OBJECTIVES:Insulin resistance (IR) is frequently observed and associated with complications of cardiovascular disease among the RA population. Triglyceride-glucose (TyG)-related indexes, serving as surrogates for assessing IR, have been significantly associated with mortality in some chronic diseases. However, their prognostic roles in the RA population have not been validated to date. METHODS:A cohort of 764 RA participants, spanning from 1999 to 2018, was recruited from the National Health and Nutrition Examination Survey (NHANES). Kaplan-Meier (KM) curves, restricted cubic splines (RCS), and the Cox proportional hazards model were used to analyse the relationship between TyG-related indexes and mortality. RESULTS:During a median follow-up of 82 months, 235 all-cause and 73 cardiovascular deaths were recorded. The survival rates for the higher TyG and TyG-WHtR groups were significantly lower compared with those in the lower group. Multivariate Cox proportional hazards analysis showed that higher TyG was significantly associated with all-cause mortality (HR = 1.60, P = 0.011) and cardiovascular mortality (HR = 2.36, P = 0.017). The RCS curves showed a significant non-linear trend between cardiovascular mortality and TyG-WHtR, TyG-WC, TyG-BMI (P for non-linearity < 0.05), with inflection points at 6.11, 869.84 and 314.01, respectively. Interaction analysis revealed significant effect modification by BMI, drinking, race and education (P for interaction < 0.05). The sensitivity analyses supported the positive associations between TyG-related indexes and mortality in the RA population. CONCLUSIONS:This study highlights the prognostic value of TyG-related indicators with thresholds for predicting mortality, which suggests that TyG-related surrogates could be effective biomarkers for risk stratification in clinical management among the RA population.

Background: Phthalate exposure has been linked to adverse cardiometabolic profiles in children, but its association with longitudinal cardiometabolic risk patterns and the modifying role of 24-h movement behaviors remain unclear. Methods: We analyzed repeated follow-up data from a school-based cohort of Chinese children from 2018 to 2020. Urinary phthalate metabolites were measured annually and averaged to represent habitual exposure. Cardiometabolic risk status was classified into five progression patterns: stable healthy, improving, fluctuating, worsening, and persistently abnormal. Multinomial logistic regression was used to examine associations between phthalate exposure quartiles and progression patterns. Effect modification by sex and adherence to the 24-h movement guidelines was evaluated, and weighted quantile sum regression was used to assess mixture effects. Results: Most phthalate metabolites showed limited or inconsistent associations with stable healthy, improving, or fluctuating patterns. In contrast, higher exposure to several high-molecular-weight phthalate metabolites was associated with increased odds of the persistently abnormal pattern, particularly for MEOHP and MEHHP. Associations with worsening patterns were generally inconsistent. Sex-stratified analyses suggested stronger associations among boys, although formal interaction evidence was limited. Adherence to the 24-h movement guidelines was associated with weaker exposure-outcome associations, but estimates were imprecise. Mixture analyses showed a positive association between overall phthalate exposure burden and the persistently abnormal pattern. Conclusions: Repeated phthalate exposure was mainly associated with persistently abnormal cardiometabolic risk in children. Healthy movement behaviors may partly mitigate these associations, although further longitudinal studies are needed.

BackgroundNon-alcoholic fatty liver disease (NAFLD) or liver fibrosis may share similar pathophysiological features with Parkinson’s disease (PD), yet their correlation was unclear. This study aimed to explore their correlation between PD and liver fibrosis using the fibrosis-4 score (FIB-4) as a surrogate marker.MethodsWe analyzed Parkinson’s Progression Markers Initiative (PPMI) data and enrolled PD patients with comprehensive baseline and 5-year follow-up time-point clinical data. Participants were categorized based on FIB-4 levels to assess the association between FIB-4 scores and various clinical scales, controlling for potential confounders. Differences in the progression of clinical scales over five years were compared using generalized linear mixed models (GLMM).ResultsBaseline FIB-4 levels positively correlated to scores of baseline section III of the Unified-Parkinson Disease Rating Scale (UPDRS III) (r = 0.145, p = 0.017), Epworth Sleepiness Scale (EPSS) (r = 0.140, P = 0.022), Hopkins Verbal Learning Test (HVLT)-delayed recall (r = 0.128, P = 0.036) and HVLT-retention (r = 0.128, p = 0.036). GLMM analysis revealed an independent correlation between FIB-4 subgroup*time and several clinical scales including the State-trait Anxiety Inventory (STAI), Symbol Digit Modalities Test (SDMT), Semantic Fluency Test (SF), HVLT-total recall, and HVLT-delayed recall, with the high FIB-4 subgroup exhibiting a greater decline in these scores compared to the low FIB-4 subgroup (all p<0.05).ConclusionElevated baseline FIB-4 correlated to more severe baseline daytime sleepiness, motor symptoms, and memory function in PD patients, along with a more rapid decline in cognitive functions such as executive function, information processing ability, and memory. Additionally, a high FIB-4 might confer a protective effect against anxiety.

