Renal outcome in patients with congenital anomalies of the kidney and urinary tract.

15openopenSanna-Cherchi S; Ravani P; Corbani V; Parodi S; Haupt R; Piaggio G; Innocenti ML; Somenzi D; Trivelli A; Caridi G; Izzi C; Scolari F; Mattioli G; Allegri L; Ghiggeri GM.Sanna Cherchi, S; Ravani, P; Corbani, V; Parodi, S; Haupt, R; Piaggio, G; Innocenti, Ml; Somenzi, D; Trivelli, A; Caridi, G; Izzi, C; Scolari, Francesco; Mattioli, G; Allegri, L; Ghiggeri, G. M

No filters, no fridges: a method for preservation of water samples for eDNA analysis

Background: Advancements in the detection of environmental DNA (eDNA) for detecting species of interest will likely allow for expanded use of these techniques in the field. One obstacle that continues to hinder applications in the field is the requirement of a cold chain of storage for water samples containing eDNA. While eDNA has been successfully preserved using Longmire’s lysis buffer applied to filters, it has yet to be tried with freshwater samples collected for eDNA detection of an invasive species. We tested the utility of Longmire’s solution (100 mM Tris, 100 mM EDTA, 10 mM NaCl, 0.5 % SDS, 0.2 % sodium azide) as an additive to freshwater samples for preservation of eDNA. Results: Environmental DNA was effectively preserved in 15 mL water samples with Longmire’s solution added; eDNA positive detection was comparable to freezing the samples at −80 °C and occurred out to 56 days at the highest concentration (5 mL Longmire’s solution: 15 mL sample water). Medium and low concentrations of Longmire’s solution added to 15 mL of sample water generally preserved eDNA out to 56 days but not as well as did freezing or application of the highest concentration of Longmire’s lysis buffer. Treatment and degradation time had a significant effect on average DNA concentration of samples, although not the interaction of treatment and time. Perfect detection occurred out to 56 days with the high Longmire’s treatment group but DNA concentration was significantly lower at this time point compared to 28 days. Conclusion: We conclude that Longmire’s lysis buffer is a viable alternative to cold chain storage that can simplify the collection of eDNA by eliminating the need for filtering and allow more time for sample collection when added at our highest concentration (1 part Longmire’s:3 parts water sample), which could translate to an increase in the chances of detecting a rare or elusive species

Evaluating Biosecurity of Physical Containment at USDA Animal Facilities to Prepare for Genetically Modified Rodent Trials

House mice and rats have been introduced to most countries and islands worldwide and represent serious threats to biodiversity, economic enterprise, and human health. Genome editing and gene drives are being explored as new genetic biocontrol methods to effectively suppress rodent pests. An essential step in the translation of this technology to field-ready tools is to administer breeding and behavioral trials with freely-interacting genetically modified (GM) rodents. Due to the potential impacts of unintended release of GM organisms, these trials will require biosecure animal facilities that are rigorously tested to ensure physical containment. This study was conducted to develop and evaluate the biosecurity of a physical containment facility for house mouse trials at USDA’s National Wildlife Research Center. First, we conducted >20 trials with 75 wild-caught (non-GM) house mice to test their ability to escape from small containment units (0.35 m2). During these trials that lasted >160 days, mouse behaviors and escape attempts were documented following exposure to attractants (high value foods and potential mates) as motivators for escape. Just two mice success­fully breached containment during early trials, and both were from chewing small holes in plastic walls that allowed escape to the other side of the containment unit. In a second series of trials, we assessed containment efficacy in a large (24 m2) arena intended to more closely replicate conditions of free-breeding wild mice. In these trials, mice were held in groups of six to 26 for up to 6 months. Across trials, only one mouse escaped the arena, an incident most likely attributable to human error during routine animal husbandry activities. This mouse was captured in the secondary containment (live-trap) within hours of breaching the primary containment. Overall, the containment strategy utilized here presents a robust design, with redundant containment mechanisms that should serve as a model for future behavioral trials using GM rodents. Additionally, our study highlights the need for rigorous staff training, careful attention to construction methods and materials, and adhering to biosecurity protocols to ensure the highest levels of containment that will be essential for testing efficacy of genetic biocontrols

Further investigation of confirmed urinary tract infection (UTI) in children under five years: a systematic review.

