Cost-Efficient Micro-Well Array-Based Colorimetric Antibiotic Susceptibility Testing (MacAST) for Bacteria from Culture or Community.

Rapid and cost-efficient antibiotic susceptibility testing (AST) is key to timely prescription-oriented diagnosis and precision treatment. However, current AST methods have limitations in throughput or cost effectiveness, and are impractical for microbial communities. Here, we developed a high-throughput micro-well array-based colorimetric AST (macAST) system equipped with a self-developed smartphone application that could efficiently test sixteen combinations of bacteria strains and antibiotics, achieving comparable AST results based on resazurin metabolism assay. For community samples, we integrated immunomagnetic separation into the macAST (imacAST) system to specifically enrich the target cells before testing, which shortened bacterial isolation time from days to only 45 min and achieved AST of the target bacteria with a low concentration (~103 CFU/mL). This proof-of-concept study developed a high-throughput AST system with an at least ten-fold reduction in cost compared with a system equipped with a microscope or Raman spectrum. Based on colorimetric readout, the antimicrobial susceptibility of the bacteria from microbial communities can be delivered within 6 h, compared to days being required based on standard procedures, bypassing the need for precise instrumentation in therapy to combat bacterial antibiotic resistance in resource-limited settings.

Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research.

In the last decade, metagenomics has greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads raised mainly from the preparation of metagenomic DNA sequencing libraries and their impacts on metagenomic assembly and binning have never been brought to attention. Here, we explicitly investigated the effects of duplicate reads on metagenomic assemblies and binning based on analyses of five groups of representative metagenomes with distinct microbiome complexities. Our results showed that deduplication considerably increased the binning yields (by 3.5% to 80%) for most of the metagenomic data sets examined thanks to the improved contig length and coverage profiling of metagenome-assembled contigs, whereas it slightly decreased the binning yields of metagenomes with low complexity (e.g., human gut metagenomes). Specifically, 411 versus 397, 331 versus 317, 104 versus 88, and 9 versus 5 metagenome-assembled genomes (MAGs) were recovered from MEGAHIT assemblies of bioreactor sludge, surface water, lake sediment, and forest soil metagenomes, respectively. Noticeably, deduplication significantly reduced the computational costs of the metagenomic assembly, including the elapsed time (9.0% to 29.9%) and the maximum memory requirement (4.3% to 37.1%). Collectively, we recommend the removal of duplicate reads in metagenomes with high complexity before assembly and binning analyses, for example, the forest soil metagenomes examined in this study. IMPORTANCE Duplicated reads in shotgun metagenomes are usually considered technical artifacts. Their presence in metagenomes would theoretically not only introduce bias into the quantitative analysis but also result in mistakes in the coverage profile, leading to adverse effects on or even failures in metagenomic assembly and binning, as the widely used metagenome assemblers and binners all need coverage information for graph partitioning and assembly binning, respectively. However, this issue was seldom noticed, and its impacts on downstream essential bioinformatic procedures (e.g., assembly and binning) remained unclear. In this study, we comprehensively evaluated for the first time the implications of duplicate reads for the de novo assembly and binning of real metagenomic data sets by comparing the assembly qualities, binning yields, and requirements for computational resources with and without the removal of duplicate reads. It was revealed that deduplication considerably increased the binning yields of metagenomes with high complexity and significantly reduced the computational costs, including the elapsed time and the maximum memory requirement, for most of the metagenomes studied. These results provide empirical references for more cost-efficient metagenomic analyses in microbiome research.

Quantitative assessment of the contribution of soil organic matter functional groups and heteroatoms to PAHs adsorption based on the COSMO-RS model.

Soil organic matter (SOM) is considered as a pivotal factor influencing the adsorption of pollutants. However, few prior quantitative investigations of the SOM functional group distribution to the contaminants' fate have been conducted. In this paper, the SOM cluster method based on COSMO-RS theory has been conducted to illustrate the chemical composition variables of SOM that affect the polycyclic aromatic hydrocarbons (PAHs) fate in quantitative terms. In the theoretical simulations, the contributions of carbonyl, carboxyl, aromatic, oxyalkyl and aliphatic groups in SOM to phenanthrene (Phe) and pyrene (Pyr) adsorption are evaluated by calculating the partition coefficients (LogP). The results show that the increase in oxyalkyl content leads to a decrease in LogP. Inversely, carbonyl and carboxyl groups of SOMs positively associated with Phe adsorption. The changes in aromatic and alkyl components have a similar magnitude of influence on LogP. Moreover, the effect of non-carbon-based functional groups in SOM on the Phe partitioning has been examined for the first time. The increase of sulfur and nitrogen content in SOM hinder Phe adsorption, while the rise of phosphorus content promotes the adsorption. In soil adsorption experiments, four natural soils, characterized by X-ray photoelectron spectroscopy (XPS) and Diffuse reflectance infrared Fourier transform (DRIFT), are selected to verify the influence of SOM functional group distribution. Comparing the experimental SOM-water partition coefficient (LogKoc) with the simulation predicted LogP suggests that the COSMO-RS based SOM cluster method can predict PAHs adsorption ability in SOM.

