Deep sequencing approach for investigating infectious agents causing fever.

Acute undifferentiated fever (AUF) poses a diagnostic challenge due to the variety of possible aetiologies. While the majority of AUFs resolve spontaneously, some cases become prolonged and cause significant morbidity and mortality, necessitating improved diagnostic methods. This study evaluated the utility of deep sequencing in fever investigation. DNA and RNA were isolated from plasma/sera of AUF cases being investigated at Cairns Hospital in northern Australia, including eight control samples from patients with a confirmed diagnosis. Following isolation, DNA and RNA were bulk amplified and RNA was reverse transcribed to cDNA. The resulting DNA and cDNA amplicons were subjected to deep sequencing on an Illumina HiSeq 2000 platform. Bioinformatics analysis was performed using the program Kraken and the CLC assembly-alignment pipeline. The results were compared with the outcomes of clinical tests. We generated between 4 and 20 million reads per sample. The results of Kraken and CLC analyses concurred with diagnoses obtained by other means in 87.5 % (7/8) and 25 % (2/8) of control samples, respectively. Some plausible causes of fever were identified in ten patients who remained undiagnosed following routine hospital investigations, including Escherichia coli bacteraemia and scrub typhus that eluded conventional tests. Achromobacter xylosoxidans, Alteromonas macleodii and Enterobacteria phage were prevalent in all samples. A deep sequencing approach of patient plasma/serum samples led to the identification of aetiological agents putatively implicated in AUFs and enabled the study of microbial diversity in human blood. The application of this approach in hospital practice is currently limited by sequencing input requirements and complicated data analysis.

Bioinformatics meets parasitology.

The advent and integration of high-throughput '-omics' technologies (e.g. genomics, transcriptomics, proteomics, metabolomics, glycomics and lipidomics) are revolutionizing the way biology is done, allowing the systems biology of organisms to be explored. These technologies are now providing unique opportunities for global, molecular investigations of parasites. For example, studies of a transcriptome (all transcripts in an organism, tissue or cell) have become instrumental in providing insights into aspects of gene expression, regulation and function in a parasite, which is a major step to understanding its biology. The purpose of this article was to review recent applications of next-generation sequencing technologies and bioinformatic tools to large-scale investigations of the transcriptomes of parasitic nematodes of socio-economic significance (particularly key species of the order Strongylida) and to indicate the prospects and implications of these explorations for developing novel methods of parasite intervention.

Bioinformatic analysis of abundant, gender-enriched transcripts of adult Ascaris suum (Nematoda) using a semi-automated workflow platform.

Expressed sequence tag (EST) data representing transcripts with a high level of differential hybridization in suppressive-subtractive hybridization (SSH)-based microarray analysis between adult female and male Ascaris suum were subjected to detailed bioinformatic analysis. A total of 361 ESTs clustered into 209 sequences, of which 52 and 157 represented transcripts that were enriched in female and male A. suum, respectively. Thirty (57.7%) of the 'female' subset of 52 sequences had orthologues/homologues in other parasitic nematodes and/or Caenorhabditis elegans, 13 (25%) exclusively in other parasitic nematodes and nine (17.3%) had no match in any other organism for which sequence data are currently available; the C. elegans orthologues encoded molecules involved in reproduction as well as embryonic and gamete development, such as vitellogenins and chitin-binding proteins. Of the 'male' subset of 157 sequences, 73 (46.5%) had orthologues/homologues in other parasitic nematodes and/or C. elegans, 57 (37.5%) in other parasitic nematodes only, and 22 (14.5%) had no significant similarity match in any other organism; the C. elegans orthologues encoded predominantly major sperm proteins (MSPs), kinases and phosphatases, actins, myosins and an Ancylostoma secreted protein-like molecule. The findings of the present study should support further genomic investigations of A. suum.

Investigating public health impacts of deer in a protected drinking water supply watershed.

The World Health Organisation's (WHO) Water Safety Plans highlight the need for preventative risk management when managing water contamination risks. As part of this approach, a management framework incorporating multiple barriers is necessary and there is a need to validate those barriers through scientific evidence. This paper reports on a study undertaken to validate the effectiveness, in terms of pathogen numbers, of having protected watersheds. The study aimed to determine if the deer population in a protected watershed carried Cryptosporidium and whether or not it was human infectious. Deer faecal samples were collected from the protected watersheds over a 12 month period and analysed using a new method, developed as part of this project, for genotyping Cryptosporidium. Early results showed the presence of Cryptosporidium, but following a refinement in the method no human infectious Cryptosporidium was detected. The results give some confidence that having protected watersheds is an effective barrier against pathogen contamination. They do not, however, imply that continued monitoring and management of the deer should cease. To maintain compliance with the Water Safety Plans, continual validation of barrier effectiveness is required.

Cryptosporidium--biotechnological advances in the detection, diagnosis and analysis of genetic variation.

