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In comparative studies, the advantage of increased sample sizes might be outweighed by detrimental effects on sample homogeneity and comparability when small numbers of hosts from a different demographic of the same species are included in samples. A mixed sample of sunfishes (Lepomis spp.) was subdivided in different ways and examined using cumulative performance curves to determine whether the exclusion of larger hosts from a single-species sample and/or the inclusion of hosts of the same size demographic from closely related host species would produce more homogeneous samples. The exclusion of larger hosts from the single-species samples tended to reduce the aggregation of the infrapopulation samples, and mixed-species samples of smaller fishes tended to have lower degrees of aggregation for a given sample size relative to the single-species sample. Cumulative performance curves for diversity and richness, in concert with nonmetric multidimensional scaling of the infracommunities, demonstrated sunfish size to be a more reliable determinant of infracommunity similarity than sunfish species in this particular sample. The results demonstrate that cumulative aggregation curves can be an effective tool for delineating homogeneous and comparable subsamples and that, under some circumstances, it is possible to offset the smaller sample sizes that result from the exclusion of older/larger hosts by the addition of congeneric or confamilial hosts within the same size/age classes as the stratified sample.

Tick-borne diseases are emerging globally, necessitating increased research and coordination of tick surveillance practices. The most widely used technique for active collection of host-seeking, human-biting tick vectors is ‘tick dragging’, by which a cloth is dragged across the top of the vegetation or forest floor and regularly checked for the presence of ticks. Use of variable dragging protocols limits the ability of researchers to combine data sets for comparative analyses or determine patterns and trends across different spatial and temporal scales. Standardization of tick drag collection and reporting methodology will greatly benefit the field of tick-pathogen studies. Based on the recommendations of the Center for Disease Control and Prevention and other ecological considerations, we propose that tick dragging should be conducted to sample at least 750 m2 along linear transects when habitat allows in a manner that reduces bias in the sampled area, and report density of each tick species and life stage separately. A protocol for constructing a standard drag cloth, establishing linear transects, and drag sampling is presented, along with a downloadable datasheet that can be modified to suit the needs of different projects. Efforts to align tick surveillance according to these standard best practices will help generate robust data on tick population biology.

We conducted an extensive literature review on studies that have used DNA sequences to detect cryptic species of parasites during the last decade. Each literature citation that included the term “cryptic” or “sibling” species was analyzed to determine the approach used by the author(s). Reports were carefully filtered to retain only those that recognized the existence of cryptic species centered on the use of DNA sequences. Based on analysis of these papers, we comment on the different ways that parasite cryptic species are discovered in studies focusing on different aspects of the host–parasite relationship, or disciplines, within parasitology. We found a lack of methodological and theoretical uniformity in the discipline for finding and delimiting cryptic species, and we draw attention to the need for standardizing these approaches. We suggest that cryptic species, in the strict sense, are always provisionally cryptic, in that the possibility does exist that new morphological studies or techniques will reveal previously unknown diagnostic structural differences which will permit rapid and practical morphological diagnosis. To avoid future taxonomic confusion, we recommend that parasitologists describe (and formally name) cryptic species following standard taxonomic practice.

Objective To compare rapid diagnostic tests (RDTs) for malaria with routine microscopy in guiding treatment decisions for febrile patients.Design Randomised trial.Setting Outpatient departments in northeast Tanzania at varying levels of malaria transmission.Participants 2416 patients for whom a malaria test was requested.Intervention Staff received training on rapid diagnostic tests; patients sent for malaria tests were randomised to rapid diagnostic test or routine microscopyMain outcome measure Proportion of patients with a negative test prescribed an antimalarial drug.Results Of 7589 outpatient consultations, 2425 (32%) had a malaria test requested. Of 1204 patients randomised to microscopy, 1030 (86%) tested negative for malaria; 523 (51%) of these were treated with an antimalarial drug. Of 1193 patients randomised to rapid diagnostic test, 1005 (84%) tested negative; 540 (54%) of these were treated for malaria (odds ratio 1.13, 95% confidence interval 0.95 to 1.34; P=0.18). Children aged under 5 with negative rapid diagnostic tests were more likely to be prescribed an antimalarial drug than were those with negative slides (P=0.003). Patients with a negative test by any method were more likely to be prescribed an antibiotic (odds ratio 6.42, 4.72 to 8.75; P<0.001). More than 90% of prescriptions for antimalarial drugs in low-moderate transmission settings were for patients for whom a test requested by a clinician was negative for malaria.Conclusions Although many cases of malaria are missed outside the formal sector, within it malaria is massively over-diagnosed. This threatens the sustainability of deployment of artemisinin combination treatment, and treatable bacterial diseases are likely to be missed. Use of rapid diagnostic tests, with basic training for clinical staff, did not in itself lead to any reduction in over-treatment for malaria. Interventions to improve clinicians' management of febrile illness are essential but will not be easy.Trial registration Clinical trials NCT00146796.

