Potential Contributions of Human Endogenous Retroviruses in Innate Immune Memory.

The phenomenon wherein innate immune cells adopt long-term inflammatory phenotypes following the first stimuli is named trained immunity and can improve host defense against infections. Transcriptional and epigenetic reprogramming are critical mechanisms of trained immunity; however, the regulatory networks are not entirely clear at present. The human endogenous retroviruses (HERVs) provide large amounts of transcriptional regulators in the regulatory pathways. In this study, we analyzed published large omics data to explore the roles of such "dark matter" of the human genome in trained and tolerant macrophages. We collected 80 RNA sequencing data and 62 sequencing data to detect histone modifications and active regulatory regions from nine published studies on trained and tolerant macrophages. By analyzing the characteristics of transcription and epigenetic modification of HERVs, as well as their association with gene expression, we found that 15.3% of HERVs were transcribed nonrandomly from noncoding regions and enriched in specific HERV families and specific chromosomes, such as chromosomes 11, 15, 17, and 19, and they were highly related with the expression of adjacent genes. We found that 295 differentially expressed HERVs are located in 50-kbp flanking regions of 142 differentially expressed genes. We found epigenetic changes of these HERVs and that overlap with predicted enhancers and identified 35 enhancer-like HERVs. The related genes were highly involved in the activation and inflammatory responses, such as the TLR pathway. Other pathways including phosphoinositide signaling and transport of folate and K+ might be also related with trained immunity, which require further study. These results demonstrated that HERVs might play important roles in trained immunity.

Heptacyclic aromatic hydrocarbon isomers with two azulene units fused.

Azulene, known for its unique electronic properties and structural asymmetry, serves as a promising building block for the design of novel non-benzenoid polycyclic aromatic hydrocarbons (PAHs). Herein, we present the synthesis, characterization, and physical properties of three diazulene-fused heptacyclic aromatic hydrocarbons, 8,17-dioctyldiazuleno[2,1-a:2',1'-h]anthracene (trans configuration), 16,18-dioctyldiazuleno[2,1-a:1',2'-j]anthracene (cis configuration) and 3,18-dioctyldiazuleno[2,1-a:1',2'-i]phenanthrene (zigzag configuration). Three compounds are configurational isomers with different fusing patterns of aromatic rings. All three isomers exhibit pronounced aromaticity, as revealed by nuclear magnetic resonance spectroscopy and theoretical calculations. They exhibit characteristics of both azulene and benzenoid PAHs and are much more stable than their all-benzene analogues. The optical and electrochemical properties of these three isomers were investigated through UV-vis absorption spectra and cyclic voltammetry, revealing distinct behaviors influenced by their molecular configurations. Furthermore, the isomer in trans configuration exhibits promising semiconducting properties with a hole mobility of up to 0.22 cm2 V-1 s-1, indicating its potential in organic electronics applications.

An increased prevalence of carbapenem-resistant hypervirulent Klebsiella pneumoniae associated with the COVID-19 pandemic.

BACKGROUND: Klebsiella pneumoniae (Kp) is a common community-acquired and nosocomial pathogen. Carbapenem-resistant and hypervirulent (CR-hvKp) variants can emerge rapidly within healthcare facilities and impacted by other infectious agents such as COVID-19 virus. METHODS: To understand the impact of COVID-19 virus on the prevalence of CR-hvKp, we accessed Kp genomes with corresponding metadata from GenBank. Sequence types (STs), antimicrobial resistance genes, and virulence genes, and those scores and CR-hvKp were identified. We analyzed population diversity and phylogenetic characteristics of five most common STs, measured the prevalence of CR-hvKp, identified CR-hvKp subtypes, and determined associations between carbapenem resistance gene subtypes with STs and plasmid types. These variables were compared pre- and during the COVID-19 pandemic. FINDINGS: The proportion of CR-hvKp isolates increased within multiple STs in different continents during the COVID-19 pandemic and persistent CR-hvKp subtypes were found in common STs. blaKPC was dominant in CG258, blaKPC-2 was detected in 97 % of the ST11 CR-hvKp, blaNDM subtypes were prominent in ST147 (87.4 %) and ST307 (70.8 %); blaOXA-48 and its subtypes were prevalent in ST15 (80.5 %). The possession of carbapenemase genes was different among subclades from different origins in different periods of time within each ST. IncFIB/IncHI1B hybrid plasmids contained virulence genes and carbapenemase genes and were predominant in ST147 (67.37 %) and ST307 (56.25 %). INTERPRETATION: The prevalence of CR-hvKp increased during the COVID-19 pandemic, which was evident by an increase in local endemic clones. This process was facilitated by the convergence of plasmids containing carbapenemase genes and virulence genes. These findings have implications for the appropriate use of antimicrobials and infection prevention and control during outbreaks of respiratory viruses and pandemic management.

