scholarly journals Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics

2021 ◽  
Vol 4 ◽  
Author(s):  
Dominik Buchner ◽  
Peter Haase ◽  
Florian Leese
Keyword(s):  
Large Scale ◽  
Best Practice ◽  
Specific Marker ◽  
Cross Contamination ◽  
Increased Risk ◽  
Single Use ◽  
Reliability And Robustness ◽  
Almost All ◽  
Negative Controls ◽  
Sample Homogenization

DNA metabarcoding is an efficient tool to characterize invertebrate species composition in environmental samples. Most metabarcoding protocols for invertebrate bulk samples start with sample homogenization, followed by DNA extraction, amplification of a specific marker region and sequencing on a high-throughput sequencer. Many of the above-mentioned laboratory steps have been verified thoroughly and best practice strategies exist. Giving the amount of research done to validate almost all laboratory steps of metabarcoding workflows it is surprising that there is no clear recommendation for the basis of almost all metabarcoding studies: the homogenization of samples itself. For homogenization, different devices are used that can be divided into two major categories: bead mills and blenders. While bead-mills accelerate small, hard particles in a closed container or tube to break down specimens into small tissue fragments, blenders work with a rapidly rotating blades that reliably slice specimens as well as other substrate of the sample. Both methods are currently used in metabarcoding studies and have downsides to consider. Bead-mills rely on single-use plastics and therefore produce a lot of waste and are expensive. In addition to that, processing times can go up to 30 minutes making them unsuitable for large scale studies. Blenders on the other hand offer the opportunity to be cleaned and can handle larger sample volumes in shorter time, with an increased risk of cross-contamination. We here aimed to develop a fast, robust, cheap and reliable sample homogenization protocol that overcomes the above-mentioned limitations of both methods, i.e. does not produce difficult to discard waste and avoid single-use plastics while reducing overall costs. We tested the performance of the new protocol using six sorted Malaise trap insect samples and six unsorted stream macroinvertebrate kick-net samples. We used 14 technical replicates of each sample and many negative controls per sample (Fig. 1) to quantify impacts of i) insufficient homogenization and ii) possible sources of cross-contamination. Our results show that homogenization is sufficient after 3 minutes of homogenization. Rinsing the blender with water is sufficient in most cases but leads to low read-numbers in some of the negative controls. These could be further reduced by rinsing the blender with self-made drain-safe sterilization solution based on bleach but far less corrosive than pure bleach. Our results suggest that rinsing 1-2 times for 20 seconds is sufficient to avoid any cross-contamination. The improvements of the protocol in terms of speed, ease of handling, overall reduction of costs as well as the documented reliability and robustness make it an important candidate for sample homogenization after sampling in particular for large-scale and regulatory metabarcoding biodiversity assessments and monitoring programs.

scholarly journals Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics

2021 ◽  
Vol 5 ◽  
Author(s):  
Dominik Buchner ◽  
Peter Haase ◽  
Florian Leese
Keyword(s):  
Large Scale ◽  
Best Practice ◽  
Specific Marker ◽  
Cross Contamination ◽  
Processing Times ◽  
Increased Risk ◽  
Single Use ◽  
Cost Efficient ◽  
Reliability And Robustness ◽  
Almost All

