Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis.

Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. ß-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis. IMPORTANCE: A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.

Pancreatic Diseases: Genetics and Modeling Using Human Pluripotent Stem Cells.

Pancreas serves endocrine and exocrine functions in the body; thus, their pathology can cause a broad range of irreparable consequences. Endocrine functions include the production of hormones such as insulin and glucagon, while exocrine functions involve the secretion of digestive enzymes. Disruption of these functions can lead to conditions like diabetes mellitus and exocrine pancreatic insufficiency. Also, the symptoms and causality of pancreatic cancer very greatly depends on their origin: pancreatic ductal adenocarcinoma is one of the most fatal cancer; however, most of tumor derived from endocrine part of pancreas are benign. Pancreatitis, an inflammation of the pancreatic tissues, is caused by excessive alcohol consumption, the bile duct obstruction by gallstones, and the premature activation of digestive enzymes in the pancreas. Hereditary pancreatic diseases, such as maturity-onset diabetes of the young and hereditary pancreatitis, can be a candidate for disease modeling using human pluripotent stem cells (hPSCs), due to their strong genetic influence. hPSC-derived pancreatic differentiation has been established for cell replacement therapy for diabetic patients and is robustly used for disease modeling. The disease modeling platform that allows interactions between immune cells and pancreatic cells is necessary to perform in-depth investigation of disease pathogenesis.

Phylogenetic lineage dynamics of global parainfluenza virus type 3 post-COVID-19 pandemic.

During the coronavirus disease 2019 (COVID-19) pandemic, outbreaks of parainfluenza virus type 3 (PIV-3) decreased due to infection control measures. However, a post-pandemic resurgence of PIV-3 has recently been observed. Nonetheless, the role of viral genetic epidemiology, possibly influenced by a genetic bottleneck effect, remains unexplored. We investigated the phylogenetic structure of the publicly available PIV-3 whole-genome and hemagglutinin-neuraminidase (HN) gene sequences spanning the last 65 years, including the COVID-19 pandemic. Sequences were retrieved from the nucleotide database of the National Center for Biotechnology Information using the search term "Human respirovirus 3." Sequence subsets covering all six genes of PIV-3 or the HN gene were designated as the whole-genome and HN surveillance data sets, respectively. Using these data sets, we constructed maximum-likelihood phylogenetic trees and performed a time-scaled analysis using a Bayesian SkyGrid coalescent prior. A total of 455 whole-genome and 1,139 HN gene sequences were extracted, revealing 10 and 11 distinct lineages, respectively, with >98% concurrence in lineage assignments. During the 2020 COVID-19 pandemic, only three single-lineage clusters were identified in Japan, Korea, and the USA. The inferred year of origin for PIV-3 was 1938 (1903-1963) for the whole-genome data set and 1955 (1930-1963) for the HN gene data set. Our study suggests that PIV-3 epidemics in the post-COVID era are likely influenced by a pandemic-driven bottleneck phenomenon and supports previous hypotheses suggesting s that PIV-3 originated during the early half of the 20th century.IMPORTANCEUsing publicly available parainfluenza virus type 3 (PIV-3) whole-genome sequences, we estimated that PIV-3 originated during the 1930s, consistent with previous hypotheses. Lineage typing and time-scaled phylogenetic analysis revealed that PIV-3 experienced a bottleneck phenomenon in Korea and the USA during the coronavirus disease 2019 pandemic. We identified the conservative hemagglutinin-neuraminidase gene as a viable alternative marker in long-term epidemiological studies of PIV-3 when whole-genome analysis is limited.

Optical grade transformation of monolayer transition metal dichalcogenides via encapsulation annealing.

