Application of Nanopore Sequencing Technology in the Clinical Diagnosis of Infectious Diseases.

Infectious diseases are an enormous public health burden and a growing threat to human health worldwide. Emerging or classic recurrent pathogens, or pathogens with resistant traits, challenge our ability to diagnose and control infectious diseases. Nanopore sequencing technology has the potential to enhance our ability to diagnose, interrogate, and track infectious diseases due to the unrestricted read length and system portability. This review focuses on the application of nanopore sequencing technology in the clinical diagnosis of infectious diseases and includes the following: (i) a brief introduction to nanopore sequencing technology and Oxford Nanopore Technologies (ONT) sequencing platforms; (ii) strategies for nanopore-based sequencing technologies; and (iii) applications of nanopore sequencing technology in monitoring emerging pathogenic microorganisms, molecular detection of clinically relevant drug-resistance genes, and characterization of disease-related microbial communities. Finally, we discuss the current challenges, potential opportunities, and future outlook for applying nanopore sequencing technology in the diagnosis of infectious diseases.

A Whole-genome Sequencing Analysis of Neisseria gonorrhoeae Isolates in China: An Observational Study.

BACKGROUND: Tracking the spread of the Neisseria gonorrhoeae strains with decreased susceptibility or resistance to cephalosporins is a major priority for global surveillance programmes. Whole-genome sequencing (WGS) has been widely used by increasing countries in North America, Europe, and Pacific to determine the decreased susceptible or resistance determinants of Neisseria gonorrhoeae, track the spread of these determinants throughout the gonococcal population at national or regional level. However, no studies to date have examined the genomic epidemiology of gonorrhea in Asia where the antimicrobial resistant strains of Neisseria gonorrhoeae appears to have emerged before disseminating the strains globally. METHODS: We obtained clinical isolates and data from the China Gonococcal Resistance Surveillance Programme (China-GRSP) from 2012 to 2013. We sequenced the genomes of 435 clinical isolates of Neisseria gonorrhoeae, including 112 (25.6%) isolates with decreased susceptibility to ceftriaxone (Cfx-DS). We assessed the association between antimicrobial resistance genotype and phenotype. We also compared our data with the whole genome data of the isolates from the USA and the UK in the GenBank. FINDINGS: The most prevalent MLST STs in our gonococcal population were MLST ST7827 (n = 74), followed by ST7365 (n = 58), ST1600 (n = 38), ST7367 (n = 35), and ST7363 (n = 29). MLST ST1901 which was reported as the predominant ST in the US was not found in our population. A total of 2512 strains, including additional 2077 published NG strains, were further included for phylogenetic analysis. It generated two distinct lineages - lineage 1 and lineage 2. Analysis of MLST ST1901 in the database indicate that most of MLST ST1901 isolates in the lineage2.6 were Cfx-DS isolates while all isolates in the lineage 2.1 were sensitive to ceftriaxone (77/110 vs. 0/13; p < 0.001). ST1901/lineage 2.6 is a ceftriaxone resistant clone which cannot distinguished by MLST genotyping. In the isolates from our study, the MICs of ceftriaxone for ST7363/lineage 2.6 isolates ranged from 0.008-0.125 mg/L (mean ±â€¯SD; 0.054 ±â€¯0.043 mg/L) while those for ST7363/lineage 2.8 isolates ranged from 0.032-0.250 mg/L (0.134 ±â€¯0.085 mg/L). All ST7363/lineage 2.8 isolates contained penA mosaic alleles. INTERPRETATION: To our knowledge, current study is the first WGS-based analysis of gonococcal population at national level in Asia. China harbors the different predominant clones associated with decreased susceptibility to ceftriaxone from those clones circulated in other regions. The findings from the study can be not only used as baseline data for future studies in China but also contributable to our understanding on spread of N. gonorrhoeae and its resistant strains at regional and global levels. FUNDING: The Chinese Academy Medical Sciences (CAMS) Initiative for Innovative Medicine.

Association between three VEGF polymorphisms and renal cell carcinoma susceptibility: a meta-analysis.

Several studies have reported an association between vascular endothelial growth factor (VEGF) gene polymorphisms rs2010963, rs3025039 and rs699947 and renal cell carcinoma (RCC). However, the results remain inconclusive and controversial. We therefore conducted a meta-analysis to evaluate this association. Electronic databases were searched for relevant case-control studies up to November 2016. RevMan 5.2 software and STATA version 12.0 were used for statistical analysis in our meta-analysis. Heterogeneity was assessed using the I2 value. Nine eligible studies were retrieved for detailed evaluation. The pooled estimates indicated that the GG genotype of VEGF rs2010963 polymorphism significantly decreased RCC risk [GG vs. GC+CC; GG vs. GC]. There was also a significant association between VEGF rs3025039 polymorphism and RCC susceptibility [CC+CT vs. TT; CC vs. TT]. Furthermore, a significant association between VEGF rs699947 polymorphism and RCC susceptibility was detected [A vs. C; AA+AC vs. CC; AA vs. AC+CC; AA vs. CC; AA vs. AC; AC vs. CC]. Subgroup analysis revealed that these associations held true especially for Asians. Our meta-analysis suggested that there may be a relationship between the VEGF rs2010963, rs3025039 and rs699947 polymorphisms and RCC susceptibility.

