Pathogenic Detection by Metagenomic Next-generation Sequencing in Skin and Soft Tissue Infection.

BACKGROUND/AIM: Skin and soft tissue infections (SSTIs) can be life-threatening, but the conventional bacterial cultures have low sensitivity and are time-consuming. Metagenomic next-generation sequencing (mNGS) is widely used as a diagnostic tool for detecting pathogens from infection sites. However, the use of mNGS for pathogen detection in SSTIs and related research is still relatively limited. PATIENTS AND METHODS: From January 2020 to October 2021, 19 SSTI samples from 16 patients were collected in a single center (Taichung Veterans General Hospital, Taichung, Taiwan). The clinical samples were simultaneously subjected to mNGS and conventional bacterial culture methods to detect pathogens. Clinical characteristics were prospectively collected through electronic chart review. The microbiological findings from conventional bacterial culture and mNGS were analyzed and compared. RESULTS: The mNGS method detected a higher proportion of multiple pathogens in SSTIs compared to conventional bacterial culture methods. Pseudomonas spp. was among the most commonly identified Gram-negative bacilli using mNGS. Additionally, the mNGS method identified several rare pathogens in patients with SSTIs, including Granulicatella adiacens, Bacillus thuringiensis, and Bacteroides fragilis. Antimicrobial resistance genes were detected in 10 samples (52.6%) using the mNGS method, including genes for extended-spectrum beta-lactamase, Ambler class C ß-lactamases, and carbapenemase. CONCLUSION: mNGS not only plays an important role in the detection of pathogens in soft tissue infections, but also informs clinical professionals about the presence of additional microbes that may be important for treatment decisions. Further studies comparing conventional pathogen culture with the mNGS method in SSTIs are required.

Tracing the footprints of MPXV in Asia: phylogenetic insights and lineage dynamics.

OBJECTIVES: The 2022 global outbreak of monkeypox virus (MPXV), previously confined to Central and West Africa, necessitates an enhanced understanding of its spread. Comprehensive genomic surveillance to understand the virus's evolution and spread is needed, particularly in Asia. METHODS: Genomic data from 169 MPXV genome sequences in Asia were analysed. Through advanced genomic sequencing of clinical samples, we analysed the distribution and mutations of MPXV lineages in Asia. RESULTS: Phylogenetic analysis revealed a distinct clustering of C.1 strains rise in Northeast Asia in 2023, while genomic examination identified specific consensus mutations like R84K, R665C and L16F in C.1 strains. The mutations, coupled with an increased rate of apolipoprotein B mRNA-editing catalytic polypeptide-like 3 motif G-to-A mutations in C.1 (OR 24.87±8.81), indicate a potential adaptation mechanism. CONCLUSIONS: Our findings underscore the need for ongoing surveillance and provide vital insights into MPXV's evolving dynamics, aiding in public health strategy formulation against this emerging infectious threat.

Characterization of CRISPR-Cas Systems in Shewanella algae and Shewanella haliotis: Insights into the Adaptation and Survival of Marine Pathogens.

CRISPR-Cas systems are adaptive immune mechanisms present in most prokaryotes that play an important role in the adaptation of bacteria and archaea to new environments. Shewanella algae is a marine zoonotic pathogen with worldwide distribution, which accounts for the majority of clinical cases of Shewanella infections. However, the characterization of Shewanella algae CRISPR-Cas systems has not been well investigated yet. Through whole genome sequence analysis, we characterized the CRISPR-Cas systems in S. algae. Our results indicate that CRISPR-Cas systems are prevalent in S. algae, with the majority of strains containing the Type I-F system. This study provides new insights into the diversity and function of CRISPR-Cas systems in S. algae and highlights their potential role in the adaptation and survival of these marine pathogens.

Talaromyces amestolkiae Infection in an AIDS Patient with Cryptococcal Meningitis.