Self-assembled metal-polyphenolic based multifunctional nanomedicine to improve therapy treatment of pancreatic cancer by inhibition of glutamine metabolism.

Cancer poses a significant threat to human health and life. Chemotherapy, immunotherapy and chemodynamic therapy (CDT) are effective treatments for cancer. However, the presence of metabolic reprogramming via glutamine in tumor cells limits their therapeutic effectiveness. Herein, we propose an effective assembly strategy to synthesize a novel metal-polyphenolic based multifunctional nanomedicine (Fe-DBEF) containing Pluronic F127 stable ferric ion crosslinked epigallocatechin gallate (EGCG) nanoparticles loaded with GLS1 inhibitor bis-2-(5-phenylacetamino-1,3,4-thiadiazole-2-yl) ethyl sulfide (BPTES) and chemotherapy drug doxorubicin (DOX). Our study demonstrates that Fe-DBEF nanomedicine exhibits high efficiency anti-proliferation properties in pancreatic cancer through a combination of in vitro cell experiments, human organoid experiments and KPC animal experiments. Notably, Fe-DBEF nanomedicine can reduce the production of glutathione (GSH) in tumor cells, thereby reducing their resistance to ROS therapy. Additionally, excessive ROS production also aggravates DNA damage caused by DOX, synergistically sensitizing chemotherapy and promoting apoptosis for efficient treatment of pancreatic cancer. Overall, our findings suggest that inhibiting glutamine metabolism to increase the sensitivity of chemotherapy/CDT using metal-polyphenolic based multifunctional nanomedicine provides a promising combination of multiple therapeutic means for treating pancreatic cancer.

Reflections on appropriately liberalizing ART for groups requiring special attention in China.

PURPOSE: The continuous advancement of assisted reproductive technologies (ART) and the evolving attitudes towards marriage and fertility among the general public have led to an increasing number of groups requiring special attention (GRSA) desiring to fulfill their reproductive needs through these technologies. These groups include single women (including single mothers without children), same-sex couples, and women in high-risk occupations, among others. The purpose of this paper is to explore the feasibility of appropriately liberalizing ART for GRSA. METHODS: This paper discusses the advantages of a moderate liberalization of ART for GRSA from two perspectives: a theoretical basis and a practical significance level. It also analyzes the current constraints on liberalizing ART and presents suggestions for moderate liberalization. RESULTS: The moderate liberalization of ART can provide technical support for respecting and realizing the reproductive freedom of GRSA, which has certain theoretical and practical significance. However, it is also subject to constraints. CONCLUSION: We call for government to keep pace with the times, based on the current stage of political, economic, and social development, to further recognize and protect citizens' reproductive rights, prioritize the practical needs of the public, and explore policies and regulations for gradually loosening the restrictions on ART for GRSA.

Simultaneous improvement of the sensitivity and resolution of CPT magnetometers based on phase delay and differential method.

We report a method to enhance the sensitivity of coherent population trapping (CPT) magnetometers using a combination of left-handed and right-handed circularly polarized light phase-delay detection and a differential detection scheme. The approach can achieve a four third-fold enhancement of the CPT dispersion signal slope and a three-fold reduction in noises. The proposed method experimentally exhibits a four third-fold magnetic field resolution enhancement in CPT open-loop measurements, and the differential method could achieve a sensitivity of 1 p T/H z at 10 Hz and a sensitivity of 0.4 p T/H z at 50-100 Hz in the CPT closed-loop measurement, which is a four-fold sensitivity enhancement compared to the single-transmitted CPT magnetometer.