Background Routine field diagnosis of malaria is a considerable challenge in rural and low resources endemic areas mainly due to lack of personnel, training and sample processing capacity. In addition, differential diagnosis of Plasmodium species has a high level of misdiagnosis. Real time remote microscopical diagnosis through on-line crowdsourcing platforms could be converted into an agile network to support diagnosis-based treatment and malaria control in low resources areas. This study explores whether accurate Plasmodium species identification—a critical step during the diagnosis protocol in order to choose the appropriate medication—is possible through the information provided by non-trained on-line volunteers. Methods 88 volunteers have performed a series of questionnaires over 110 images to differentiate species ( Plasmodium falciparum, Plasmodium ovale, Plasmodium vivax, Plasmodium malariae, Plasmodium knowlesi ) and parasite staging from thin blood smear images digitalized with a smartphone camera adapted to the ocular of a conventional light microscope. Visual cues evaluated in the surveys include texture and colour, parasite shape and red blood size. Results On-line volunteers are able to discriminate Plasmodium species ( P. falciparum , P. malariae, P. vivax , P. ovale , P. knowlesi ) and stages in thin-blood smears according to visual cues observed on digitalized images of parasitized red blood cells. Friendly textual descriptions of the visual cues and specialized malaria terminology is key for volunteers learning and efficiency. Conclusions On-line volunteers with short-training are able to differentiate malaria parasite species and parasite stages from digitalized thin smears based on simple visual cues (shape, size, texture and colour). While the accuracy of a single on-line expert is far from perfect, a single parasite classification obtained by combining the opinions of multiple on-line volunteers over the same smear, could improve accuracy and reliability of Plasmodium species identification in remote malaria diagnosis.

In recent decades, parasite community ecology has produced hundreds of studies on an ever-growing number of host species, and developed into an active sub-discipline of parasitology. However, this growth has been characterized by a lack of standards in the practices used by researchers, with many common approaches being flawed, unjustified or misleading. Here, in the hope of promoting advances in the study of parasite community ecology, I identify some of the most common errors or weaknesses in past studies, and propose ten simple rules for best practice in the field. They cover issues including, among others, taxonomic resolution, proper and justifiable analytical methods, higher-level replication, controlling for sampling effort or species richness, accounting for spatial distances, using experimental approaches, and placing raw data in the public domain. While knowledge of parasite communities has expanded in breadth, with more and more host species being studied, true progress has been very limited with respect to our understanding of fundamental general processes shaping these communities. It is hoped that the guidelines presented here can direct researchers away from the entrenched use of certain approaches flawed in design, analysis or interpretation, by offering a more rigorous and standardized set of practices, and, hopefully, a way forward.

The performance of a 400-μm-mesh-size sieve (sieve400) has not previously been compared with that of a 180-μm-mesh-size sieve (sieve180). Using pork samples spiked with 0 to 10 Trichinella muscle larvae and an artificial digestion method, sieve performance was evaluated for control of Trichinella in meat-producing animals. The use of a sieve400 resulted in 12% lower larval counts, 147% more debris, and 28% longer counting times compared with the use of a sieve180. Although no false-negative results were obtained, prolonged counting times with the sieve400 may have an impact on performance in a high-throughput environment such as a slaughterhouse laboratory. Based on our results, the sieve180 remains the sieve of choice for Trichinella control in meat in slaughterhouse laboratories, according to the European Union reference method (European Commission regulation 2075/2005). Furthermore, the results of the present study contribute to the discussion of harmonization of meat inspection requirements among countries.