Cryptosporidiosis is predominantly a gastrointestinal disease of humans and other animals, caused by various species of protozoan parasites representing the genus Cryptosporidium. This disease, transmitted mainly via the faecal-oral route (in water or food), is of major socioeconomic importance worldwide. The diagnosis and genetic characterization of the different species and population variants (usually recognised as "genotypes" or "subgenotypes") of Cryptosporidium is central to the prevention, surveillance and control of cryptosporidiosis, particularly given that there is presently no broadly applicable treatment regimen for this disease. Although traditional phenotypic techniques have had major limitations in the specific diagnosis of cryptosporidiosis, there have been major advances in the development of molecular analytical and diagnostic tools. This article provides a concise account of Cryptosporidium and cryptosporidiosis, and focuses mainly on recent advances in nucleic acid-based approaches for the diagnosis of cryptosporidiosis and analysis of genetic variation within and among species of Cryptosporidium. These advances represent a significant step toward an improved understanding of the epidemiology as well as the prevention and control of cryptosporidiosis.

Local climate aridity influences the distribution of thelastomatoid nematodes of the Australian giant burrowing cockroach.

In this study, we examined the effects of local climate aridity on the richness and composition of the thelastomatoid (Nematoda: Oxyurida) guild parasitizing the Australian giant burrowing cockroach, Macropanesthia rhinoceros (Blattodea: Geoscapheinae). In total, 9 thelastomatoid species parasitized this cockroach in north-eastern Australia (Queensland). Local observed richness ranged from 3 species (in Cooktown, Magnetic Island, Maiden Springs and Whitsunday Island) to 7 species (in Rochford Scrub). The lowest richness occurred in both relatively wet and dry climates, and the highest richness was in moderate climates. Three species, Cordonicola gibsoni, Leidynemella fusiformis and Travassosinema jaidenae, were found at all 13 collection sites. One species, Geoscaphenema megaovum, was found exclusively in dry to moderate climates. The remaining species, Blattophila sphaerolaima, Coronostoma australiae, Desmicola ornata, Hammerschmidtiella hochi and Jaidenema rhinoceratum, were found in moderate climates only. We hypothesize that the egg is the stage in the thelastomatoid life-cycle most vulnerable to the effects of adverse climate and that the geographical distribution for each species is, in part, bound by environments that are too dry, resulting in egg desiccation, and by environments that are too wet, resulting in decreased oxygen uptake across the egg-shell and in osmotic lysing.

A comprehensive analysis of the biogeography of the thelastomatoid pinworms from Australian burrowing cockroaches (Blaberidae: Geoscapheinae, Panesthiinae): no evidence of coevolution.

We report 21 thelastomatoid species parasitizing 31 described and 5 undescribed geoscapheine and panesthiine cockroaches, representing all but 1 of the known species of these subfamilies in Australia. The nematodes have 3 distinct patterns of host distribution: dominant, moderate and rare. The 4 dominant species, Cordonicola gibsoni, Leidynemella fusiformis, Travassosinema jaidenae and Aoruroides queenslandensis, are highly prevalent, found in nearly all host species examined, and broadly distributed. The 8 moderate species have lower prevalences but are still widely distributed. Many of these species are more common in one host subfamily than the other. The remaining 9 rare species have highly restricted host and geographical distributions. Six of the 21 species are exclusive to geoscapheines, 5 to panesthiines and 10 are shared. These patterns suggest that most of the reported thelastomatoid species are generalists rather than specialists, that host-specificity within this group is low and that co-evolutionary speciation has had little, if any, impact on structuring the thelastomatoid fauna of Australian burrowing cockroaches. In a broader context, this study provides the first comprehensive examination of the role of coevolutionary speciation and host specificity in regulating the distribution of pinworms in arthropods.

Molecular characterization of Thelastomatoidea (Nematoda: Oxyurida) from cockroaches in Australia.

A molecular approach was used to genetically characterize 5 species (Aoruroides queenslandensis, Blattophila sphaerolaima, Cordonicola gibsoni, Desmicola ornata and Leidynemella fusiformis) belonging to the superfamily Thelastomatoidea (Nematoda: Oxyurida), a group of pinworms that parasitizes terrestrial arthropods. The D3 domain of the large subunit of nuclear ribosomal RNA (LSU) was sequenced for individual specimens, and the analysis of the sequence data allowed the genetic relationships of the 5 species to be studied. The sequence variation in the D3 domain within individual species (0-1.8%) was significantly less than the differences among species (4.3-12.4%). Phylogenetic analyses, using maximum parsimony, maximum likelihood, and neighbour-joining, tree-building methods, established relationships among the 5 species of Thelastomatoidea and Oxyuris equi (a species of the order Oxyurida). The molecular approach employed provides the prospect for developing DNA tools for the specific identification of the Thelastomatoidea, irrespective of developmental stage and sex, as a basis for systematic, ecological and/or population genetic investigations of members within this superfamily.