Green pepper fruits counting based on improved DeepSort and optimized Yolov5s.

Introduction: Green pepper yield estimation is crucial for establishing harvest and storage strategies. Method: This paper proposes an automatic counting method for green pepper fruits based on object detection and multi-object tracking algorithm. Green pepper fruits have colors similar to leaves and are often occluded by each other, posing challenges for detection. Based on the YOLOv5s, the CS_YOLOv5s model is specifically designed for green pepper fruit detection. In the CS_YOLOv5s model, a Slim-Nick combined with GSConv structure is utilized in the Neck to reduce model parameters while enhancing detection speed. Additionally, the CBAM attention mechanism is integrated into the Neck to enhance the feature perception of green peppers at various locations and enhance the feature extraction capabilities of the model. Result: According to the test results, the CS_YOLOv5s model of mAP, Precision and Recall, and Detection time of a single image are 98.96%, 95%, 97.3%, and 6.3 ms respectively. Compared to the YOLOv5s model, the Detection time of a single image is reduced by 34.4%, while Recall and mAP values are improved. Additionally, for green pepper fruit tracking, this paper combines appearance matching algorithms and track optimization algorithms from SportsTrack to optimize the DeepSort algorithm. Considering three different scenarios of tracking, the MOTA and MOTP are stable, but the ID switch is reduced by 29.41%. Based on the CS_YOLOv5s model, the counting performance before and after DeepSort optimization is compared. For green pepper counting in videos, the optimized DeepSort algorithm achieves ACP (Average Counting Precision), MAE (Mean Absolute Error), and RMSE (Root Mean Squared Error) values of 95.33%, 3.33, and 3.74, respectively. Compared to the original algorithm, ACP increases by 7.2%, while MAE and RMSE decrease by 6.67 and 6.94, respectively. Additionally, Based on the optimized DeepSort, the fruit counting results using YOLOv5s model and CS_YOLOv5s model were compared, and the results show that using the better object detector CS_YOLOv5s has better counting accuracy and robustness.

Integrated optical rotation detection scheme for chip-scale atomic magnetometer empowered by silicon-rich SiNx metalens.

High-performance atomic magnetometers (AMs) rely on the measurement of optical rotation, which requires a set of bulky polarization optics that limit their applications in scenarios where portability and compactness are necessary. In this study, a miniaturized AM is constructed based on a cubic 87Rb vapor cell and monolithic metalens, which provides an integrated scheme to achieve optical rotation detection induced by the circular birefringence of polarized atoms. The designed metalens achieves polarization splitting with deflection angles of ±10∘ and focusing with efficiencies of approximately 30% for orthogonal linear polarizations. The sensitivity of our compact device is ∼30 fT/Hz1/2 with a dynamic range of around ±1.45 nT. We envision that the presented approach paves the way for the chip integration of emerging atomic devices, which are in demand for applications such as biomagnetic imaging and portable atomic gyroscopes.

DEAD-Box Helicase 17 exacerbates non-alcoholic steatohepatitis via transcriptional repression of cyp2c29, inducing hepatic lipid metabolism disorder and eliciting the activation of M1 macrophages.