Effect of pharmaceutical care on the treatment of COVID-19: A protocol for systematic review and meta analysis.

BACKGROUND: We aimed to conduct a meta-analysis to assess the effect of pharmaceutical care on the treatment of coronavirus disease 2019 (COVID-19). METHODS: All case-controlled studies related to pharmaceutical care on the treatment of COVID-19 will be included in this review. We will use index words related to pharmaceutical care and COVID-19 to perform literature searches in PubMed, Embase, MEDLINE, CNKI, and Wanfang databases, to include articles indexed as of October 20, 2020 in English and Chinese language. Two reviewers will select trials independently for inclusion and assess trial quality. Two pairs of review authors will independently extract information for each included trials. Primary outcomes are clinical outcomes, average hospital stays, costs, patient satisfaction, and incidence of adverse drug reactions. We will evaluate the risk of bias of the included studies based on Cochrane assessment tool. Revman 5.3 (the Cochrane collaboration, Oxford, UK) will be used for heterogeneity assessment, generating funnel-plots, data synthesis, subgroup analysis, and sensitivity analysis. RESULTS: We will provide targeted and practical results assessing the effect of pharmaceutical care on the treatment of COVID-19. CONCLUSION: The stronger evidence about the effect of pharmaceutical care on the treatment of COVID-19 will be provided for clinicians. SYSTEMATIC REVIEW REGISTRATION NUMBER: PROSPERO CRD42020214223 ETHICS AND DISSEMINATION:: There is no need for ethical approval, and the review will be reported in a peer-reviewed journal.

Comprehensive insights into the key components of bacterial assemblages in pharmaceutical wastewater treatment plants.

Due to complexity and variety of pharmaceutical wastewater composition, little is known as for functionally important microflora of pharmaceutical wastewater treatment plants (pWWTPs). We compared bacterial composition and diversity of pWWTPs (27 sludge samples collected from 12 full-scale pWWTPs) with those of other industrial (iWWTPs) (27 samples) and municipal wastewater treatment plants (mWWTPs) (27 samples) through meta-analysis based on 16S rRNA gene amplicon sequencing, and identified putatively important organisms and their ecological correlations. Non-metric multidimensional scaling indicated that the pWWTPs, iWWTPs and mWWTPs showed distinctive differences in bacterial community composition (P < 1e-04), and the pWWTPs had significantly lower bacterial diversity than the mWWTPs (P < 1e-06). Thermotogae and Synergistetes phyla only strictly dominated in the pWWTPs, and 26, 30 and 6 specific genera were identified in the pWWTPs, mWWTPs and iWWTPs, respectively. Totally, 15 and 1300 OTUs were identified as core and occasional groups, representing 23.2% and 66.2% of the total read abundance of the pWWTPs, respectively. Permutational multivariate analysis of variance revealed that the bacterial components were clearly clustered corresponding to the types of pharmaceutical wastewater, and a total of 129 local specific OTUs were identified in the pWWTPs, among which anticancer antibiotics pWWTPs had the highest number of specific OTUs (40 ones). Co-occurrence network revealed that the species dominating in the same type of pWWTPs tended to co-occur much more frequently than theoretical random expectation. The results may extend our knowledge regarding the ecological status and correlation of the key microflora in pWWTPs.

Portable, low cost smartphone-based potentiostat system for the salivary α-amylase detection in stress paradigm.

The aim of this study was to explore a novel, low-cost smartphone-based biosensor system and establish an efficient analysis method for the detection of potential stress biomarker, salivary α-amylase(sAA). This system consists of Smartphone with sAA-detection, Screen-printed electrodes(SPEs) and potentiostat module. The presented technique that using a small perturbation to obtain a linearized response could affect the composition of the sample as to cyclic voltammetry which repeatedly reduces and oxidizes the sample. For application, 6 healthy graduate students took a 5 minutes Trier Social Stress Test(TSST). Results show that this method could detect sAA activities conveniently and accurately. Calibration curve of sAA whose quantitative range is from 50 and 1200 U mL-1 with a limit of detection(LOD) of 1.6 U mL-1, is Y=-52.324X+295.63, R^2=0.9933. After psychological stress, sAA secretion was significant verified. It is concluded that this smartphone-based sAA detection system is reliable for determination of Salivary α-amylase and useful in the assessment of Psychological stress.

