Prospective evaluation of a rapid clinical metagenomics test for bacterial pneumonia

Background: The diagnosis of bacterial pathogens in lower respiratory tract infections (LRI) using conventional culture methods remains challenging and time-consuming.  Objectives: To evaluate the clinical performance of a rapid nanopore-sequencing based metagenomics test for diagnosis of bacterial pathogens in common LRIs through a large-scale prospective study.  Methods: We enrolled 292 hospitalized patients suspected to have LRIs between November 2018 and June 2019 in a single-center, prospective cohort study. Rapid clinical metagenomics test was performed on-site, and the results were compared with those of routine microbiology tests.  Results: 171 bronchoalveolar lavage fluid (BAL) and 121 sputum samples were collected from patients with six kinds of LRIs. The turnaround time (from sample registration to result) for the rapid metagenomics test was 6.4 ± 1.4 hours, compared to 94.8 ± 34.9 hours for routine culture. Compared with culture and real-time PCR validation tests, rapid metagenomics achieved 96.6% sensitivity and 88.0% specificity and identified pathogens in 63 out of 161 (39.1%) culture-negative samples. Correlation between enriched anaerobes and lung abscess was observed by Gene Set Enrichment Analysis. Moreover, 38 anaerobic species failed in culture was identified by metagenomics sequencing. The hypothetical impact of metagenomics test proposed antibiotic de-escalation in 34 patients compared to 1 using routine culture.  Conclusions: Rapid clinical metagenomics test improved pathogen detection yield in the diagnosis of LRI. Empirical antimicrobial therapy could be de-escalated if rapid metagenomics test results were hypothetically applied to clinical management

Effect of Quinoa Seeds (Chenopodium quinoa) in Diet on some Biochemical Parameters and Essential Elements in Blood of High Fructose-Fed Rats

The effect of Chenopodium quinoa seeds on lipid profile, glucose level, protein metabolism and selected essential elements (Na, K, Ca, Mg) level was determined in high—fructose fed male Wistar rats. Fructose decreased significantly LDL [42%, p < 0.01] and activity of alkaline phosphatase [20%, p < 0.05], and increased triglycerides level [86%, p < 0.01]. The analysis of blood of rats fed quinoa indicated, that these seeds effectively reduced serum total cholesterol [26%, p < 0.05], LDL [57%, p < 0.008] and triglycerides [11%, p < 0.05] when compared to the control group. Quinoa seeds also significantly reduced the level of glucose [10%, p < 0.01] and plasma total protein level [16%, p < 0.001]. Fructose significantly decreased HDL [15%, p < 0.05] level in control group but when the quinoa seeds were added into the diet the decrease of HDL level was inhibited. Quinoa seeds did not prevent any adverse effect of increasing triglyceride level caused by fructose. It was shown in this study that quinoa seeds can reduce most of the adverse effects exerted by fructose on lipid profile and glucose level

First-Principles Investigation of Mercury Adsorption on the α‑Fe₂O₃(11̅02) Surface

Theoretical investigations using density functional theory (DFT) have been carried out to understand the interaction between mercury (Hg) and hematite (α-Fe₂O₃), both of which are released during the coal combustion processes. A clean α-Fe₂O₃(11̅02) surface was chosen as a representative hematite model in this study based upon a previous <i>ab initio</i> thermodynamics study showing the high stability of this surface in the temperature range of typical flue gases. In order to determine the effect of chlorine (Cl) during Hg adsorption, the most probable adsorption sites of Hg, Cl, and HgCl on the clean α-Fe₂O₃ surface termination were found based on adsorption energy calculations, and the oxidation states of the adsorbates were determined by Bader charge analysis. Additionally, the projected density of states (PDOS) analysis characterizes the surface–adsorbate bonding mechanism. The adsorption energy of −0.103 eV indicates that Hg physisorbs to the clean α-Fe₂O₃ surface, and the subsequent Bader analysis confirms that the Hg becomes oxidized. Adding Cl to the Hg-adsorbed surface further enhances the strength of Hg adsorption, as evidenced by a shortened Hg–surface equilibrium distance. Bader charge and PDOS analyses also suggest that the presence of Cl enhances the charge transfer between the hematite surface and the adsorbate, thereby increasing the adsorption strength

Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis

Abstract Background Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susceptibility profile of patient samples without culturing, offering a powerful method to deal with culture-negative cases. Methods To assess the feasibility of a metagenomic approach to detect the causative pathogens in resected valves from IE patients, we employed both next-generation sequencing and Oxford Nanopore Technologies MinION nanopore sequencing for pathogens and antimicrobial resistance detection in seven culture-negative IE patients. Using our in-house developed bioinformatics pipeline, we analyzed the sequencing results generated from both platforms for the direct identification of pathogens from the resected valves of seven clinically culture-negative IE patients according to the modified Duke criteria. Results Our results showed both metagenomics methods can be applied for the causative pathogen detection in all IE samples. Moreover, we were able to simultaneously characterize respective antimicrobial resistance features. Conclusion Metagenomic methods for IE detection can provide clinicians with valuable information to diagnose and treat IE patients after valve replacement surgery. However, more efforts should be made to optimize protocols for sample processing, sequencing and bioinformatics analysis