Computer tomography imaging findings of adrenal cavernous hemangiomas: a report of 10 cases.

BACKGROUND: Cavernous hemangiomas (CHs) of the adrenal gland are extremely rare. To date, only a few studies of adrenal CH imaging have been reported. PURPOSE: To analyze the computed tomography (CT) imaging findings of adrenal CHs. MATERIAL AND METHODS: Ten cases of adrenal CHs confirmed by a histopathological examination were retrospectively analyzed. All of the patients had undergone unenhanced and enhanced CT examinations, and eight had also undergone multiphase CT enhancement examinations. CT characteristics, including shape, size, margin, attenuation, and enhancement patterns, were analyzed. RESULTS: The study included six women and four men with a mean age of 49.2 years (age range, 25-62 years) and no signs of abnormal endocrine activity. The unenhanced CTs showed well-defined, heterogeneous (n = 8) or homogeneous (n = 2) density masses with scattered (n = 8) or spread calcifications (n = 2) in six tumors. In the contrast-enhanced CTs, seven tumors appeared to be marked with heterogeneous enhancement, whereas three cases exhibited no obvious enhancement. The evaluation of the pattern of dynamic enhancement in eight patients revealed that the tumors showed early peripheral enhancement (n = 4), early central enhancement (n = 1), and mixed enhancement (n = 1) with progressive partial filling-in, and no obvious enhancement in any phases (n = 2). CONCLUSION: Adrenal CHs should be included in the differential diagnosis when an adrenal neoplasm is incidentally found and appears as a well-defined, heterogeneous mass with calcifications and various enhancement patterns, including heterogeneous enhancement with characteristic progressive partial filling-in, as well as lack of enhancement in any phase.

Mapping the Electronic Structure of Each Ingredient Oxide Layer of High-T\{c} Cuprate Superconductor Bi{2}Sr{2}CaCu{2}O{8+δ}.

Understanding the mechanism of high transition temperature (T{c}) superconductivity in cuprates has been hindered by the apparent complexity of their multilayered crystal structure. Using a cryogenic scanning tunneling microscopy (STM), we report on layer-by-layer probing of the electronic structures of all ingredient planes (BiO, SrO, CuO{2}) of Bi{2}Sr{2}CaCu_2}O{8+δ} superconductor prepared by argon-ion bombardment and annealing technique. We show that the well-known pseudogap (PG) feature observed by STM is inherently a property of the BiO planes and thus irrelevant directly to Cooper pairing. The SrO planes exhibit an unexpected van Hove singularity near the Fermi level, while the CuO{2} planes are exclusively characterized by a smaller gap inside the PG. The small gap becomes invisible near T{c}, which we identify as the superconducting gap. The above results constitute severe constraints on any microscopic model for high T{c} superconductivity in cuprates.

Quantum Griffiths singularity of superconductor-metal transition in Ga thin films.

The Griffiths singularity in a phase transition, caused by disorder effects, was predicted more than 40 years ago. Its signature, the divergence of the dynamical critical exponent, is challenging to observe experimentally. We report the experimental observation of the quantum Griffiths singularity in a two-dimensional superconducting system. We measured the transport properties of atomically thin gallium films and found that the films undergo superconductor-metal transitions with increasing magnetic field. Approaching the zero-temperature quantum critical point, we observed divergence of the dynamical critical exponent, which is consistent with the Griffiths singularity behavior. We interpret the observed superconductor-metal quantum phase transition as the infinite-randomness critical point, where the properties of the system are controlled by rare large superconducting regions.

Detection of a superconducting phase in a two-atom layer of hexagonal Ga film grown on semiconducting GaN(0001).

The recent observation of the superconducting state at atomic scale has motivated the pursuit of exotic condensed phases in two-dimensional (2D) systems. Here we report on a superconducting phase in two-monolayer crystalline Ga films epitaxially grown on wide-band-gap semiconductor GaN(0001). This phase exhibits a hexagonal structure and only 0.552 nm in thickness, nevertheless, brings about a superconducting transition temperature Tc as high as 5.4 K, confirmed by in situ scanning tunneling spectroscopy and ex situ electrical magnetotransport and magnetization measurements. The anisotropy of critical magnetic field and Berezinski-Kosterlitz-Thouless-like transition are observed, typical for the 2D superconductivity. Our results demonstrate a novel platform for exploring atomic-scale 2D superconductors, with great potential for understanding the interface superconductivity.