Monolayer transition metal dichalcogenides (TMDs) have emerged as highly promising candidates for optoelectronic applications due to their direct band gap and strong light-matter interactions. However, exfoliated TMDs have demonstrated optical characteristics that fall short of expectations, primarily because of significant defects and associated doping in the synthesized TMD crystals. Here, we report the improvement of optical properties in monolayer TMDs of MoS2, MoSe2, WS2, and WSe2, by hBN-encapsulation annealing. Monolayer WSe2 showed 2000% enhanced photoluminescence quantum yield (PLQY) and 1000% increased lifetime after encapsulation annealing at 1000 °C, which are attributed to dominant radiative recombination of excitons through dedoping of monolayer TMDs. Furthermore, after encapsulation annealing, the transport characteristics of monolayer WS2 changed from n-type to ambipolar, along with an enhanced hole transport, which also support dedoping of annealed TMDs. This work provides an innovative approach to elevate the optical grade of monolayer TMDs, enabling the fabrication of high-performance optoelectronic devices.

Reduced Defect Density in MOCVD-Grown MoS2 by Manipulating the Precursor Phase.

Advancements in the synthesis of large-area, high-quality two-dimensional transition metal dichalcogenides such as MoS2 play a crucial role in the development of future electronic and optoelectronic devices. The presence of defects formed by sulfur vacancies in MoS2 results in low photoluminescence emission and imparts high n-type doping behavior, thus substantially affecting material quality. Herein, we report a new method in which single-phase (liquid) precursors are used for the metal-organic chemical vapor deposition (MOCVD) growth of a MoS2 film. Furthermore, we fabricated a high-performance photodetector (PD) and achieved improved photoresponsivity and faster photoresponse in the spectral range 405-637 nm compared to those of PDs fabricated by the conventional MOCVD method. In addition, the fabricated MoS2 thin film showed a threshold voltage shift in the positive gate bias direction owing to the reduced number of S vacancy defects in the MoS2 lattice. Thus, our method significantly improved the synthesis of monolayer MoS2 and can expand the application scope of high-quality, atomically thin materials in large-scale electronic and optoelectronic devices.

1D Magnetic MX3 Single-Chains (M = Cr, V and X = Cl, Br, I).

Magnetic materials in reduced dimensions are not only excellent platforms for fundamental studies of magnetism, but they play crucial roles in technological advances. The discovery of intrinsic magnetism in monolayer 2D van der Waals systems has sparked enormous interest, but the single-chain limit of 1D magnetic van der Waals materials has been largely unexplored. This paper reports on a family of 1D magnetic van der Waals materials with composition MX3 (M = Cr, V, and X = Cl, Br, I), prepared in fully-isolated fashion within the protective cores of carbon nanotubes. Atomic-resolution scanning transmission electron microscopy identifies unique structures that differ from the well-known 2D honeycomb lattice MX3 structure. Density functional theory calculations reveal charge-driven reversible magnetic phase transitions.

Low-temperature growth of MoS2 on polymer and thin glass substrates for flexible electronics.

Recent advances in two-dimensional semiconductors, particularly molybdenum disulfide (MoS2), have enabled the fabrication of flexible electronic devices with outstanding mechanical flexibility. Previous approaches typically involved the synthesis of MoS2 on a rigid substrate at a high temperature followed by the transfer to a flexible substrate onto which the device is fabricated. A recurring drawback with this methodology is the fact that flexible substrates have a lower melting temperature than the MoS2 growth process, and that the transfer process degrades the electronic properties of MoS2. Here we report a strategy for directly synthesizing high-quality and high-crystallinity MoS2 monolayers on polymers and ultrathin glass substrates (thickness ~30 µm) at ~150 °C using metal-organic chemical vapour deposition. By avoiding the transfer process, the MoS2 quality is preserved. On flexible field-effect transistors, we achieve a mobility of 9.1 cm2 V-1 s-1 and a positive threshold voltage of +5 V, which is essential for reducing device power consumption. Moreover, under bending conditions, our logic circuits exhibit stable operation while phototransistors can detect light over a wide range of wavelengths from 405 nm to 904 nm.

Type-II Red Phosphorus: Wavy Packing of Twisted Pentagonal Tubes.