Currently, there is a substantial amount of research on the impact of long-term exposure to printing shop particles (PSPs) on worker health. However, the effects of short-term exposure to PSPs on consumer health and the appropriate exposure metric for assessing the health risks of PSPs remain unclear. In this study, a two-stage crossover experiment was conducted, in which 20 healthy adults were randomly exposed to different size distributions of PSPs during two separate experimental periods. Lung function of the participants was tested before and after PSP exposure, and blood samples were collected for analysis. The results indicated that, compared to traditional particle exposure metrics such as mass and number concentration, the ratio of PM10 to PM1 mass concentration (PMC10/PMC1) was a more suitable metric for evaluating PSP exposure risks. After exposure to PSPs, participants showed a decline in lung function. As the PMC10/PMC1 ratio increased in two experimental periods, lung function indicators associated with small airways, such as forced expiratory volume in 1 s (FEV1), FEV3, forced expiratory flow at 25% of FVC exhaled (FEF25), FEF75, and FEF25-75%, significantly decreased. Blood biochemical test results revealed an increase in potassium levels in the serum of participants, potentially related to small airway damage caused by PSPs. In summary, this study proposes a more suitable exposure metric to evaluate the health impact of PSPs and other nanoparticles, offering epidemiological evidence on the health effects of short-term exposure to these substances.

To investigate the joint associations between various body fat distribution parameters and high blood pressure (HBP) using the Bayesian Kernel Machine Regression (BKMR) model in school-aged children. A diverse sample of 7 ∼ 17 years old (N = 1423; 50.25

Chronic widespread pain (CWP) remains challenging due to its heterogenous causes and complex mechanisms. We analysed 2,923 plasma proteins from 29,254 UK Biobank participants. We first identified 811 proteins correlated with the presence of CWP cross-sectionally. We then created a sparse (top 10 proteins) and intricate (all significant proteins) proteomic-based score (ProtS) for CWP, both outperforming and improving the traditional clinical score (AUC: 0.82 and 0.88 vs 0.81 individually, and 0.87 and 0.92 in combination). Prospectively, the ProtS was associated with increased risks of a spectrum of pain traits, including dimensions from pain onset, progression and intensity, up to 13-years of follow-up; More importantly, we identified distinct proteomic signatures for nociplastic pain compared to nociceptive and neuropathic pain. For the individual proteins, carbonic anhydrase 14 (CA14) and leptin appeared as promising casual CWP biomarkers as triangulated by Mendelian randomisation and colocalization analyses. Lastly, our drug-repurposing analysis identified ten potential candidates for CWP therapies, calling for further research including randomised controlled trials. Although no CA14 agonists are currently available, CA14 remains a promising target, warranting further efforts to explore its role in pain modulation. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement DPA and JX received partial support from the Oxford National Institute for Health and care Research (NIHR) Biomedical Research Centre. The present study was supported by China National Natural Science Foundation of China (Grant 82103865 and 82373593 to Yanhui Dong) and Natural Science Foundation of Beijing (Grant 7222244 to Yanhui Dong), Peking University Talent Introduction Program Project (BMU2023YJ011 to Yanhui Dong). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: https://www.ukbiobank.ac.uk I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors

Background This study aimed to develop and apply a novel computational pipeline combining SELFormer, a transformer architecture-based chemical language model, with advanced deep learning techniques to predict natural compounds (NCs) with potential in Alzheimer's disease (AD) treatment. The NCs were identified based on activity related to seven AD-specific genes, including acetylcholinesterase (AChE), amyloid precursor protein (APP), beta-secretase 1 (BACE1), and presenilin-1 (PSEN1). Methods We implemented a computational pipeline using SELFormer and deep learning techniques, conducted optimal clustering and quantitative structure-activity relationship (QSAR) analyses, and performed a uniform manifold approximation and projection (UMAP) to categorize compounds based on bioactivity levels. Molecular docking analysis was carried out on selected compounds. To validate the computational predictions, we conducted in vitro studies using nerve growth factor (NGF)-differentiated PC12 cells. Finally, we mapped the relationships between food sources containing the identified compounds and their target proteins. Results Optimal clustering analysis revealed five distinct groups of NCs, while QSAR analysis highlighted variations in molecular properties across clusters. The UMAP projection identified 17 highly active NCs (pIC50>7). Molecular docking analysis showed that cowanin, β-caryophyllene, and L-citronellol demonstrated decreased binding energy across target proteins. In vitro studies confirmed significant biological activities of these compounds, including increased cell viability, decreased AChE activity, reduced lipid peroxidation and tumor necrosis factor (TNF)-α mRNA expression, and increased brain-derived neurotrophic factor (BDNF) mRNA expression compared to the control. The study also identified natural sources of these compounds, such as anatidae, mangosteen, and celery, providing insights into potential dietary interventions. Conclusion This integrated computational and experimental approach offers a promising framework for identifying potential NCs for AD treatment. The results contribute to exploring effective therapeutic strategies against AD.

Phthalates (PAEs) are synthetic compounds extensively employed in consumer products. Blood pressure (BP) in children can vary, the degree of visit-to-visit BP variability (VVV) is at least partially independent of BP. The interactions between PAEs exposure, pubertal-related genetic susceptibility and lifestyles on childhood VVV are not investigated. This study utilized data from a cohort collected from Oct 2017-2020 in Xiamen, China. Seven urine PAE metabolites were measured. The long-term VVV was characterized employing the standard deviation (SD) and average real variability. We constructed a genetic risk score (GRS) of pubertal-related genes and healthy lifestyle scores. Exposed to high levels of mono-2-ethyl-5-hydroxyhexyl phthalate (MEHHP) (OR=1.43, =1.43, 95 % CI=1.07, =1.07, 1.92) and mono-2-ethyl-5-oxohexyl phthalate (OR=1.36, =1.36, 95 % CI=1.01, =1.01, 1.83) was related to increased SBP-SD, and the OR for high SBP-SD related to high GRS was 1.38 (95 % CI=1.02, =1.02, 1.85). Compared to participants who had low GRS and low MEHHP exposure, participants exhibiting high GRS and MEHHP levels were more likely to experience high SBP-SD (OR=2.00, =2.00, P <0.05). Individuals exhibiting low GRS, low MEHHP levels, and adhering to healthy lifestyles were associated with the least probability of experiencing high SBP-SD (OR=0.31, =0.31, P <0.05). Increased PAEs exposure could elevate childhood systolic VVV, and exacerbated the adverse impact of pubertal-related genetic susceptibility on the high VVV of SBP; however, healthy lifestyles might alleviate these adverse effects. Promoting healthy lifestyles and reducing PAEs exposure for preventing elevated BP variability among children is important, especially for individuals with greater genetic susceptibility to early pubertal onset. Environmental implication: Blood pressure (BP) in children can vary, as a noninvasive, inexpensive and applicable method, the extent of visit-to-visit variability (VVV) is at least partially independent of BP. The interactions between phthalates (PAEs) exposure, variants of puberty-related genes and lifestyles on VVV are not investigated. Increased childhood systolic VVV might be associated with PAEs exposure, with the associations more pronounced combined with pubertal genetic susceptibility. Yet, healthy habits could partly eliminate such adverse effects. Our study underscores the importance of advocating for healthy lifestyles and reducing exposure to PAEs, especially among individuals with high genetic susceptibility to early puberty onset.