Molecular beam epitaxy growth and post-growth annealing of FeSe films on SrTiO3: a scanning tunneling microscopy study.

Low temperature scanning tunneling microscopy and spectroscopy are used to investigate the atomic and electronic structure evolution of FeSe films grown on SrTiO3 as a function of post-growth annealing. Single unit cell FeSe films are found to bond strongly with the underlying substrate, and become superconductive with diminishing chemical bond disorders at the interface via post-annealing. For thicker FeSe films, post-annealing removes excess Se in the films and leads to a transition from semiconductor into metallic behaviors. In double and multilayer films, strain-induced complex textures are observed and suggested to be the main cause for the absent superconductivity.

Abnormal regional homogeneity of resting-state brain activity in patients with HBV-related cirrhosis without overt hepatic encephalopathy.

BACKGROUND: Many studies have reported that cognitive deficits exist in cirrhotic patients without overt hepatic encephalopathy (OHE). However, the neurobiological mechanisms underlying these deficits are still not fully understood. AIM: To investigate regional activity abnormalities in patients with hepatitis B virus-related cirrhosis (HBV-RC) without OHE using resting-state functional MRI (Rs-fMRI), and to examine the relationship between regional activity abnormalities and impaired cognition. METHODS: A newly reported regional homogeneity (ReHo) approach was used to compare the local synchronization of Rs-fMRI signals in 32 patients with HBV-RC without OHE and 32 well-matched healthy controls. Cognition was measured in all patients using psychometric hepatic encephalopathy score (PHES) tests, and the relationship between ReHo variation and PHES was analysed. RESULTS: Relative to healthy controls, the cirrhosis group showed high ReHo in the prefrontal cortex, and widespread low ReHo in visual association areas (left lingual gyrus, middle temporal gyrus and right middle occipital gyrus), motor association areas (bilateral precentral gyrus and paracentral lobule) and the bilateral precuneus. Correlation analysis of the mean ReHo values in different brain areas and PHES in cirrhotic patients revealed a significantly positive correlation in the left lingual gyrus (r = 0.352; P = 0.048), right middle occipital gyrus (r = 0.453; P = 0.009) and bilateral precentral gyrus (left: r = 0.436, P = 0.013; right: r = 0.582, P < 0.001), paracentral lobule (r = 0.485; P = 0.005) and precuneus (r = 0.468; P = 0.007). CONCLUSIONS: Our results provide information on the pathophysiological mechanisms underlying cognitive alterations in cirrhotic patients and demonstrate the feasibility of using Rs-fMRI with ReHo analysis as a noninvasive modality with which to detect the progression of cognitive changes in cirrhotic patients.

Transcriptional profile of the Shigella flexneri response to an alkaloid: berberine.

Berberine, a natural isoquinoline alkaloid found in many medicinal herbs, has been shown to be active against a variety of microbial infections. To examine the potential effects of berberine on Shigella flexneri, a whole-genome DNA microarray was constructed and a transcriptome analysis of the cellular responses of S. flexneri when exposed to berberine chloride (BC) was performed. Our data revealed that BC upregulated a group of genes involved in DNA replication, repair and division. Intriguingly, the expression of many genes related to cell envelope biogenesis was increased. In addition, many genes involved in cell secretion, nucleotide metabolism, translation, fatty acid metabolism and the virulence system were also induced by the drug. However, more genes from the functional classes of carbohydrate metabolism, energy production and conversion as well as amino acid metabolism were significantly repressed than were induced. These results provide a comprehensive view of the changes in gene expression when S. flexneri was exposed to BC, and shed light on its complicated effects on this pathogen.

[Development of the cDNA chip for SARS virus and a primary study on the possible molecular mechanism of interferon alpha2b inhibiting the SARS virus replication].

BACKGROUND: To study the molecular mechanism of interferon alpha2b(IFNalpha2b) inhibiting the SARS virus replication. SARS-associated coronavirus (SARS virus) cDNA chip was developed and applied to detect the virus RNA transcription levels in the interferon-treated and untreated cell cultures, and the mechanism of anti-SARS virus activity of interferon alpha2b in cell culture system was explored. METHODS: SARS virus cDNA chip was prepared by comparing the published SARS virus genome sequence, and the cDNA chip was used to study the interferon alpha2b function during SARS virus replication. RESULTS: SARS virus cDNA chip was successfully prepared by using PCR method. The results showed that the cDNA chip could be used to detect the viral RNA transcription level. Interferon alpha2b could inhibit almost all the SARS virus gene transcription. An unknown gene at the position 28130-28426 bp, named as U gene, may play an important role during the viral replication. CONCLUSION: A SARS virus whole genome cDNA chip was established. It could be used to study the virus molecular biology and antiviral drug screening. The results also showed that interferon alpha2b could inhibit almost the whole virus gene transcription by using the cDNA chip.