Elemental phosphorus exhibits fascinating structural varieties and versatile properties. The unique nature of phosphorus bonds can lead to the formation of extremely complex structures, and detailed structural information on some phosphorus polymorphs is yet to be investigated. In this study, we investigated an unidentified crystalline phase of phosphorus, type-II red phosphorus (RP), by combining state-of-the-art structural characterization techniques. Electron diffraction tomography, atomic-resolution scanning transmission electron microscopy (STEM), powder X-ray diffraction, and Raman spectroscopy were concurrently used to elucidate the hidden structural motifs and their packing in type-II RP. Electron diffraction tomography, performed using individual crystalline nanowires, was used to identify a triclinic unit cell with volume of 5330 Å3 , which is the largest unit cell for elemental phosphorus crystals up to now and contains approximately 250 phosphorus atoms. Atomic-resolution STEM imaging, which was performed along different crystal-zone axes, confirmed that the twisted wavy tubular motif is the basic building block of type-II RP. Our study discovered and presented a new variation of building blocks in phosphorus, and it provides insights to clarify the complexities observed in phosphorus as well as other relevant systems.

Tuning the Sharing Modes and Composition in a Tetrahedral GeX2 (X = S, Se) System via One-Dimensional Confinement.

The packing and connectivity of tetrahedral units are central themes in the structural and electronic properties of a host of solids. Here, we report one-dimensional (1D) chains of GeX2 (X = S or Se) with modification of the tetrahedral connectivity at the single-chain limit. Precise tuning of the edge- and corner-sharing modes between GeX2 blocks is achieved by diameter-dependent 1D confinement inside a carbon nanotube. Atomic-resolution scanning transmission electron microscopy directly confirms the existence of two distinct types of GeX2 chains. Density functional theory calculations corroborate the diameter-dependent stability of the system and reveal an intriguing electronic structure that sensitively depends on tetrahedral connectivity and composition. GeS2(1-x)Se2x compound chains are also realized, which demonstrate the tunability of the system's semiconducting properties through composition engineering.

Population-level impacts of antibiotic usage on the human gut microbiome.

The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.

Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets.

Research on the gut microbiota in irritable bowel syndrome (IBS) shows discordant results due to inconsistent study designs or small sample sizes. This study aimed to characterize how gut microbiota in IBS patients differs from that in healthy controls by performing a case-control study and cross- and mega-cohort analysis. Multiple publicly shared data sets were examined by using a unified analytical approach. We performed 16S rRNA gene (V3-4) sequencing and taxonomic profiling of the gut bacterial communities. Fecal samples from children with IBS (n = 19) and age-matched healthy controls (n = 24) were used. Next, we analyzed 10 separate data sets using a unified data-processing and analytical approach. In total, 567 IBS patients and 487 healthy controls were examined. In our data sets, no significant differences existed in stool α-diversity between IBS patients and healthy controls. After combining all the data sets using a unified data-processing method, we found significantly lower α-diversity in IBS patients than in healthy controls. In addition, the relative abundance of 21 bacterial species differed between the IBS patients and healthy participants. Although the causal relationship is uncertain, gut bacterial dysbiosis is associated with IBS. Further functional studies are needed to assess whether the change in gut microorganisms contributes to the development of IBS. IMPORTANCE Research on the gut bacteria in irritable bowel syndrome (IBS) shows discordant results due to inconsistent study designs or small sample sizes. To overcome these issues, we analyzed microbiota of 567 IBS patients and 487 healthy people from 10 shared data sets using a unified method. We demonstrated that gut bacteria are less diverse in IBS patients than in healthy people. In addition, the abundance of 21 bacterial species is different between the two groups. Altered bacterial balance, called dysbiosis, has been reported in several disease states. Although the causal relationship is uncertain, gut bacterial dysbiosis also seems to be associated with IBS.

Cytoplasmic molecular chaperones in Pseudomonas species.