Concurrent infections caused by multiple fungal pathogens in immunocompromised patients can pose diagnostic and treatment challenges. Here, we presented the first reported case in Taiwan of an AIDS patient who had concurrent infection with Cryptococcus neoformans meningitis and Talaromyces amestolkiae lymphadenopathy. The patient presented with an enlarged inguinal lymph node and was diagnosed with T. amestolkiae lymphadenitis. The species T. amestolkiae was identified using DNA sequencing, which had the capability of differentiating it from other Talaromyces species. The patient was discharged from the hospital following treatment with amphotericin B and subsequent administration of voriconazole. This case highlights the importance of maintaining a suspicion of co-infections and utilizing appropriate diagnostic tools, such as DNA sequencing, to identify possible pathogens. Further studies are needed to determine the optimal treatment for T. amestolkiae and other co-infecting fungal pathogens.

Clinical metagenomics-assisted diagnosis of relapsed HIV-associated cryptococcal meningitis.

To date, the identification of crypotococcal relapse remains clinically challenging as it often has similar manifestation with paradoxical immune reconstitution inflammatory syndrome. This study reports on the use of metagenomics assisted next generation sequencing to aid in diagnosing recurrent cryptococcal meningitis in an person living with HIV experiencing recurring symptoms, despite negative culture results for Cryptococcus neoformans in the cerebrospinal fluid. Although fungal culture was negative, when reads from metagenomic and metatranscriptomic sequencing performed on the Day 308 cerebrospinal fluid sample were mapped onto the genome from the Day 4 isolate, 589 specific reads were identified. NCBI BLAST search also revealed Cryptococcus-specific 18S/25S/28S ribosomal RNA, indicating a relapse of the disease.

Insight into the Mechanisms of Carbapenem Resistance in Klebsiella pneumoniae: A Study on IS26 Integrons, Beta-Lactamases, Porin Modifications, and Plasmidome Analysis.

The emergence of carbapenem-resistant Klebsiella pneumoniae poses a significant threat to public health. In this study, we aimed to investigate the distribution and genetic diversity of plasmids carrying beta-lactamase resistance determinants in a collection of carbapenem-resistant K. pneumoniae blood isolates. Blood isolates of carbapenem-resistant K. pneumoniae bacteremia were collected and identified. Whole-genome sequencing, assembly and analysis were performed for the prediction of antimicrobial resistance determinants. Plasmidome analysis was also performed. Our plasmidome analysis revealed two major plasmid groups, IncFII/IncR and IncC, as key players in the dissemination of carbapenem resistance among carbapenem-resistant K. pneumoniae. Notably, plasmids within the same group exhibited conservation of encapsulated genes, suggesting that these plasmid groups may serve as conservative carriers of carbapenem-resistant determinants. Additionally, we investigated the evolution and expansion of IS26 integrons in carbapenem-resistant K. pneumoniae isolates using long-read sequencing. Our findings revealed the evolution and expansion of IS26 structure, which may have contributed to the development of carbapenem resistance in these strains. Our findings indicate that IncC group plasmids are associated with the endemic occurrence of carbapenem-resistant K. pneumoniae, highlighting the need for targeted interventions to control its spread. Although our study focuses on the endemic presence of carbapenem-resistant K. pneumoniae, it is important to note that carbapenem-resistant K. pneumoniae is indeed a global problem, with cases reported in multiple regions worldwide. Further research is necessary to better understand the factors driving the worldwide dissemination of carbapenem-resistant K. pneumoniae and to develop effective strategies for its prevention and control.

Kolb's experiential learning theory and marine debris education: Effects of different stages on learning.

Marine debris is a vital issue in ocean governance. While education outreach can promote individual learning and develop pro-environmental behavior, research on marine debris education remains scarce. Kolb's experiential learning theory may provide a holistic model for marine debris education; therefore, this study developed an experiential-learning based marine debris (ELBMD) beach cleanup curriculum and analyzed the participants' performance during Kolb's four-stage cycle. The results revealed that (1) the ELBMD curriculum deepened the participants' understanding of marine debris, created a sense of responsibility, and increased their confidence in analytical skills and intention to act responsibly. (2) Reflection (Stage II) encouraged participants to think deeply about the human-environment relationship, which induced pro-environmental behavior and awareness of political engagement (Stage IV). (3) Peer discussion (Stage III) induced participants to refine their conception architecture, form values, and practice pro-environmental behavior (Stage IV). The results may aid the development of future marine debris education.

The Impact of the COVID-19 Pandemic on Respiratory Syncytial Virus Infection: A Narrative Review.