OBJECTIVE: Our study was to elucidate the role of RNA helicase DEAD-Box Helicase 17 (DDX17) in NAFLD and to explore its underlying mechanisms. METHODS: We created hepatocyte-specific Ddx17-deficient mice aim to investigate the impact of Ddx17 on NAFLD induced by a high-fat diet (HFD) as well as methionine and choline-deficient l-amino acid diet (MCD) in adult male mice. RNA-seq and lipidomic analyses were conducted to depict the metabolic landscape, and CUT&Tag combined with chromatin immunoprecipitation (ChIP) and luciferase reporter assays were conducted. RESULTS: In this work, we observed a notable increase in DDX17 expression in the livers of patients with NASH and in murine models of NASH induced by HFD or MCD. After introducing lentiviruses into hepatocyte L02 for DDX17 knockdown or overexpression, we found that lipid accumulation induced by palmitic acid/oleic acid (PAOA) in L02 cells was noticeably weakened by DDX17 knockdown but augmented by DDX17 overexpression. Furthermore, hepatocyte-specific DDX17 knockout significantly alleviated hepatic steatosis, inflammatory response and fibrosis in mice after the administration of MCD and HFD. Mechanistically, our analysis of RNA-seq and CUT&Tag results combined with ChIP and luciferase reporter assays indicated that DDX17 transcriptionally represses Cyp2c29 gene expression by cooperating with CCCTC binding factor (CTCF) and DEAD-Box Helicase 5 (DDX5). Using absolute quantitative lipidomics analysis, we identified a hepatocyte-specific DDX17 deficiency that decreased lipid accumulation and altered lipid composition in the livers of mice after MCD administration. Based on the RNA-seq analysis, our findings suggest that DDX17 could potentially have an impact on the modulation of lipid metabolism and the activation of M1 macrophages in murine NASH models. CONCLUSION: These results imply that DDX17 is involved in NASH development by promoting lipid accumulation in hepatocytes, inducing the activation of M1 macrophages, subsequent inflammatory responses and fibrosis through the transcriptional repression of Cyp2c29 in mice. Therefore, DDX17 holds promise as a potential drug target for the treatment of NASH.

ST218 Klebsiella pneumoniae became a high-risk clone for multidrug resistance and hypervirulence.

BACKGROUND: The occurrence of multidrug-resistant and hypervirulent Klebsiella pneumoniae (MDR-hvKp) worldwide poses a great challenge for public health. Few studies have focused on ST218 MDR-hvKp. METHODS: Retrospective genomic surveillance was conducted at the Peking University Third Hospital from 2017 and clinical information was obtained. To understand genomic and microbiological characteristics, antimicrobial susceptibility testing, plasmid conjugation and stability, biofilm formation, serum killing, growth curves and whole-genome sequencing were performed. We also assessed the clinical and microbiological characteristics of ST218 compared with ST23. RESULTS: A total of eleven ST218 Kp isolates were included. The most common infection type was lower respiratory tract infection (72.7%, 8/11) in our hospital, whereas ST23 hvKp (72.7%, 8/11) was closely associated with bloodstream infection. Notably, nosocomial infections caused by ST218 (54.5%, 6/11) was slightly higher than ST23 (36.4%, 4/11). All of the ST218 and ST23 strains presented with the virulence genes combination of iucA + iroB + peg344 + rmpA + rmpA2. Interestingly, the virulence score of ST218 was lower than ST23, whereas one ST218 strain (pPEKP3107) exhibited resistance to carbapenems, cephalosporins, ß-lactamase/inhibitors and quinolones and harbored an ~ 59-kb IncN type MDR plasmid carrying resistance genes including blaNDM-1, dfrA14 and qnrS1. Importantly, blaNDM-1 and qnrS1 were flanked with IS26 located within the plasmid that could successfully transfer into E. coli J53. Additionally, PEKP2044 harbored an ~ 41-kb resistance plasmid located within tetA indicating resistance to doxycycline. CONCLUSION: The emergence of blaNDM-1 revealed that there is great potential for ST218 Kp to become a high-risk clone for MDR-hvKp, indicating the urgent need for enhanced genomic surveillance.

Dynamic within-host cefiderocol heteroresistance caused by blaSHV-12 amplification in pandrug-resistant and hypervirulent Klebsiella pneumoniae sequence type 11.