Most metabarcoding protocols for invertebrate bulk samples start with sample homogenisation, followed by DNA extraction, amplification of a specific marker region, and sequencing. Many of the above-mentioned laboratory steps have been verified thoroughly and best practice strategies exist, yet, no clear recommendation for the basis of almost all metabarcoding studies exists: the homogenisation of samples itself. Two different categories of devices are typically used for homogenisation: bead mills or blenders. Both have upsides and downsides. Bead mills rely on single-use plastics and therefore produce a lot of waste and are expensive. In addition to that, processing times can go up to 30 minutes making them unsuitable for large-scale studies. Blenders can handle larger sample volumes in a shorter time, and be cleaned – yet suffer from an increased risk of cross-contamination. We aimed to develop a fast, robust, cheap, and reliable sample homogenisation protocol that overcomes limitations of both approaches, i.e. does not produce difficult to discard waste and avoid single-use plastics while reducing overall costs. We tested the performance of the new protocol using six size-sorted Malaise trap samples and six unsorted stream macroinvertebrate kick-net samples. We used 14 replicates per sample and included many negative controls at different steps of the protocol to quantify the impacts of i) insufficient homogenisation and ii) cross-contamination. Our results show that 3-min homogenisation is sufficient to recover about 80% of OTUs per sample in each replicate and that a non-hazardous DIY cleaning solution provides an effective and efficient way of cleaning. The improvements of the protocol in terms of speed, ease of handling, an overall reduction of costs as well as the documented reliability and robustness make it an important candidate for sample homogenisation after sampling in particular for large-scale and regulatory metabarcoding but also metagenomics biodiversity assessments and monitoring.

Quantification of Transfer of Salmonella from Citrus Fruits to Peel, Edible Portion, and Gloved Hands during Hand Peeling

2017 ◽  
Vol 80 (6) ◽  
pp. 933-939 ◽  
Author(s):  
Jiin Jung ◽  
Loretta M. Friedrich ◽  
Michelle D. Danyluk ◽  
Donald W. Schaffner
Keyword(s):  
Citrus Fruit ◽  
Cross Contamination ◽  
Citrus Paradisi ◽  
Citrus Fruits ◽  
Fruit Peel ◽  
Edible Portion ◽  
Latex Gloves ◽  
Edible Fruit ◽  
Single Use ◽  
Almost All

ABSTRACT Although studies have quantified bacterial transfer between hands and various materials, cross-contamination between the surface of fresh citrus fruit and the edible portions during hand peeling has not been reported. This study quantifies transfer of Salmonella to the edible portion of citrus fruit from a contaminated peel during hand peeling. Citrus fruits used for this study were Citrus sinensis (sweet orange) cultivars ‘Valencia' and ‘Navel’, Citrus unshiu (Satsuma mandarins), Citrus reticulata × Citrus paradisi (‘Minneola' tangelo or ‘Honeybell'), and C. paradisi (grapefruit) cultivar ‘Marsh’. An avirulent Salmonella Typhimurium LT2 (ATCC 700720) resistant to rifampin was used for all experiments. The inoculum containing approximately 9 log CFU/mL (50 μL) was spot inoculated onto the equator, stem, or styler of each fruit and allowed to dry for 24 h. Six volunteers put on single-use latex gloves and peeled inoculated fruit. Peel, edible fruit portion, and gloves were collected and enumerated separately. Three replicates of the study were performed in which each volunteer peeled two inoculated fruit of each variety (n = 36 fruit per variety). Cross-contamination from contaminated surface of citrus fruits to edible portion or gloved hands during peeling was affected by inoculation sites. Average Salmonella transfer to the edible portion ranged from 0.16% (Valencia inoculated at the equator) to 5.41% (navel inoculated at the stem). Average Salmonella transfer to gloved hands ranged from 0.41% (grapefruit inoculated at the stem) to 8.97% (navel inoculated at the stem). Most Salmonella remained on the peel of citrus fruits. The average level of Salmonella remaining on the peel ranged from 5.37% (Minneola inoculated at the equator) to 66.3% (Satsuma inoculated at the styler). When grapefruit was inoculated, the Salmonella that remained on the peel showed a bimodal pattern in which some individuals left almost all Salmonella on the peel, while others left substantially less.