Left and right ventricular strain and strain rate measurement in normal adults using velocity vector imaging: an assessment of reference values and intersystem agreement.

Velocity vector imaging (VVI) software permits quantitative assessment of ventricular function through measurement of myocardial strain (S) and strain rate (SR). The purpose of this study was to define a reference range of ventricular S and SR values in normal adults using VVI software, and to describe the variability among observers and systems. Two-dimensional echocardiography was performed in 186 healthy adults free of cardiovascular disease or risk factors, followed by comprehensive ventricular S and SR analysis using VVI software. Images were acquired using three commercial ultrasound systems. The mean age of patients was 44 ± 16 years, and 114 (61 %) were female. Mean global left ventricular (LV) longitudinal, circumferential, and radial S and SR, and right ventricular (RV) longitudinal S and SR values are presented. Significant segmental variation in regional LV and RV S and SR was detected. Multivariate regression analysis demonstrated global longitudinal LV (p = 0.05) and RV (p = 0.002) S values decline significantly with age. The overall variability of S and SR values accounted for by patient demographic and hemodynamic variables was low (16 and 8 % for LV longitudinal S and SR, respectively). Interobserver agreement was very good, but was lowest for LV radial S and SR. There were no significant differences of LV and RV S and SR between ultrasound systems. Comprehensive reference values for the normal ranges of LV and RV S and SR measured using VVI software are presented. The ultrasound system used for image acquisition did not significantly influence results.

Role of serial quantitative assessment of right ventricular function by strain in pulmonary arterial hypertension.

The aim of this study was to assess whether serial quantitative assessment of right ventricular (RV) function by speckle-based strain imaging is affected by pulmonary hypertension-specific therapies and whether there is a correlation between serial changes in RV strain and clinical status. RV longitudinal systolic function was assessed using speckle-tracking echocardiography in 50 patients with pulmonary arterial hypertension (PAH) before and after the initiation of therapy. The mean interval to follow-up was 6 ± 2 months. Subsequent survival was assessed over 4 years. Patients demonstrated a mean increase in RV systolic strain from -15 ± 5 before to -20 ± 7% (p = 0.0001) after PAH treatment. Persistence of or progression to a severe reduction in free wall systolic strain (<-12.5%) at 6 months was associated with greater disease severity (100% were in functional class III or IV vs 42%, p = 0.005), greater diuretic use (86% vs 40%, p = 0.02), higher mean pulmonary artery pressure (67 ± 20 vs 46 ± 17 mm Hg, p = 0.006), and poorer survival (4-year mortality 43% vs 23%, p = 0.002). After adjusting for age, functional class, and RV strain at baseline, patients with ≥ 5% improvement in RV free wall systolic strain had a greater than sevenfold lower mortality risk at 4 years (hazard ratio 0.13, 95% confidence interval 0.03 to 0.50, p = 0.003). In conclusion, serial echocardiographic assessment of RV longitudinal systolic function by quantitative strain imaging independently predicts clinical deterioration and mortality in patients with PAH after the institution of medical therapy.

[An evaluation of net carbon sink effect and cost/benefits of a rice-rape rotation ecosystem under long-term fertilization from Tai Lake region of China].

Taking a long-term fertilized rice-rape rotation system in Taihu Lake as test objective, its annual C balance and economic benefit were estimated, based on the measurement of past years grain yield, litter C content, and field CO2 emission as well as the investigation of material and management inputs. The calculated annual C sink under different fertilizations ranged from 0.9 t C x hm(-2) x a(-1) to 7.5 t C x hm(-2) x a(-1), and the net C sink effect under combined inorganic/organic fertilization was three folds as that under chemical fertilization. The C cost of material input ranged from 0.37 t C x hm(-2) x a(-1) to 1.13 t C x hm(-2) x a(-1), and that of management input ranged from 1.69 t C x hm(-2) x a(-1) to 1.83 t C x hm(-2) x a(-1). The annual economic benefit ranged from 5.8 x 10(3) CNY x hm(-2) x a(-1) to 16.5 x 10(3) CNY x hm(-2) x a(-1), and was 2.1 times higher under combined fertilization than under chemical fertilization. Comparing with that under chemical fertilization, the marginal cost for per ton C sink under combined inorganic/organic fertilization was estimated as 217.1 CNY x t(-1) C, very close to the C price of 20 Euro x t(-1) C in the EU. In sum, under combined inorganic/organic fertilization, this rice paddy ecosystem could not only have higher productivity, but also present greater net C sink effect and higher economic benefit, compared with under chemical fertilizer fertilization.