against gastrointestinal nematodes and can interfere with parasite growth and development. Here, we report that at least two natural genetic variants of LGALS-11 exist in sheep, and demonstrate fundamental differences in anti-parasitic activity, correlated with their ability to dimerise. This study improves our understanding of the role of galectins in the host immune and inflammatory responses against parasitic nematodes and provides a basis for genetic studies toward selective breeding of animals for resistance to parasites.
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http://dx.doi.org/10.1038/s42003-020-01179-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7442640PMC
August 2020