Swimming on Peritoneal Dialysis: Recommendations from Australian PD Units

2019 ◽  
Vol 39 (6) ◽  
pp. 527-531 ◽  
Author(s):  
Anna Lee
Keyword(s):  
Peritoneal Dialysis ◽  
Cross Section ◽  
Best Practice ◽  
Sea Water ◽  
Risk Of Infection ◽  
Exit Site ◽  
Practice Recommendations ◽  
Increased Risk ◽  
Almost All ◽  
Infective Complications

Background There is no evidence to support the need for protection of the peritoneal dialysis (PD) catheter and exit site for people on PD who want to swim. Swimming with a PD catheter is perceived to potentially put that person at increased risk of infection. Objectives of this study were to determine the proportion of Australian PD units supporting swimming for people on PD, recommendations made to protect the PD catheter, and exit site and any subsequent infective complications. Method Phone surveys were conducted with PD nurses from a cross section of 39 Australian PD units. Results Almost all units reported that patients on PD do swim despite only 77% of units advocating swimming. Swimming in sea water (85%) or a private swimming pool (90%) is mostly recommended. Covering the exit site and PD catheter is recommended with a waterproof film dressing or colostomy bag. Performing routine exit-site care after swimming is recommended (100%). There were 7 reported exit-site infections and 2 episodes of peritonitis perceived to be associated with swimming with a PD catheter. Conclusion Most PD units in Australia report that patients on PD swim. Swimming is recommended in either sea water or private swimming pools. The PD catheter and exit site should be covered with either a clear waterproof dressing or colostomy bag. Routine exit-site care should be performed after swimming. Infections were rarely reported in those who swim. Until further research is available, best practice recommendations are warranted for the safety of those on PD who want to swim.

scholarly journals Copper-oxide impregnated respiratory masks may significantly reduce the risk of SARS-CoV-2 cross-contamination

2020 ◽  
Author(s):  
Gadi Borkow ◽  
Danny Lustiger ◽  
Eyal Melamed ◽  
Vicki Herrera ◽  
Daniel Ackerman ◽  
...  
Keyword(s):  
General Population ◽  
Copper Oxide ◽  
Nonwoven Fabric ◽  
Viral Transmission ◽  
Cross Contamination ◽  
Risk Of Infection ◽  
Increased Risk ◽  
Surgical Masks ◽  
Single Use ◽  
Pcr Assays

Abstract The use of protective respiratory face masks has been adopted universally as an important measure in the fight against COVID-19. Masks become contaminated by symptomatic and asymptomatic SARS-CoV-2 infected individuals and the virus can remain viable on the surface of the masks for several days. Although the regular respiratory face masks are single use disposable masks, these masks are being largely reused and not often discarded after use by the general population. Mask touching during use, reuse and disposal occurs frequently, and this can lead to increased risk of infection and further transmission. N95s and regular surgical masks were produced in which the external layers were made with nonwoven fabric impregnated with copper-oxide microparticles. The masks reduced the infectious titers of SARS-CoV-2 by more than 99.9% within 1 minute of contact, as determined by TCID50 assay and serial PCR assays. The use of masks capable of rendering the SARS-CoV-2 non-infectious within minutes, may significantly reduce the risk of viral transmission and infection.

Study of Biochemical and Clinical Markers in Steatohepatitis Related to Obesity

2018 ◽  
Vol 69 (6) ◽  
pp. 1501-1505
Author(s):  
Roxana Maria Livadariu ◽  
Radu Danila ◽  
Lidia Ionescu ◽  
Delia Ciobanu ◽  
Daniel Timofte
Keyword(s):  
Liver Disease ◽  
Liver Biopsy ◽  
Large Scale ◽  
Biological Data ◽  
Obese Patients ◽  
Clinical Markers ◽  
Mean Values ◽  
Nonalcoholic Fatty Liver ◽  
Obstructive Sleep ◽  
Increased Risk

