Vector-based risk assessment is a powerful and efficient management approach for nonindigenous species (NIS). By managing a vector, an entire assemblage of associated NIS is simultaneously ...considered. The majority of current risk assessment frameworks have been conducted for a single, or selected few, target species and thus are not useful for managing vectors transporting a large number of potentially unknown species. Here we develop a predictive framework to assess relative invasion risk for a vector (ballast water) transporting an unknown species assemblage, using the Canadian Arctic as a case study. Ballast water discharge is a known high-risk vector globally, but its magnitude in the Arctic has not been well characterized. Our framework determined relative invasion risks between different transit pathways by quantifying the probability of NIS successfully transiting all stages of the invasion process and the magnitude of consequences of introduction to those ports. Churchill, Manitoba was ranked at ‘higher’ invasion risk via ballast water discharged by international merchant vessels than any other recipient port studied. The overall pattern of ballast water discharge suggests that water originating from coastal domestic sources carried by international merchant vessels may be important for dispersal of NIS. In addition, ballast-mediated NIS are more likely to arrive to the Hudson Bay region during summer months. These results can be useful for developing prevention and early detection programs for the region. Our risk assessment framework is not limited to ballast water and could be applied to other vectors for effective management of NIS.
and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The ...pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553
and 274 non-
spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.
To assess the validity of the Market Basket Analysis Tool (MBAT) for food environment quality within various retail environments compared to the Nutrition Environment Measures Survey in Stores ...(NEMS-S).
In-store assessments using the MBAT and the NEMS-S on the same day in a given store were conducted in grocery stores, corner stores, pharmacies, and dollar stores in a metropolis, and urban and rural counties across 4 states: Louisiana, Mississippi, North Carolina, and Virginia. Descriptive statistics, correlations, and ANOVAs were used to assess store location, store type differences, and MBAT and NEMS-S scores.
Market Basket Analysis Tool and NEMS-S data were collected from 114 stores. Market Basket Analysis Tool and NEMS-S total and all individual component scores were significantly correlated (r = 0.84, P ≤ 0.0001; r range, 0.51–0.88; P ≤ 0.0001).
The MBAT offers a methodology to measure the food retail environment focusing on the availability of healthful food items with a reduced training time and streamlined data collection compared with the NEMS-S. Future work can assess the completion time of the MBAT compared with the NEMS-S and the ability of the MBAT to detect changes in food environment quality post healthy food retail interventions.
Background
Accurate diagnosis of coronavirus disease 2019 is essential to limiting transmission within healthcare settings. The aim of this study was to identify patient demographic and clinical ...characteristics that could impact the clinical sensitivity of the nasopharyngeal severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV2) reverse transcription polymerase chain reaction (RT‐PCR) test.
Methods
We conducted a retrospective, matched case‐control study of patients who underwent repeated nasopharyngeal SARS‐CoV2 RT‐PCR testing at a tertiary care academic medical center between March 1 and July 23, 2020. The primary endpoint was conversion from negative to positive PCR status within 14 days. We conducted conditional logistic regression modeling to assess the associations between demographic and clinical features and conversion to test positivity.
Results
Of 51,116 patients with conclusive SARS‐CoV2 nasopharyngeal RT‐PCR results, 97 patients converted from negative to positive within 14 days. We matched those patients 1:2 to 194 controls by initial test date. In multivariate analysis, clinical suspicion for a respiratory infection (adjusted odds ratio aOR 20.9, 95% confidence interval CI: 3.1–141.2) and lack of pulmonary imaging (aOR 4.7, 95% CI: 1.03–21.8) were associated with conversion, while a lower burden of comorbidities trended toward an increased odds of conversion (aOR 2.2, 95% CI: 0.9–5.3).
Conclusions
Symptoms consistent with a respiratory infection, especially in relatively healthy individuals, should raise concerns about a clinical false‐negative result. We have identified several characteristics that should be considered when creating institutional infection prevention guidelines in the absence of more definitive data and should be included in future studies.