AIMS: Although cefiderocol (FDC) is not prescribed in China, FDC-resistant pandrug-resistant hypervirulent Klebsiella pneumoniae (PDR-hvKp) is emerging. In this study, we performed FDC susceptibility testing of clinical Kp isolates to explore the prevalence of FDC-resistant isolates and the mechanism of FDC-resistance. METHODS: We retrospectively selected 151 carbapenem-resistant Kp isolates to assess FDC susceptibility. Seven isolates harboring blaSHV-12 from two patients were enrolled for whole-genome sequencing. The antimicrobial resistance, virulence, blaSHV-12 expression, and fitness costs in different media were examined. The amplification of blaSHV-12 was further investigated by qPCR and long-read sequencing. RESULTS: The 151 isolates showed a low MIC50/MIC90 (1/4 mg/L) of FDC. The seven isolates were ST11 PDR-hvKp, and two represented FDC-resistance (MIC=32 mg/L). The IncR/IncFII plasmids of two FDC-resistant isolates harbored 6 and 15 copies of blaSHV-12, whereas four FDC-susceptible isolates carried one copy and one harbored three copies. These blaSHV-12 genes concatenated together and were located within the same 7.3 kb fragment flanked by IS26, which contributed to the increased expression and FDC resistance without fitness costs. The amplification of blaSHV-12 and FDC resistance could be induced by FDC in vitro and reversed during continuous passage. CONCLUSIONS: The amplification of blaSHV-12 and the consequent dynamic within-host heteroresistance are important concerns for the rational application of antibiotics. Long-read sequencing might be a superior way to detect resistance gene amplification rapidly and accurately.

USP11 potentiates HGF/AKT signaling and drives metastasis in hepatocellular carcinoma.

USP11 is a member of the ubiquitin-specific protease family and plays a crucial role in tumor progression in various cancers. However, the precise mechanism by which USP11 promotes EMT and metastasis in hepatocellular carcinoma (HCC) is not fully understood. In this study, we demonstrated that the USP11 expression was dramatically upregulated in HCC tissues and cell lines. Increased USP11 expression was closely associated with tumor number, vascular invasion, and poor prognosis. Functional experiments demonstrated that USP11 markedly promoted metastasis and EMT in HCC via induction of the transcription factor Snail. Mechanistically, USP11 interacted with and deubiquitinated eEF1A1 on Lys439, thereby inhibiting its ubiquitin-mediated degradation. Subsequently, the elevated expression of eEF1A1 resulted in its binding to SP1, which in turn drove the binding of SP1 to its target HGF gene promoter to increase its transcription. This led to an enhanced expression of HGF and the activation of the downstream PI3K/AKT signaling pathway. We demonstrated that USP11 promotes EMT and metastasis in HCC via eEF1A1/SP1/HGF dependent-EMT. Our findings suggest that the USP11/ eEF1A1/SP1/HGF axis contributes to metastasis in HCC, and therefore, could be considered as a potential therapeutic target for the treatment of HCC.

Dynamic evolution and transmission of a blaNDM-1-bearing fusion plasmid in a clinical Escherichia coli.

Plasmids are the main driving forces for the rapid dissemination of blaNDM-1. In recent years, blaNDM-1-carrying fusion plasmids have been frequently reported. However, the evolutionary patterns of blaNDM-1-carrying fusion plasmids remain largely unknown. Herein, we reported a blaNDM-1-bearing fusion plasmid pZX35-269k possessing IncFII and IncA/C2 replicons from clinical ST349 E. coli 13ZX35. The backbone of pZX35-269k was structurally unstable, which was manifested in different types of structural dissociation during conjugation and passage, thereby forming various daughter plasmids. Moreover, the same events were observed in the clinical setting as well. We found that pZX35-269k exhibited highly identical to two plasmids (pZX30-70k and pZX30-192k) in 13ZX30, both of which were isolated from the same hospital. Sequence analysis highlighted that two plasmids in 13ZX30 evolved from pZX35-269k through homologous recombination of a 4856-bp fragment. Collectively, this study confirmed the transmission and structural evolution of a blaNDM-1-bearing fusion plasmid in both laboratory and clinical settings, and provided clear evidence of plasmid spread and evolution in clinical settings. Such versatile plasmids may represent a potential risk for the public health.

Senkyunolide I ameliorates thoracic aortic aneurysm and dissection in mice via inhibiting the oxidative stress and apoptosis of endothelial cells.