Nonalcoholic fatty liver disease (NAFLD) is highly associated to obesity and comprises several liver diseases, from simple steatosis to steatohepatitis (NASH) with increased risk of developing progressive liver fibrosis, cirrhosis and hepatocellular carcinoma. Liver biopsy is the gold standard in diagnosing the disease, but it cannot be used in a large scale. The aim of the study was the assessment of some non-invasive clinical and biological markers in relation to the progressive forms of NAFLD. We performed a prospective study on 64 obese patients successively hospitalised for bariatric surgery in our Surgical Unit. Patients with history of alcohol consumption, chronic hepatitis B or C, other chronic liver disease or patients undergoing hepatotoxic drug use were excluded. All patients underwent liver biopsy during sleeve gastrectomy. NAFLD was present in 100% of the patients: hepatic steatosis (38%), NASH with the two forms: with fibrosis (31%) and without fibrosis (20%), cumulating 51%; 7 patients had NASH with vanished steatosis. NASH with fibrosis statistically correlated with metabolic syndrome (p = 0.036), DM II (p = 0.01) and obstructive sleep apnea (p = 0.02). Waist circumference was significantly higher in the steatohepatitis groups (both with and without fibrosis), each 10 cm increase increasing the risk of steatohepatitis (p = 0.007). The mean values of serum fibrinogen and CRP were significantly higher in patients having the progressive forms of NAFLD. Simple clinical and biological data available to the practitioner in medicine can be used to identify obese patients at high risk of NASH, aiming to direct them to specialized medical centers.

Should all Hypertensive Patients be Screened for Primary Aldosteronism?

2019 ◽  
Vol 15 (1) ◽  
pp. 54-56
Author(s):  
Stelina Alkagiet ◽  
Konstantinos Tziomalos
Keyword(s):  
Resistant Hypertension ◽  
Primary Aldosteronism ◽  
Large Scale ◽  
Controlled Trial ◽  
The Other ◽  
Limited Data ◽  
Hypertensive Patients ◽  
Randomized Controlled ◽  
Increased Risk ◽  
Prospective Randomized Controlled Trial

Primary aldosteronism (PA) is not only a leading cause of secondary and resistant hypertension, but is also quite frequent in unselected hypertensive patients. Moreover, PA is associated with increased cardiovascular risk, which is disproportionate to BP levels. In addition, timely diagnosis of PA and prompt initiation of treatment attenuate this increased risk. On the other hand, there are limited data regarding the usefulness of screening for PA in all asymptomatic or normokalemic hypertensive patients. More importantly, until now, no well-organized, large-scale, prospective, randomized controlled trial has proved the effectiveness of screening for PA for improving clinical outcome. Accordingly, until more relevant data are available, screening for PA should be considered in hypertensive patients with spontaneous or diuretic-induced hypokalemia as well as in those with resistant hypertension. However, screening for PA in all hypertensive patients cannot be currently recommended.

scholarly journals COVID-19 and Its Symptoms’ Panoply: A Case-Control Study of 919 Suspected Cases in Locked-Down Ovar, Portugal

2021 ◽  
pp. 1-8
Author(s):  
Regina Sá ◽  
Tiago Pinho-Bandeira ◽  
Guilherme Queiroz ◽  
Joana Matos ◽  
João Duarte Ferreira ◽  
...  
Keyword(s):  
Large Scale ◽  
Case Control Study ◽  
Statistical Significance ◽  
Case Control ◽  
Case Definition ◽  
Suspected Case ◽  
Risk Characteristics ◽  
Increased Risk ◽  
Wide Range ◽  
Control Study