Respiratory syncytial virus (RSV) is one of the most common respiratory viruses. It not only affects young children but also the elderly and immunocompromised patients. After the emergence of SARS-CoV-2 and the corona virus disease 2019 (COVID-19) era, a dramatic reduction in RSV activity was found, which coincided with the implementation of public health and social measures (PHSMs). However, the correlation is more complicated than we initially thought. After PHSMs were gradually lifted, a seasonality shift and a delayed RSV outbreak with greater number of infected patients were found in numerous countries, such as Israel, Australia, South Africa, New Zealand, France, United States, and Japan. Several hypotheses and possible reasons explaining the interaction between SARS-CoV-2 and RSV were mentioned. Since RSV vaccinations are still under investigation, administration of palivizumab should be considered in high-risk patients. In the post-COVID-19 era, greater attention should be paid to a further resurgence of RSV. In this narrative review, we conducted a thorough review of the current knowledge on the epidemiology of RSV during the COVID-19 era, the out-of-season outbreak of RSV, and the data on co-infection with RSV and SARS-CoV-2.

Motivating Individuals to Take Responsible Ocean Action: The Mediatory Effects of Attitude toward the Ocean.

When considering how to improve public literacy and behavior related to specific themes, top priority is usually given to strategies that enhance relevant knowledge. Fostering attitude comes later. Understanding the mechanisms of behavior may help us develop better policy and educational strategies. However, how knowledge and attitude impact behavior is still under investigation. The aim of this study is to explore the relationships among ocean knowledge, attitude toward the ocean, and the intention to behave responsibly in the marine setting. Specifically, we investigated a potential mediation mechanism by recruiting a total of 266 participants, whose ocean knowledge, attitudes toward the ocean, and intention to behave responsibly were evaluated using questionnaires. The results indicate that a person's attitude toward the ocean may indeed be a mediating factor between ocean knowledge and their intention to show positive marine behavior. In order to engage people in responsible ocean behavior, other forms of assistance from marine policy and education are recommended. Additionally, it would be of interest for future studies to investigate the effects of attitude and attitude-related knowledge in the development of ocean actions.

Blood Culture Negative Endocarditis: A Review of Laboratory Diagnostic Approaches.

Infective endocarditis is a potentially fatal condition, and identifying the pathogen is crucial to optimizing antibiotic treatment. While a blood culture takes time and may yield negative results, it remains the gold standard for diagnosis, blood culture-negative endocarditis, which accounts for up to 20% of infective endocarditis cases, poses a clinical challenge with increasing mortality. To better understand the etiology of blood culture-negative infective endocarditis, we reviewed non-culture-based strategies and compared the results. Serology tests work best in limited pathogens, such as Coxiella burnetii and Bartonella infections. Most of the pathogens identified by broad-range PCR tests are Streptococcus spp, Staphylococcus spp and Propionibacterium spp. adding specific real-time PCR assays to the systematic PCR testing of patients with blood culture-negative endocarditis will increase the efficiency of diagnosis. Recently, metagenomic next-generation sequencing has also shown promising results.

Antibiotic resistance in Enterobacter hormaechei.

Enterobacter hormaechei, a member of the Enterobacter cloacae complex, has emerged as an important pathogen in healthcare-associated infections. Advancements in phylogenetic analyses and whole-genome sequencing techniques have led to the identification of E. hormaechei in numerous locations worldwide. The emergence of antibiotic-resistant E. hormaechei isolates, including those that produce extended-spectrum ß-lactamases (ESBLs), AmpC ß-lactamases and carbapenemases, has been reported worldwide. In this article, we review the different resistance genes of antibiotic-resistant E. hormaechei.

COVID-19 Associated Bacteremia with Chryseobacterium indologenes Co-Harboring bla IND-2, bla CIA and bla CcrA.

We report a COVID-19 case with carbapenem resistant Chryseobacterium indologenes bacteremia. Whole genome sequencing identified the presence of bla IND-2, bla CIA and bla CcrA. To our knowledge, this is the first report of Chryseobacterium indologenes complicating COVID-19 and the detection of bla CcrA in C. indologenes. The presence of bla CcrA in Chryseobacterium was overlooked previously may related to substantial sequence divergence with the original allele in Bacteroides fragilis. Antimicrobial resistance (AMR) is a challenge to global health in the age of COVID-19 pandemic. Further study and surveillance of underlying mechanisms is needed.