BACKGROUND: Thoracic aortic aneurysm and aortic dissection (TAAD) is one of the most fatal cardiovascular diseases. Senkyunolide I (SEI) is a component of traditional Chinese medicine with remarkable anti-inflammatory properties and exhibits remarkable protective effects, but its impact on TAAD remains unclear. Our study aimed to explore the role of SEI in a murine model of TAAD and further explore the immunopharmacological mechanism. METHODS AND MATERIALS: The in vivo model were assessed using echocardiography, gross anatomy, and tissue staining. Western blot and immunofluorescence were performed to evaluate the effects of SEI in vivo and in vitro. A SEI solution injection containing 1 % dimethyl sulfoxide (DMSO) was administered intraperitoneally to the TAAD model group, while a normal saline injection comprising 1 % DMSO was administered to the sham group. RESULTS: SEI prevented TAAD formation induced by BAPN/Ang II and reduced the TAAD incidence in mice. SEI treatment significantly inhibited the degradation of collagen and elastin fibers in the extracellular matrix. Furthermore, it reduced the expression of inflammatory factors in the aortic intima. Western blot analysis revealed that SEI-treated mice showed a significant decrease in apoptosis-related protein levels in the aorta compared with the TAAD group. PI3K, Akt, and mTOR in the SEI treatment group were significantly lower than in the model group. SEI could also attenuate H2O2-induced Human umbilical vein endothelial cells (HUVECs) damage and reverse the decline in migrant cells. The apoptosis of HUVECs was considerably reduced by the SEI treatment. CONCLUSIONS: Conclusively, SEI may alleviate the progression of TAAD by suppressing the PI3K/Akt/NF-κB signaling pathway. The SEI's ability to inhibit inflammation and oxidative stress opens the way to restore the function of endothelial cells and vascular homeostasis, and thus to provide novel and promising options for the treatment of TAAD patients.

Thoracic aneurysm and dissection gene variants increase the risk of aortic-related adverse events in early-onset isolated Stanford type B aortic dissection after endovascular aortic repair.

Background: Researches on Marfan syndrome and Ehlers-Danlos syndrome leading to early-onset aortic dissection (AD) emphasize the importance of gene variants, but the genetic pathogenesis, clinical characteristics and outcomes of early-onset isolated Stanford type B aortic dissection (iTBAD) patients remain unclear and need to be further elucidated. Methods: Isolated type B AD patients with an onset age of less than 50 years were enrolled in this study. Whole exome sequencing (WES) was performed to detect 11 known thoracic aortic aneurysm and dissection (TAAD) gene variants. Clinical characteristics and outcomes were compared between patients with and without gene variants. Multivariate Cox regression analysis was performed to identify independent risk factors for aortic-related adverse events (ARAEs) after endovascular aortic repair. Results: A total of 37 patients were included. Ten patients carried 10 variants in five TAAD genes, four of whom carried pathogenic or likely pathogenic variants. Compared to patients without the variants, patients with variants had a lower incidence of hypertension (50.0% vs. 88.9%, P=0.021), a higher incidence of other vascular abnormalities (60.0% vs. 18.5%, P=0.038), all-cause mortality (40.0% vs. 3.7%, P=0.014) and aortic related mortality (30.0% vs. 3.7%, P=0.052). Multivariate analysis confirmed the presence of TAAD gene variants as the only independent risk factor for ARAEs [hazard ratio (HR) =4.00; 95% confidence interval (CI): 1.26-12.74; P=0.019]. Conclusions: Routine genetic testing is necessary for early-onset iTBAD patients. Individuals with a high risk of ARAEs can be identified by detecting TAAD gene variants, which is important for risk stratification and proper management.

Long-read metagenomic sequencing reveals that high-copy small plasmids shape the highly prevalent antibiotic resistance genes in animal fecal microbiome.