Pseudomonas is widespread in various environmental and host niches. To promote rejuvenation, cellular protein homeostasis must be finely tuned in response to diverse stresses, such as extremely high and low temperatures, oxidative stress, and desiccation, which can result in protein homeostasis imbalance. Molecular chaperones function as key components that aid protein folding and prevent protein denaturation. Pseudomonas, an ecologically important bacterial genus, includes human and plant pathogens as well as growth-promoting symbionts and species useful for bioremediation. In this review, we focus on protein quality control systems, particularly molecular chaperones, in ecologically diverse species of Pseudomonas, including the opportunistic human pathogen Pseudomonas aeruginosa, the plant pathogen Pseudomonas syringae, the soil species Pseudomonas putida, and the psychrophilic Pseudomonas antarctica.

Imaging Findings of Peripheral Arterial Disease on Lower-Extremity CT Angiography Using a Virtual Monoenergetic Imaging Algorithm.

Peripheral arterial disease (PAD) is common in elderly patients. Lower-extremity CT angiography (LE-CTA) can be useful for detecting PAD and planning its treatment. PAD can also be accurately evaluated on reconstructed monoenergetic images (MEIs) from low kiloelectron volt (keV) to high keV images using dual-energy CT. Low keV images generally provide higher contrast than high keV images but also feature more severe image noise. The noise-reduced virtual MEI reconstruction algorithm, called the Mono+ technique, was recently introduced to overcome such image noise. Therefore, this pictorial review aimed to present the imaging findings of PAD on LE-CTA and compare low and high keV images with those subjected to the Mono+ technique. We found that, in many cases, the overall and segmental image qualities were better and metal artifacts and venous contamination were decreased in the high keV images.

Genomic and evolutionary study from SARS-CoV-2 virus isolates from Bangladesh during the early stage of pandemic strongly correlate with European origin and not with China.

The goal of this study was to identify the genomic variants and determine molecular epidemiology of SARS-CoV-2 virus during the early pandemic stage in Bangladesh. Viral RNA was extracted, converted to cDNA, and amplified using Ion AmpliSeq™ SARS-CoV-2 Research Panel. 413 unique mutants from 151 viral isolates were identified. 80% of cases belongs to 8 mutants: 241C toT, 1163A toT, 3037C toT, 14408C toT, 23403A toG, 28881G toA, 28,882 G toA, and 28883G toC. Observed dominance of GR clade variants that have strong presence in Europe, suggesting European channel a possible entry route. Among 37 genomic mutants significantly associated with clinical symptoms, 3916CtoT (associated with sore-throat), 14408C to T (associated with cough-protection), 28881G to A, 28882G to A, and 28883G to C (associated with chest pain) were notable. These findings may inform future research platforms for disease management and epidemiological study.

Colistin-degrading proteases confer collective resistance to microbial communities during polymicrobial infections.

BACKGROUND: The increasing prevalence of resistance against the last-resort antibiotic colistin is a significant threat to global public health. Here, we discovered a novel colistin resistance mechanism via enzymatic inactivation of the drug and proposed its clinical importance in microbial communities during polymicrobial infections. RESULTS: A bacterial strain of the Gram-negative opportunistic pathogen Stenotrophomonas maltophilia capable of degrading colistin and exhibiting a high-level colistin resistance was isolated from the soil environment. A colistin-degrading protease (Cdp) was identified in this strain, and its contribution to colistin resistance was demonstrated by growth inhibition experiments using knock-out (Δcdp) and complemented (Δcdp::cdp) mutants. Coculture and coinfection experiments revealed that S. maltophilia carrying the cdp gene could inactivate colistin and protect otherwise susceptible Pseudomonas aeruginosa, which may seriously affect the clinical efficacy of the drug for the treatment of cystic fibrosis patients with polymicrobial infection. CONCLUSIONS: Our results suggest that Cdp should be recognized as a colistin resistance determinant that confers collective resistance at the microbial community level. Our study will provide vital information for successful clinical outcomes during the treatment of complex polymicrobial infections, particularly including S. maltophilia and other colistin-susceptible Gram-negative pathogens such as P. aeruginosa. Video abstract.

Impact of Wildfire Smoke Exposure on Health in Korea.

