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Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page (http://PathoTracker.pku.edu.cn/) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg. This study constructed a database and platform for the characterization of Klebsiellapneumoniae in clinical metagenomic Nanopore sequencing and developed a website for online analysis. [ABSTRACT FROM AUTHOR]

Flow chemistry offers high reaction yield, kinetic control, improved safety, reliability, scalability, and greater degree of process control. Herein, hyperbranched polymer-grafted silica microparticles (HP-SMPs) are synthesized in a commercially available flow reactor through atom transfer radical polymerization. Initiator-anchored silica microparticles are obtained by in situ silanization in the flow reactor. Hyperbranched poly[2-(dimethylamino)ethylmethacrylate] chains are grafted onto the initiator-anchored SMPs through inimer–monomer ratio control. To demonstrate the efficiency and universality of this approach in grafting polymers onto SMPs, multiple hyperbranched polymeric structures are obtained by varying the inimer concentration. Dye absorption test is conducted to demonstrate the potential applications of HP-SMPs. [ABSTRACT FROM AUTHOR]

The mobile resistance gene blaNDM encodes the NDM enzyme which hydrolyses carbapenems, a class of antibiotics used to treat some of the most severe bacterial infections. The blaNDM gene is globally distributed across a variety of Gram-negative bacteria on multiple plasmids, typically located within highly recombining and transposon-rich genomic regions, which leads to the dynamics underlying the global dissemination of blaNDM to remain poorly resolved. Here, we compile a dataset of over 6000 bacterial genomes harbouring the blaNDM gene, including 104 newly generated PacBio hybrid assemblies from clinical and livestock-associated isolates across China. We develop a computational approach to track structural variants surrounding blaNDM, which allows us to identify prevalent genomic contexts, mobile genetic elements, and likely events in the gene's global spread. We estimate that blaNDM emerged on a Tn125 transposon before 1985, but only reached global prevalence around a decade after its first recorded observation in 2005. The Tn125 transposon seems to have played an important role in early plasmid-mediated jumps of blaNDM, but was overtaken in recent years by other elements including IS26-flanked pseudo-composite transposons and Tn3000. We found a strong association between blaNDM-carrying plasmid backbones and the sampling location of isolates. This observation suggests that the global dissemination of the blaNDM gene was primarily driven by successive between-plasmid transposon jumps, with far more restricted subsequent plasmid exchange, possibly due to adaptation of plasmids to their specific bacterial hosts. Gene blaNDM, conferring resistance to carbapenem antibiotics, is globally distributed across Gram-negative bacteria on multiple plasmids. Here, Acman et al. study the dynamics underlying blaNDM dissemination across over 6000 bacterial genomes, and identify mobile genetic elements and specific mobilisation events likely involved in the gene's global spread. [ABSTRACT FROM AUTHOR]

Hospital-acquired pneumonia (HAP) is a significant nosocomial infection; data on the distribution and antimicrobial resistance profiles of HAP in China are limited. We included 2827 adult patients with HAP from the Chinese Antimicrobial Resistance Surveillance of Nosocomial Infections network admitted in 15 Chinese teaching hospitals between 2007 and 2016. Clinical data and antimicrobial susceptibility of isolated pathogens were obtained from the medical records and central laboratory, respectively. Multivariable logistic regression was performed to determine the risk factors for mortality and multidrug resistance (MDR). A total of 386 (13.7%) patients died in the hospital, while 1181 (41.8%) developed ventilator-associated pneumonia (VAP). Active immunosuppressant therapy (OR 1.915 (95% CI 1.475–2.487)), solid tumor (OR 1.860 (95% CI 1.410–2.452)), coma (OR 1.783 (95% CI 1.364–2.333)), clinical pulmonary infection score ≥7 (OR 1.743 (95% CI 1.373–2.212)), intensive care unit stay (OR 1.652 (95% CI 1.292–2.111)), age ≥65 years (OR 1.621 (95% CI 1.282–2.049)), and tracheal cannula insertion (OR 1.613 (95% CI 1.169–2.224)) were independent risk factors for in-hospital mortality. Liver cirrhosis (OR 3.120 (95% CI 1.436–6.780)) and six other variables were independent predictors of MDR. Acinetobacter baumannii (25.6%), Pseudomonas aeruginosa (20.1%), Klebsiella pneumoniae (15.4%), and Staphylococcus aureus (12.6%) were the most common pathogens (MDR prevalence 64.9%). Isolates from VAP patients showed more A. baumannii and less K. pneumoniae and E. coli strains (p < 0.001, respectively) than those from patients without VAP. The proportion of methicillin-resistant S. aureus strains decreased; that of carbapenem-resistant A. baumannii and Enterobacterales strains increased. There had been changes in the antibiotic resistance profiles of HAP pathogens in China. Risk factors for mortality and MDR are important for the selection of antimicrobials for HAP in China. [ABSTRACT FROM AUTHOR]

Objective: Many studies have confirmed the glucose-lowering effect of berberine in type 2 diabetes patients. Although the mechanism of action of berberine involves the improvement of insulin sensitivity, its hypoglycemic mechanism remains elusive. Here we show a new mechanism by which berberine antagonizes glucagon signaling and find that SIRT3 is involved in the hypoglycemic effect of berberine.Methods: Gene knockout and overexpression were used to assess the inhibitory effect of berberine on SIRT3. Downstream signaling pathways and the hypoglycemic effect of SIRT3 were evaluated by immunoblotting and metabolic monitoring.Results: We found that berberine led to mitochondrial dysfunction and AMP accumulation by inhibiting deacetylase SIRT3. We confirmed that AMP accumulation activated the AMPK signaling pathway and further promoted glucose uptake. Simultaneously, AMP accumulation reduced cyclic AMP (cAMP) levels and abrogated the phosphorylation of critical protein targets of protein kinase A (PKA). Furthermore, we found that phosphoenolpyruvate carboxykinase 1 (PEPCK1) is a key gluconeogenesis enzyme that can be stabilized by glucagon. Berberine caused significant PEPCK1 ubiquitination and degradation by antagonizing glucagon and was accompanied by high levels of PEPCK1 acetylation. Interestingly, berberine-induced glucagon inhibition is independent of AMPK activation. The in vivo data from sirt3 knockout mice were further confirmed by the in vitro experiments.Conclusions: Berberine promotes glucose uptake and inhibits gluconeogenesis by inhibiting SIRT3, and regulating mitochondria-related pathways may provide a novel approach to the development of antidiabetic drugs. [ABSTRACT FROM AUTHOR]