Background: Further investigation of confirmed UTI in children aims to prevent renal scarring and future complications. Methods: We conducted a systematic review to determine the most effective approach to the further investigation of confirmed urinary tract infection (UTI) in children under five years of age. Results: 73 studies were included. Many studies had methodological limitations or were poorly reported. Effectiveness of further investigations: One study found that routine imaging did not lead to a reduction in recurrent UTIs or renal scarring. Diagnostic accuracy: The studies do not support the use of less invasive tests such as ultrasound as an alternative to renal scintigraphy, either to rule out infection of the upper urinary tract (LR- = 0.57, 95%CI: 0.47, 0.68) and thus to exclude patients from further investigation or to detect renal scarring (LR+ = 3.5, 95% CI: 2.5, 4.8). None of the tests investigated can accurately predict the development of renal scarring. The available evidence supports the consideration of contrast-enhanced ultrasound techniques for detecting vesico-ureteric reflux (VUR), as an alternative to micturating cystourethrography (MCUG) (LR+ = 14.1, 95% CI: 9.5, 20.8; LR- = 0.20, 95%CI: 0.13, 0.29); these techniques have the advantage of not requiring exposure to ionising radiation. Conclusion: There is no evidence to support the clinical effectiveness of routine investigation of children with confirmed UTI. Primary research on the effectiveness, in terms of improved patient outcome, of testing at all stages in the investigation of confirmed urinary tract infection is urgently required

Picky eaters are rare: DNA-based blood meal analysis of \u3ci\u3eCulicoides\u3c/i\u3e (Diptera: Ceratopogonidae) species from the United States

Background: Biting midges in the genus Culicoides (Diptera; Ceratopogonidae) have been implicated in the transmission of a number of parasites and highly pathogenic viruses. In North America, the complete transmission cycles of many of these pathogens need further elucidation. One way to increase our knowledge about the evolution and ecology of Culicoides species and the pathogens they transmit is to document the diversity of vertebrate hosts that Culicoides feed upon. Our objective was to identify the diversity of Culicoides hosts in the United States. Results: We sequenced two vertebrate mitochondrial genes (cytochrome c oxidase subunit 1 and cytochrome b) from blood-engorged Culicoides to identify Culicoides species and their blood meals. We detected the mitochondrial DNA of 12 host species from seven different Culicoides species from three states. The majority of the identified blood meals were from the C. variipennis species complex in California. The hosts included both mammals and birds. We documented new host records for some of the Culicoides species collected. The majority of the mammalian hosts were large ungulate species but we also detected a lagomorph and a carnivore. The bird species that were detected included house finch and emu; the latter is evidence that the species in the C. variipennis species complex are not strictly mammalophilic. Conclusions: These results demonstrate that Culicoides will feed on multiple classes of vertebrates and may be more opportunistic in regards to host choice than previously thought. This knowledge can help with identification of susceptible host species, pathogen reservoirs, and new vector species which, in turn, will improve disease outbreak risk assessments

Pupillometry via smartphone for low-resource settings

The photopupillary reflex regulates the pupil reaction to changing light conditions. Being controlled by the autonomic nervous system, it is a proxy for brain trauma and for the conditions of patients in critical care. A prompt evaluation of brain traumas can save lives. With a simple penlight, skilled clinicians can do that, whereas less specialized ones have to resort to a digital pupilometer. However, many low-income countries lack both specialized clinicians and digital pupilometers. This paper presents the early results of our study aiming at designing, prototyping and validating an app for testing the photopupillary reflex via Android, following the European Medical Device Regulation and relevant standards. After a manual validation, the prototype underwent a technical validation against a commercial Infrared pupilometer. As a result, the proposed app performed as well as the manual measurements and better than the commercial solution, with lower errors, higher and significant correlations, and significantly better Bland-Altman plots for all the pupillometry-related measures. The design of this medical device was performed based on our expertise in low-resource settings. This kind of environments imposes more stringent design criteria due to contextual challenges, including the lack of specialized clinicians, funds, spare parts and consumables, poor maintenance, and harsh environmental conditions, which may hinder the safe operationalization of medical devices. This paper provides an overview of how these unique contextual characteristics are cascaded into the design of an app in order to contribute to the Sustainable Development Goal 3 of the World Health Organization: Good health and well-being

How does study quality affect the results of a diagnostic meta-analysis?