PURPOSE: The characteristic topography and climate often affect the occurrence of large-scale wildfires in the Eastern Gangwon-do region of Korea. However, there are no studies on the health effects of these wildfires in Korea. This study aimed to analyze the differences in medical use between a wildfire-affected area and an adjacent non-affected area before and after a wildfire in 2019 in Gangwon-do, Korea. MATERIALS AND METHODS: We used medical usage data from the Korean National Health Insurance Corporation. Rates of medical use were determined for citizens of a wildfire-affected area in the Eastern Yeongdong region and a non-affected area in the Western Yeongseo region. Logistic regression analysis was performed considering an increase in medical use per individual as a dependent variable; age, sex, income, smoking, drinking, and exercise were included as confounding variables. RESULTS: The odds ratio for medical use in Yeongdong region increased significantly after 3 days, 3 months, and 1 year after a fire occurred, compared with Yeongseo region. CONCLUSION: The results of this study confirmed that the use of medical care increased for residents of a wildfire-affected area, compared with those of an adjacent non-affected area. This is the first study on the relationship between wildfires and inpatient medical use in Korea.

Atomically Sharp, Closed Bilayer Phosphorene Edges by Self-Passivation.

Two-dimensional crystals' edge structures not only influence their overall properties but also dictate their formation due to edge-mediated synthesis and etching processes. Edges must be carefully examined because they often display complex, unexpected features at the atomic scale, such as reconstruction, functionalization, and uncontrolled contamination. Here, we examine atomic-scale edge structures and uncover reconstruction behavior in bilayer phosphorene. We use in situ transmission electron microscopy (TEM) of phosphorene/graphene specimens at elevated temperatures to minimize surface contamination and reduce e-beam damage, allowing us to observe intrinsic edge configurations. The bilayer zigzag (ZZ) edge was found to be the most stable edge configuration under e-beam irradiation. Through first-principles calculations and TEM image analysis under various tilting and defocus conditions, we find that bilayer ZZ edges undergo edge reconstruction and so acquire closed, self-passivated edge configurations. The extremely low formation energy of the closed bilayer ZZ edge and its high stability against e-beam irradiation are confirmed by first-principles calculations. Moreover, we fabricate bilayer phosphorene nanoribbons with atomically sharp closed ZZ edges. The identified bilayer ZZ edges will aid in the fundamental understanding of the synthesis, degradation, reconstruction, and applications of phosphorene and related structures.

STEM Image Analysis Based on Deep Learning: Identification of Vacancy Defects and Polymorphs of MoS2.

Scanning transmission electron microscopy (STEM) is an indispensable tool for atomic-resolution structural analysis for a wide range of materials. The conventional analysis of STEM images is an extensive hands-on process, which limits efficient handling of high-throughput data. Here, we apply a fully convolutional network (FCN) for identification of important structural features of two-dimensional crystals. ResUNet, a type of FCN, is utilized in identifying sulfur vacancies and polymorph types of MoS2 from atomic resolution STEM images. Efficient models are achieved based on training with simulated images in the presence of different levels of noise, aberrations, and carbon contamination. The accuracy of the FCN models toward extensive experimental STEM images is comparable to that of careful hands-on analysis. Our work provides a guideline on best practices to train a deep learning model for STEM image analysis and demonstrates FCN's application for efficient processing of a large volume of STEM data.

Complete Multipartite Genome Sequence of the Cupriavidus basilensis Type Strain, a 2,6-Dichlorophenol-Degrading Bacterium.

We report the complete 8.94-Mb genome sequence of the type strain of Cupriavidus basilensis (DSM 11853T = CCUG 49340T = RK1T), formed by two chromosomes and six putative plasmids, which offers insights into its chloroaromatic-biodegrading capabilities.

QSER1 protects DNA methylation valleys from de novo methylation.

DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to regulate the methylation landscape remains a central question. Using a knockin DNA methylation reporter, we performed a genome-wide CRISPR-Cas9 screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene, QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate genetic and biochemical interactions of QSER1 and TET1, supporting their cooperation to safeguard transcriptional and developmental programs from DNMT3-mediated de novo methylation.