Regulatory discharge standards stipulating a maximum allowable number of viable organisms in ballast water have led to a need for rapid, easy and accurate compliance assessment tools and protocols. ...Some potential tools presume that organisms present in ballast water samples display the same characteristics of life as the native community (e.g. rates of fluorescence). This presumption may not prove true, particularly when ships' ballast tanks present a harsh environment and long transit times, negatively impacting organism health. Here, we test the accuracy of a handheld pulse amplitude modulated (PAM) fluorometer, the Hach BW680, for detecting photosynthetic protists at concentrations above or below the discharge standard (<10 cells·ml−1) in comparison to microscopic counts using fluorescein diacetate as a viability probe. Testing was conducted on serial dilutions of freshwater harbour samples in the lab and in situ untreated ballast water samples originating from marine, freshwater and brackish sources utilizing three preprocessing techniques to target organisms in the size range of ≥10 and <50μm. The BW680 numeric estimates were in agreement with microscopic counts when analyzing freshly collected harbour water at all but the lowest concentrations (<38 cells·ml−1). Chi-square tests determined that error is not independent of preprocessing methods: using the filtrate method or unfiltered water, in addition to refining the conversion factor of raw fluorescence to cell size, can decrease the grey area where exceedance of the discharge standard cannot be measured with certainty (at least for the studied populations). When examining in situ ballast water, the BW680 detected significantly fewer viable organisms than microscopy, possibly due to factors such as organism size or ballast water age. Assuming both the BW680 and microscopy with FDA stain were measuring fluorescence and enzymatic activity/membrane integrity correctly, the observed discrepancy between methods may simply reflect that the two methods are measuring different characteristics of life. This is the first study to conduct proof-of-concept testing for a rapid compliance detection tool using freshly collected harbour water concomitantly with in situ ballast water; our results demonstrate that it is important to challenge potential compliance tools with water samples spanning a range of biotic and abiotic conditions.
•For fresh harbour water, BW680 and microscopy yield similar concentration estimates.•Results were disparate for in situ untreated ballast water samples.•Organism size and ballast age likely contribute to differences in results.•The BW680 might be more sensitive to earlier stages of death than viability probes.
The unintentional release of aquatic nonindigenous species (NIS) via ballast water has long been recognized as a primary vector of biological invasions. To reduce the risk of ballast-mediated ...invasions, the International Maritime Organization (IMO) will direct ships to meet standards regarding the maximum number of viable organisms discharged in ballast water, with most ships expected to install ballast water management systems (BWMSs). Currently, filtration + ultraviolet (UV) irradiation is utilized as a common BWMS. There are issues, however, with enumerating viable phytoplankton after treatment at the low UV doses used onboard ships because the physiological effect occurs at the DNA level—organisms are reproductively sterilized but may remain alive for hours or days after treatment. The objective of this study is to examine three techniques to measure the number of viable phytoplankton cells following filtration + UV treatment: pulse amplitude modulation (PAM) fluorometry, epifluorescence microscopy using fluorescein diacetate (FDA) stain, and the serial dilution culture most probable number (MPN) method. PAM and staining techniques demonstrated similar patterns of phytoplankton reduction after UV irradiation. After 14 days, the MPN method confirmed viability of treated samples in enriched culture medium incubations and may be used to indicate potential recovery of damaged cells (i.e., “re-growth”). All cells that survived treatment and showed detectable growth after 14 days of incubation were smaller than 10 µm, as determined by microscopy. Combinations of direct and/or indirect measurements and culture-based methods might be the best solution to improve detection strategies and eliminate nonindigenous species.
•Recurrence strongly associated with liver and renal failure, diabetes and immune-suppressive drugs.•A persistent focus was judged the primary reason for recurrence in 23(74%).•A risk score based on ...BMI, Immunosuppression, Renal disease, Diabetes, Liver disease predicted recurrence.•Older age and higher neutrophil counts predicted early treatment failure and S. aureus-attributed mortality.