Review of an intelligent indoor environment monitoring and management system for COVID-19 risk mitigation.

The coronavirus disease (COVID-19) outbreak has turned the world upside down bringing about a massive impact on society due to enforced measures such as the curtailment of personal travel and limitations on economic activities. The global pandemic resulted in numerous people spending their time at home, working, and learning from home hence exposing them to air contaminants of outdoor and indoor origins. COVID-19 is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which spreads by airborne transmission. The viruses found indoors are linked to the building's ventilation system quality. The ventilation flow in an indoor environment controls the movement and advection of any aerosols, pollutants, and Carbon Dioxide (CO2) created by indoor sources/occupants; the quantity of CO2 can be measured by sensors. Indoor CO2 monitoring is a technique used to track a person's COVID-19 risk, but high or low CO2 levels do not necessarily mean that the COVID-19 virus is present in the air. CO2 monitors, in short, can help inform an individual whether they are breathing in clean air. In terms of COVID-19 risk mitigation strategies, intelligent indoor monitoring systems use various sensors that are available in the marketplace. This work presents a review of scientific articles that influence intelligent monitoring development and indoor environmental quality management system. The paper underlines that the non-dispersive infrared (NDIR) sensor and ESP8266 microcontroller support the development of low-cost indoor air monitoring at learning facilities.

Bacteriophages and phage-delivered CRISPR-Cas system as antibacterial therapy.

Multidrug-resistant (MDR) bacterial infections in humans are increasing worldwide. The global spread of antimicrobial resistance poses a considerable threat to human health. Phage therapy is a promising approach to combat MDR bacteria. An increasing number of reports have been published on phage therapy and the successful application of antibacterials derived using this method. Additionally, the CRISPR-Cas system has been used to develop antimicrobials with bactericidal effects in vivo. The CRISPR-Cas system can be delivered into target bacteria in various ways, with phage-based vectors being reported as an effective method. In this review, we briefly summarise the results of randomised control trials on bacteriophage therapy. Moreover, we integrated mechanisms of the CRISPR-Cas system antimicrobials in a schematic diagram and consolidated the research on phage-delivered CRISPR-Cas system antimicrobials.

Association of CaMK2A and MeCP2 signaling pathways with cognitive ability in adolescents.

The glutamatergic signaling pathway is involved in molecular learning and human cognitive ability. Specific single variants (SNVs, formerly single-nucleotide polymorphisms) in the genes encoding N-methyl-D-aspartate receptor subunits have been associated with neuropsychiatric disorders by altering glutamate transmission. However, these variants associated with cognition and mental activity have rarely been explored in healthy adolescents. In this study, we screened for SNVs in the glutamatergic signaling pathway to identify genetic variants associated with cognitive ability. We found that SNVs in the subunits of ionotropic glutamate receptors, including GRIA1, GRIN1, GRIN2B, GRIN2C, GRIN3A, GRIN3B, and calcium/calmodulin-dependent protein kinase IIα (CaMK2A) are associated with cognitive function. Plasma CaMK2A level was correlated positively with the cognitive ability of Taiwanese senior high school students. We demonstrated that elevating CaMK2A increased its autophosphorylation at T286 and increased the expression of its downstream targets, including GluA1 and phosphor- GluA1 in vivo. Additionally, methyl-CpG binding protein 2 (MeCP2), a downstream target of CaMK2A, was found to activate the expression of CaMK2A, suggesting that MeCP2 and CaMK2A can form a positive feedback loop. In summary, two members of the glutamatergic signaling pathway, CaMK2A and MeCP2, are implicated in the cognitive ability of adolescents; thus, altering the expression of CaMK2A may affect cognitive ability in youth.

2019 novel coronavirus disease (COVID-19) in Taiwan: Reports of two cases from Wuhan, China.

We reported two cases with community-acquired pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) who returned from Wuhan, China in January, 2020. The reported cases highlight non-specific clinical presentations of 2019 novel coronavirus disease (COVID-19) as well as the importance of rapid laboratory-based diagnosis.