Background Rapid diagnostic tests (RDT) and real-time PCR (qPCR) assays are sensitive for diagnosing malaria, but because they detect antigen and DNA, respectively, positivity may not reflect active infection. Performance characteristics of RDT and qPCR in Plasmodium falciparum positive specimens were evaluated over time to elucidate duration of positivity following conversion to microscopy negative. Methods Specimens from patients with at least one specimen that was positive for P. falciparum by microscopy, and at least one specimen that was negative for P. falciparum within a 1-month period were identified. Survival distributions of the diagnostic tests over time were compared. Performance characteristics for each test were calculated. Results Ninety specimens were included, with 48 initially positive for P. falciparum , and 42 subsequently negative. Of 42 specimens that converted to microscopy-negative following an initial positive, 26 (61.9 %) and 41 (97.6 %) were positive by qPCR and RDT, respectively. Survival curves of microscopy versus qPCR, as well as microscopy vs RDT differed significantly (p = 0.0002 and p < 0.0001, respectively). Compared to microscopy, sensitivity of qPCR was 100.0 % (95 % CI 90.8–100.0 %), and that of RDT was 100.0 % (95 % CI 90.8–100.0 %). Conclusions Due to slow clearance of circulating antigen and DNA from bloodstream, RDT and qPCR have low positive predictive value for clinically relevant asexual parasitaemia in post-treatment specimens. Thus, microscopy remains the only available malaria diagnostic that can reliably distinguish true asexual parasitaemia from prolonged clearance of antigen and nucleic acid in a convalescing patient.

There is a growing concern both inside and outside the scientific community over the lack of reproducibility of experiments. The depth and detail of reported methods are critical to the reproducibility of findings, but also for making it possible to compare and integrate data from different studies. In this study, we evaluated in detail the methods reporting in a comprehensive set of trypanosomiasis experiments that should enable valid reproduction, integration and comparison of research findings. We evaluated a subset of other parasitic (Leishmania, Toxoplasma, Plasmodium, Trichuris and Schistosoma) and non-parasitic (Mycobacterium) experimental infections in order to compare the quality of method reporting more generally. A systematic review using PubMed (2000-2012) of all publications describing gene expression in cells and animals infected with Trypanosoma spp was undertaken based on PRISMA guidelines; 23 papers were identified and included. We defined a checklist of essential parameters that should be reported and have scored the number of those parameters that are reported for each publication. Bibliometric parameters (impact factor, citations and h-index) were used to look for association between Journal and Author status and the quality of method reporting. Trichuriasis experiments achieved the highest scores and included the only paper to score 100% in all criteria. The mean of scores achieved by Trypanosoma articles through the checklist was 65.5% (range 32-90%). Bibliometric parameters were not correlated with the quality of method reporting (Spearman's rank correlation coefficient <-0.5; p>0.05). Our results indicate that the quality of methods reporting in experimental parasitology is a cause for concern and it has not improved over time, despite there being evidence that most of the assessed parameters do influence the results. We propose that our set of parameters be used as guidelines to improve the quality of the reporting of experimental infection models as a pre-requisite for integrating and comparing sets of data.

Yeasts can be used to convert organic food wastes to protein-rich animal feed in order to recapture nutrients. However, the reuse of animal-derived waste poses a risk for the transmission of infectious prions that can cause neurodegeneration and fatality in humans and animals. The aim of this study was to investigate the ability of yeasts to reduce prion activity during the biotransformation of waste substrates—thereby becoming a biosafety hurdle in such a circular food system. During pre-screening, 30 yeast isolates were spiked with Classical Scrapie prions and incubated for 72 h in casein substrate, as a waste substitute. Based on reduced Scrapie seeding activity, waste biotransformation and protease activities, intact cells and cell extracts of 10 yeasts were further tested. Prion analysis showed that five yeast species reduced Scrapie seeding activity by approximately 1 log10 or 90%. Cryptococcus laurentii showed the most potential to reduce prion activity since both intact and extracted cells reduced Scrapie by 1 log10 and achieved the highest protease activity. These results show that select forms of yeast can act as a prion hurdle during the biotransformation of waste. However, the limited ability of yeasts to reduce prion activity warrants caution as a sole barrier to transmission as higher log reductions are needed before using waste-cultured yeast in circular food systems.