Adjunctive rifampicin did not reduce failure/recurrence/death as a composite endpoint in the ARREST trial of Staphylococcus aureus bacteraemia, but did reduce recurrences. We investigated clinically-defined 14-day treatment failure, and recurrence and S. aureus-attributed/unattributed mortality by 12-weeks to further define their predictors.
A post-hoc exploratory analysis using competing risks models was conducted to identify sub-groups which might benefit from rifampicin. A points-based recurrence risk score was developed and used to compare rifampicin's benefits.
Recurrence was strongly associated with liver and renal failure, diabetes and immune-suppressive drugs (p < 0.005); in contrast, failure and S. aureus-attributed mortality were associated with older age and higher neutrophil counts. Higher SOFA scores predicted mortality; higher Charlson scores and deep-seated initial infection focus predicted failure. Unexpectedly, recurrence risk increased with increasing BMI in placebo (p = 0.04) but not rifampicin (p = 0.60) participants (pheterogeneity = 0.06). A persistent focus was judged the primary reason for recurrence in 23(74%). A 5-factor risk score based on BMI, Immunosuppression, Renal disease, Diabetes, Liver disease (BIRDL) strongly predicted recurrence (p < 0.001).
Rifampicin reduces recurrences overall; those with greatest absolute risk reductions were identified using a simple risk score. Source control and adequate duration of antibiotic therapy remain essential to prevent recurrence and improve outcomes.
Degenerative cervical myelopathy is a spinal disorder resulting in progressive cord compression and neurological deficits that are assessed using the modified Japanese Orthopedic Association (mJOA) ...questionnaire. It is difficult to predict which patients will recover neurological function after surgery, making it challenging for clinicians to set postoperative patient expectations. In this study, we used mJOA subscores to identify patterns of recovery and recovery timelines in patients with moderate and severe myelopathy.
Fifty-three myelopathy patients were enrolled and completed the mJOA questionnaire both pre-surgery, and six weeks and six months post-surgery. Pearson chi-square tests were performed to assess relationships of both recovery patterns and recovery timelines with severity of disease.
Moderate myelopathy patients were significantly more likely than severe myelopathy patients to experience full recovery of upper extremity, lower extremity, and sensory domains. Disease severity did not significantly impact the timeline during which recovery occurs. Overall, >90% of patients experienced at least partial recovery by six months post surgery, 80% of which demonstrated it within the first six weeks.
This study shows the more severe the disease experienced by myelopathy patients, the more likely they will be left with permanent disabilities despite surgery. Early identification and treatment are therefore necessary to prevent worsening quality of life and increased costs of functional dependence. The recovery timelines for each subscore are similar and provide new values to guide patient expectations in their potential post-operative recovery. The overall recovery timeline is more generalizable though potentially lacking the specificity patients seek.
Biological invasions by nonindigenous species (NIS) can have adverse effects on economically important goods and services, and sometimes result in an 'invisible tax' on natural resources (e.g. ...reduced yield). The combined economic costs of NIS may be significant, with implications for environmental policy and resource management; yet economic impact assessments are rare at a national scale. Impacts of nuisance NIS may be direct (e.g. loss of hardwood trees) or indirect (e.g. alteration of ecosystem services provided by growing hardwoods). Moreover, costs associated with these effects may be accrued to resources and services with clear 'market' values (e.g. crop production) and to those with more ambiguous, 'non-market' values (e.g. aesthetic value of intact forest). We characterised and projected economic costs associated with nuisance NIS in Canada, through a combination of case-studies and an empirical model derived from 21 identified effects of 16 NIS. Despite a severe dearth of available data, characterised costs associated with ten NIS in Canadian fisheries, agriculture and forestry totalled $187 million Canadian (CDN) per year. These costs were dwarfed by the 'invisible tax' projected for sixteen nuisance NIS found in Canada, which was estimated at between $13.3 and $34.5 billion CDN per year. Canada remains highly vulnerable to new nuisance NIS, but available manpower and financial resources appear insufficient to deal with this problem.
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