The emergence and prevalence of animal-derived antibiotic resistance genes (ARGs) pose a great threat to public health globally. Long-read metagenomic sequencing is increasingly being used to decipher the fate of environmental ARGs. However, the investigations of the distribution, co-occurrence patterns, and host information of animal-derived environmental ARGs with long-read metagenomic sequencing have received little attention. To cover the gap, we employed a novel QitanTech nanopore long-read metagenomic sequencing method to perform a comprehensive and systematic investigation of the microbial communities and antibiotic resistance profiles, as well as to analyze the host information and genetic structures of ARGs in the feces of laying hens. Our results showed that highly abundant and diverse ARGs were detected in the feces of different ages of laying hens, indicating that feeding animal feces was an important reservoir for the enrichment and maintenance of ARGs. The distribution pattern of chromosomal ARGs was more strongly associated with fecal microbial communities than plasmid-mediated ARGs. Further long-read host tracking analysis revealed that ARGs from Proteobacteria are commonly located on plasmids, whereas in Firmicutes, they are usually carried by chromosomes. Co-occurrence analysis displayed that co-selection phenomena of different ARGs were common occurrences and highly active insertion sequences (ISs) could result in the serious prevalence of many ARGs. Notably, small high-copy plasmids played a significant role in the dissemination of several ARGs, such as floR and tet(L), which could disturb the compositions of fecal ARGs. Overall, our findings significantly expand our knowledge of the comprehensive landscape of feeding animal feces resistome, which is important for the prevention and management of multi-drug resistant bacteria in laying hens.

[Application and Prospect of Nanopore Sequencing Technology in Etiological Diagnosis of Blood Stream Infection].

Blood stream infection (BSI),a blood-borne disease caused by microorganisms such as bacteria,fungi,and viruses,can lead to bacteremia,sepsis,and infectious shock,posing a serious threat to human life and health.Identifying the pathogen is central to the precise treatment of BSI.Traditional blood culture is the gold standard for pathogen identification,while it has limitations in clinical practice due to the long time consumption,production of false negative results,etc.Nanopore sequencing,as a new generation of sequencing technology,can rapidly detect pathogens,drug resistance genes,and virulence genes for the optimization of clinical treatment.This paper reviews the current status of nanopore sequencing technology in the diagnosis of BSI.

Prevalence and Genomic Characteristics of mcr-Positive Escherichia coli Strains Isolated from Humans, Pigs, and Foods in China.

Colistin is one of the last-resort antibiotics for treating infections caused by multidrug-resistant (MDR) Gram-negative bacteria. However, mcr genes conferring resistance to colistin have been widely identified, which is considered a global threat to public health. Here, we investigated the prevalence and characteristics of mcr-harboring Escherichia coli strains isolated from humans, animals, and foods in China by PCR, antimicrobial susceptibility testing, conjugation experiments, molecular typing, genome sequencing, and bioinformatics analysis. In total, 135 mcr-1-harboring E. coli isolates were acquired from 847 samples, and 6 isolates carried mcr-3. Among them, 131 isolates were MDR bacteria. Sixty-five resistance genes conferring resistance to multiple antimicrobials were identified in 135 isolates. The diverse pulsed-field gel electrophoresis (PFGE) patterns and sequence types (STs) of mcr-1-carrying isolates demonstrated that clonal dissemination was not the dominant mode of mcr-1 transmission. Seven types of plasmids were able to carry mcr-1 in this study, including IncI2, IncX4, IncHI2, p0111, IncY, and two hybrid plasmids. The genetic structures carrying mcr-1 of 60 isolates were successfully transferred into the recipient, including 25 IncI2 plasmids, 23 IncX4 plasmids, and an IncHI2 plasmid. mcr-1-pap2 was the dominant mcr-1-bearing structure, followed by ISApl1-mcr-1-pap2-ISApl1 (Tn6330) and ISApl1-mcr-1-pap2, among 7 mcr-1-bearing structures of 135 isolates. In conclusion, IncI2, IncX4, and IncHI2 plasmids were the major vectors spreading mcr-1 from different geographical locations and sources. The prevalence of Tn6330 may accelerate the transmission of mcr-1. Continuous surveillance of mcr-1 and variants in bacteria is vital for evaluating the public health risk posed by mcr genes. IMPORTANCE The spread of polymyxin-resistant Enterobacteriaceae poses a significant threat to public health and challenges the therapeutic options for treating infections on a global level. In this study, mcr-1-bearing ST10 E. coli was isolated from pigs, pork, and humans simultaneously, which demonstrated that ST10 E. coli was an important vehicle for the spread of mcr-1 among animals, foods, and humans. The high prevalence of mcr-1-positive E. coli strains in pigs and pork and the horizontal transmission of mcr-1-bearing plasmids in diverse E. coli strains suggest that pigs and pork are important sources of mcr-1-positive strains in humans and pose a potential threat to public health. Additional research on the prevalence and characteristics of mcr-1-positive E. coli is still required to facilitate early warning to improve polymyxin management in hospitals.