Background: The use of systematic literature review to inform evidence based practice in diagnostics is rapidly expanding. Although the primary diagnostic literature is extensive, studies are often of low methodological quality or poorly reported. There has been no rigorously evaluated, evidence based tool to assess the methodological quality of diagnostic studies. The primary objective of this study was to determine the extent to which variations in the quality of primary studies impact the results of a diagnostic meta-analysis and whether this differs with diagnostic test type. A secondary objective was to contribute to the evaluation of QUADAS, an evidence-based tool for the assessment of quality in diagnostic accuracy studies. Methods: This study was conducted as part of large systematic review of tests used in the diagnosis and further investigation of urinary tract infection (UTI) in children. All studies included in this review were assessed using QUADAS, an evidence-based tool for the assessment of quality in systematic reviews of diagnostic accuracy studies. The impact of individual components of QUADAS on a summary measure of diagnostic accuracy was investigated using regression analysis. The review divided the diagnosis and further investigation of UTI into the following three clinical stages: diagnosis of UTI, localisation of infection, and further investigation of the UTI. Each stage used different types of diagnostic test, which were considered to involve different quality concerns. Results: Many of the studies included in our review were poorly reported. The proportion of QUADAS items fulfilled was similar for studies in different sections of the review. However, as might be expected, the individual items fulfilled differed between the three clinical stages. Regression analysis found that different items showed a strong association with test performance for the different tests evaluated. These differences were observed both within and between the three clinical stages assessed by the review. The results of regression analyses were also affected by whether or not a weighting (by sample size) was applied. Our analysis was severely limited by the completeness of reporting and the differences between the index tests evaluated and the reference standards used to confirm diagnoses in the primary studies. Few tests were evaluated by sufficient studies to allow meaningful use of meta-analytic pooling and investigation of heterogeneity. This meant that further analysis to investigate heterogeneity could only be undertaken using a subset of studies, and that the findings are open to various interpretations. Conclusion: Further work is needed to investigate the influence of methodological quality on the results of diagnostic meta-analyses. Large data sets of well-reported primary studies are needed to address this question. Without significant improvements in the completeness of reporting of primary studies, progress in this area will be limited

Detection and persistence of environmental DNA from an invasive, terrestrial mammal

Invasive Sus scrofa, a species commonly referred to as wild pig or feral swine, is a destructive invasive species with a rapidly expanding distribution across the United States. We used artificial wallows and small waterers to determine the minimum amount of time needed for pig eDNA to accumulate in the water source to a detectable level. We removed water from the artificial wallows and tested eDNA detection over the course of 2 weeks to understand eDNA persistence. We show that our method is sensitive enough to detect very low quantities of eDNA shed by a terrestrial mammal that has limited interaction with water. Our experiments suggest that the number of individuals shedding into a water system can affect persistence of eDNA. Use of an eDNA detection technique can benefit management efforts by providing a sensitive method for finding even small numbers of individuals that may be elusive using other methods

Accounting for observation processes across multiple levels of uncertainty improves inference of species distributions and guides adaptive sampling of environmental DNA

Understanding factors that influence observation processes is critical for accurate assessment of underlying ecological processes. When indirect methods of detection, such as environmental DNA, are used to determine species presence, additional levels of uncertainty from observation processes need to be accounted for. We conducted a field trial to evaluate observation processes of a terrestrial invasive species (wild pigs‐ Sus scrofa) from DNA in water bodies. We used a multi‐scale occupancy analysis to estimate different levels of observation processes (detection, p): the probability DNA is available per sample (θ), the probability of capturing DNA per extraction (γ), and the probability of amplification per qPCR run (δ). We selected four sites for each of three water body types and collected 10 samples per water body during two months (September and October 2016) in central Texas. Our methodology can be used to guide sampling adaptively to minimize costs while improving inference of species distributions. Using a removal sampling approach was more efficient than pooling samples and was unbiased. Availability of DNA varied by month, was considerably higher when water pH was near neutral, and was higher in ephemeral streams relative to wildlife guzzlers and ponds. To achieve a cumulative detection probability \u3e90% (including availability, capture, and amplification), future studies should collect 20 water samples per site, conduct at least two extractions per sample, and conduct five qPCR replicates per extraction. Accounting for multiple levels of uncertainty of observation processes improved estimation of the ecological processes and provided guidance for future sampling designs