<b><i>Background:</i></b> Ovar was the first Portuguese municipality to declare active community transmission of SARS-CoV-2, with total lockdown decreed on March 17, 2020. This context provided conditions for a large-scale testing strategy, allowing a referral system considering other symptoms besides the ones that were part of the case definition (fever, cough, and dyspnea). This study aims to identify other symptoms associated with COVID-19 since it may clarify the pre-test probability of the occurrence of the disease. <b><i>Methods:</i></b> This case-control study uses primary care registers between March 29 and May 10, 2020 in Ovar municipality. Pre-test clinical and exposure-risk characteristics, reported by physicians, were collected through a form, and linked with their laboratory result. <b><i>Results:</i></b> The study population included a total of 919 patients, of whom 226 (24.6%) were COVID-19 cases and 693 were negative for SARS-CoV-2. Only 27.1% of the patients reporting contact with a confirmed or suspected case tested positive. In the multivariate analysis, statistical significance was obtained for headaches (OR 0.558), odynophagia (OR 0.273), anosmia (OR 2.360), and other symptoms (OR 2.157). The interaction of anosmia and odynophagia appeared as possibly relevant with a borderline statistically significant OR of 3.375. <b><i>Conclusion:</i></b> COVID-19 has a wide range of symptoms. Of the myriad described, the present study highlights anosmia itself and calls for additional studies on the interaction between anosmia and odynophagia. Headaches and odynophagia by themselves are not associated with an increased risk for the disease. These findings may help clinicians in deciding when to test, especially when other diseases with similar symptoms are more prevalent, namely in winter.

scholarly journals Effects of B.1.1.7 and B.1.351 on COVID-19 Dynamics: A Campus Reopening Study

2021 ◽  
Author(s):  
Kevin Linka ◽  
Mathias Peirlinck ◽  
Amelie Schäfer ◽  
Oguz Ziya Tikenogullari ◽  
Alain Goriely ◽  
...  
Keyword(s):  
Online Education ◽  
The United States ◽  
Wild Type ◽  
Seir Model ◽  
Population Mixing ◽  
Santa Clara County ◽  
Increased Risk ◽  
Controversial Topic ◽  
Almost All ◽  
Local Reproduction

AbstractThe timing and sequence of safe campus reopening has remained the most controversial topic in higher education since the outbreak of the COVID-19 pandemic. By the end of March 2020, almost all colleges and universities in the United States had transitioned to an all online education and many institutions have not yet fully reopened to date. For a residential campus like Stanford University, the major challenge of reopening is to estimate the number of incoming infectious students at the first day of class. Here we learn the number of incoming infectious students using Bayesian inference and perform a series of retrospective and projective simulations to quantify the risk of campus reopening. We create a physics-based probabilistic model to infer the local reproduction dynamics for each state and adopt a network SEIR model to simulate the return of all undergraduates, broken down by their year of enrollment and state of origin. From these returning student populations, we predict the outbreak dynamics throughout the spring, summer, fall, and winter quarters using the inferred reproduction dynamics of Santa Clara County. We compare three different scenarios: the true outbreak dynamics under the wild-type SARS-CoV-2, and the hypothetical outbreak dynamics under the new COVID-19 variants B.1.1.7 and B.1.351 with 56% and 50% increased transmissibility. Our study reveals that even small changes in transmissibility can have an enormous impact on the overall case numbers. With no additional countermeasures, during the most affected quarter, the fall of 2020, there would have been 203 cases under baseline reproduction, compared to 4727 and 4256 cases for the B.1.1.7 and B.1.351 variants. Our results suggest that population mixing presents an increased risk for local outbreaks, especially with new and more infectious variants emerging across the globe. Tight outbreak control through mandatory quarantine and test-trace-isolate strategies will be critical in successfully managing these local outbreak dynamics.

scholarly journals An Emulation of Randomized Trials of Administrating Antipsychotics in PTSD Patients for Outcomes of Suicide-Related Events

2021 ◽  
Vol 11 (3) ◽  
pp. 178
Author(s):  
Noah R. Delapaz ◽  
William K. Hor ◽  
Michael Gilbert ◽  
Andrew D. La ◽  
Feiran Liang ◽  
...  
Keyword(s):  
Randomized Clinical Trials ◽  
Previous History ◽  
Current Treatment ◽  
Careful Consideration ◽  
P Value ◽  
Post Traumatic Stress ◽  
Increased Risk ◽  
History Of ◽  
Almost All