Multiple epigenetic biomarkers for evaluation of students' academic performance.

Several reports have shown that methyl CpG-binding protein 2 (MeCP2), brain-derived neurotrophic factor (BDNF), phospho-cAMP response element-binding protein (p-CREB) and microRNAs may be important in regulating academic performance because of their roles in neuropsychiatry and cognitive diseases. The first goal of this study was to explore the associations among MeCP2, BDNF, CREB and academic performance. This study also examined the pathway responsible for the effects of MeCP2, BDNF, p-CREB and microRNAs on academic performance. Scores from the basic competency test, an annual national competitive entrance examination, were used to evaluate academic performance. Subjects' plasma RNA was extracted and analyzed. This study determined that participants in the higher academic performance group had a significant difference in MECP2 mRNA expression compared with the lower academic performance group. We then used neuronal human derived neuroblastoma cell line (SH-SY5Y) cells with inducible MeCP2 expression from a second copy of the gene as a gain-of-function model and found that MeCP2 overexpression positively affected p-CREB and BDNF expression initially. After negative feedback, the p-CREB and BDNF levels subsequently decreased. In the neuronal phenotype examination, we found a significant reduction in total outgrowth and branches in MeCP2-induced cells compared with noninduced cells. This work describes pathways that may be responsible for the effects of MeCP2, BDNF, p-CREB and microRNAs on academic performance. These results may shed light on the development of promising clinical treatment strategies in the area of neuropsychological adjustment.

Analyses of EEG Oscillatory Activities during Slow and Fast Repetitive Movements using Holo-Hilbert Spectral Analysis.

Neural oscillatory activities existing in multiple fre-quency bands usually represent different levels of neurophysiolog-ical meanings, from micro-scale to macro-scale organizations. In this study, we adopted Holo-Hilbert spectral analysis (HHSA) to study the amplitude-modulated (AM) and frequency-modulated (FM) components in sensorimotor Mu rhythm, induced by slow- and fast-rate repetitive movements. The HHSA-based approach is a two-layer empirical mode decomposition (EMD) architecture, which firstly decomposes the EEG signal into a series of frequency-modulated intrinsic mode functions (IMF) and then decomposes each frequency-modulated IMF into a set of amplitude-modulated IMFs. With the HHSA, the FM and AM components were incor-porated with their instantaneous power to achieve full-informa-tional spectral analysis. We observed that the instantaneous power induced by slow-rate movements was significantly higher than that induced by fast-rate movements (p < 0.01, Wilcoxon signed rank test). The alpha-band AM frequencies induced by slow-rate movements were higher than those induced by fast-rate move-ments, while no statistical difference was found in beta-band AM frequencies. In addition, to study the functional coupling between the primary sensorimotor area and other brain regions, spectral coherence was applied and statistical difference was found in frontal area in slow-rate versus fast-rate movements. The discrep-ancy between slow- and fast-rate movements might be owing to the change of motor functional modes from default mode network (DMN) to automatic timing with the increase of movement rates. The use of HHSA for oscillatory activity analysis can be an effi-cient tool to provide informative interaction among different fre-quency bands.

Study of Repetitive Movements Induced Oscillatory Activities in Healthy Subjects and Chronic Stroke Patients.

Repetitive movements at a constant rate require the integration of internal time counting and motor neural networks. Previous studies have proved that humans can follow short durations automatically (automatic timing) but require more cognitive efforts to track or estimate long durations. In this study, we studied sensorimotor oscillatory activities in healthy subjects and chronic stroke patients when subjects were performing repetitive finger movements. We found the movement-modulated changes in alpha and beta oscillatory activities were decreased with the increase of movement rates in finger lifting of healthy subjects and the non-paretic hands in stroke patients, whereas no difference was found in the paretic-hand movements at different movement rates in stroke patients. The significant difference in oscillatory activities between movements of non-paretic hands and paretic hands could imply the requirement of higher cognitive efforts to perform fast repetitive movements in paretic hands. The sensorimotor oscillatory response in fast repetitive movements could be a possible indicator to probe the recovery of motor function in stroke patients.