Insertion sequences mediate clinical ST34 monophasic Salmonella enterica serovar Typhimurium plasmid polymorphism.

Hybrid plasmids can combine the genetic elements of multiple plasmids, with the potential to carry a variety of antibiotic resistance genes and virulence genes, causing a great public health concern. Hybrid plasmids formed by fusion events may further exacerbate the spread of antibiotic resistance genes as well as plasmid evolution. Salmonella enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium, which is one of the major causes of foodborne disease outbreaks worldwide. To assess the risk of transmission due to plasmid structure changes, we investigated the structural diversity of plasmids in two S. 4,[5],12:i:- isolates. Nanopore long-read sequencing was performed for plasmid comparison between original plasmids (donor isolates) and reorganized plasmids. We found that the IncHI2-IncHI2A multidrug resistance (MDR) plasmids in S. 4,[5],12:i:- possessed high plasticity, and could undergo recombination with other plasmids to form fusion plasmids of different sizes. Plasmid structural polymorphisms were mainly mediated by insertion sequences such as IS26 and ISPa40, and led to the rearrangement of the plasmid internal structures. To the best of our knowledge, this is the first report of the fusion of the IncHI2-IncHI2A and IncB/O/K/Z plasmids in S. 4,[5],12:i:- mediated by IS26. In addition, we also found that the mcr-1 gene was able to generate duplication during conjugation. Polymorphic changes in MDR plasmids during conjugation may further reduce the choice of clinical therapeutic agents. Therefore, continuous monitoring regarding plasmid polymorphic changes during transmission in both in vitro and in vivo is urgently needed to decipher the MDR plasmid evolution.

Genomic Epidemiology of Streptococcus pneumoniae Isolated in a Tertiary Hospital in Beijing, China, from 2018 to 2022.

Streptococcus pneumoniae is one of the most common bacterial pathogens of a wide range of community-acquired infections. It has been more and more recognized that this bacterium could also play a role as a cause of nosocomial infections. In this study, by retrospective analysis of the phenotypic resistance characteristics and genomic characteristics of 52 S. pneumoniae isolates in a hospital in Beijing, China, from 2018 to 2022, we explored the carriage of resistance genes and mutations in penicillin-binding proteins corresponding to the resistances, and identified the population diversity based on the prediction of serotypes and identification of sequence types (STs). The isolates displayed resistances to erythromycin (98%), tetracycline (96%), sulfonamide (72%) and penicillin G (42%). Among the 52 isolates, 41 displayed multiple-drug resistance. In total, 37 STs and 21 serotypes were identified, and the clonal complex 271 serogroup 19 was the most prevalent subtype. Only 24 isolates (46.2%) of 7 serotypes were covered by the 13-valent pneumococcal conjugate vaccination. The isolates showed high carriages of resistance genes, including tet(M) (100%) and erm(B) (98.1%); additionally, 32 isolates (61.5%) had mutations in penicillin-binding proteins. We also observed 11 healthcare-associated infections and 3 cases infected by different subtypes of isolates. We did not find nosocomial transmissions between the patients, and these cases might be associated with the asymptomatic colonization of S. pneumoniae in the human population. Our results called for further active surveillance of these subtypes, as well as the continuous optimization of the treatment protocols.