Post-traumatic stress disorder (PTSD) is a prevalent mental disorder marked by psychological and behavioral changes. Currently, there is no consensus of preferred antipsychotics to be used for the treatment of PTSD. We aim to discover whether certain antipsychotics have decreased suicide risk in the PTSD population, as these patients may be at higher risk. A total of 38,807 patients were identified with a diagnosis of PTSD through the ICD9 or ICD10 codes from January 2004 to October 2019. An emulation of randomized clinical trials was conducted to compare the outcomes of suicide-related events (SREs) among PTSD patients who ever used one of eight individual antipsychotics after the diagnosis of PTSD. Exclusion criteria included patients with a history of SREs and a previous history of antipsychotic use within one year before enrollment. Eligible individuals were assigned to a treatment group according to the antipsychotic initiated and followed until stopping current treatment, switching to another same class of drugs, death, or loss to follow up. The primary outcome was to identify the frequency of SREs associated with each antipsychotic. SREs were defined as ideation, attempts, and death by suicide. Pooled logistic regression methods with the Firth option were conducted to compare two drugs for their outcomes using SAS version 9.4 (SAS Institute, Cary, NC, USA). The results were adjusted for baseline characteristics and post-baseline, time-varying confounders. A total of 5294 patients were eligible for enrollment with an average follow up of 7.86 months. A total of 157 SREs were recorded throughout this study. Lurasidone showed a statistically significant decrease in SREs when compared head to head to almost all the other antipsychotics: aripiprazole, haloperidol, olanzapine, quetiapine, risperidone, and ziprasidone (p < 0.0001 and false discovery rate-adjusted p value < 0.0004). In addition, olanzapine was associated with higher SREs than quetiapine and risperidone, and ziprasidone was associated with higher SREs than risperidone. The results of this study suggest that certain antipsychotics may put individuals within the PTSD population at an increased risk of SREs, and that careful consideration may need to be taken when prescribed.

scholarly journals The DWQ-EMR Embedded Tool to Enhance the Family Physician-Caregiver Connection: A Pilot Case Study

Geriatrics ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 29
Author(s):  
Kristina Marie Kokorelias ◽  
Einat Danieli ◽  
Sheila Dunn ◽  
Sid Feldman ◽  
David Patrick Ryan ◽  
...  
Keyword(s):  
Family Caregivers ◽  
Best Practice ◽  
Data Gathering ◽  
Family Physicians ◽  
Efficient Manner ◽  
Efficient Access ◽  
Increased Risk ◽  
Starting Point ◽  
To Receive

The number of family caregivers to individuals with dementia is increasing. Family physicians are often the first point of access to the health care system for individuals with dementia and their caregivers. Caregivers are at an increased risk of developing negative physical, cognitive and affective health problems themselves. Caregivers also describe having unmet needs to help them sustain care in the community. Family physicians are in a unique position to help support caregivers and individuals with dementia, but often struggle with keeping up with best practice dementia service knowledge. The Dementia Wellness Questionnaire was designed to serve as a starting point for discussions between caregivers and family physicians by empowering caregivers to communicate their needs and concerns and to enhance family physicians’ access to specific dementia support information. The DWQ aims to alert physicians of caregiver and patient needs. This pilot study aimed to explore the experiences of physicians and caregivers of people using the Questionnaire in two family medicine clinics in Ontario, Canada. Interviews with physicians and caregivers collected data on their experiences using the DWQ following a 10-month data gathering period. Data was analyzed using content analysis. Results indicated that family physicians may have an improved efficacy in managing dementia by having dementia care case specific guidelines integrated within electronic medical records. By having time-efficient access to tailored supports, family physicians can better address the needs of the caregiver–patient dyad and help support family caregivers in their caregiving role. Caregivers expressed that the Questionnaire helped them remember concerns to bring up with physicians, in order to receive help in a more efficient manner.

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