The relationship between childhood phthalates (PAEs) exposure, DNA methylation, and cardiometabolic risk (CMR) factors is not well understood. Children were included from a longitudinal cohort 2018-2020 in Xiamen, China. A nest case-control study was additionally conducted, and methylation in lysyl oxidase-like 3 (LOXL3) and solute Carrier Family 6 Member 19 (SLC6A19) were measured. Generalized linear models were used to estimate the associations between PAEs exposure and CMR factors, and mediation analyses of DNA methylation were conducted. The longitudinal study included 835 children aged 7-11 years, and the nest case-control study included 120 cases and 120 controls. Exposure to higher PAEs was correlated with increased CMR scores at baseline (beta = 0.299, 95 %CI = 0.114, 0.485) and the final visit (beta = 0.202, 95 %CI = 0.008, 0.397). In nest case control study, higher mono-n-butyl phthalate (MnBP) exposure was related with elevated triglycerides (TG) (beta = 0.283, 95 %CI = 0.025, 0.540). A decrement of methylation of CpG 33.34 of LOXL3 was found in response to MnBP exposure (beta =-0.014, 95 %CI =-0.027,-0.001). Furthermore, increased methylation of LOXL3_CpG 33.34 and SLC6A19_CpG 11.12 was related to reduced TG. De-methylation of LOXL3_CpG 33.34 and SLC6A19_CpG 11.12 could mediate MnBP-TG pathways. Childhood exposure to PAEs was associated with increased CMR scores, and mediation of PAE exposure on childhood cardiometabolic health by LOXL3 and SLC6A19 de-methylation was observed.

BackgroundIdentifying the diagnosis as well as prognosis for patients presented with community-acquired pneumonia (CAP) remains challenging. We aimed to identify the role of lysophosphatidylcholine acyl-transferase (LPCAT) for CAP along with assessing this protein’s effectiveness as a biomarker for severity of disease and mortality.MethodsProspective multicenter research study was carried out among hospitalized patients. A total of 299 CAP patients (including 97 severe CAP patients [SCAP]) and 20 healthy controls (HC) were included. A quantitative enzyme-linked immunosorbent test kit was employed for detecting the LPCAT level in plasma. We developed a deep-learning-based binary classification (SCAP or non-severe CAP [NSCAP]) model to process LPCAT levels and other laboratory test results.ResultsThe level of LPCAT in patients with SCAP and death outcome was significantly higher than that in other patients. LPCAT showed the highest predictive value for SCAP. LPCAT was able to predict 30-day mortality among CAP patients, combining LPCAT values with PSI scores or CURB-65 further enhance mortality prediction accuracy.ConclusionThe on admission level of LPCAT found significantly raised among SCAP patients and strongly predicted SCAP patients but with no correlation to etiology. Combining the LPCAT value with CURB-65 or PSI improved the 30-day mortality forecast significantly.Trial registrationNCT03093220 Registered on March 28th, 2017.

Purpose Patients with bacterial, fungal, and viral community-acquired pneumonia (CAP) were studied to determine their metabolic profiles.Methods Loop-mediated isothermal amplification technology and nucleic acid sequence-dependent amplification combined with microfluidic chip technology were applied to screen multiple pathogens from respiratory tract samples. Eighteen patients with single bacterial infection (B-CAP), fifteen with single virus infection (V-CAP), twenty with single fungal infection (F-CAP), and twenty controls were enrolled. UHPLC-MS/MS analysis of untargeted serum samples for metabolic profiles. Multiple linear regression and Spearman’s rank correlation analysis were used to determine associations between metabolites and clinical parameters. The sensitivity and specificity of the screened metabolites were also examined, along with their area under the curve.Results The metabolic signatures of patients with CAP infected by bacteria, viruses, and fungi were markedly different from those of controls. The abundances of 45, 56, and 79 metabolites were significantly unbalanced. Among these differential metabolites, 11, 13, and 29 were unique to the B-CAP, V-CAP, and F-CAP groups, respectively. Bacterial infections were the only known causes of disturbances in the pentose and glucuronate and aldarate and ascorbate metabolism interconversions metabolic pathway.Conclusions Serum metabolomic techniques based on UHPLC-MS/MS may identify differences between individuals with CAP who have been infected by various pathogens, and they can also build a metabolite signature for early detection of the origin of infection and prompt care.

Staphylococcus lugdunensis (S. lugdunensis) is a coagulase-negative Staphylococcus comprising the normal skin microbiota, primarily colonizing the lower abdomen and extremities.[1]S. lugdunensis has attracted substantial attention in recent years since the discovery of lugdunin by Zipperer et al[2] in 2016. Lugdunin is a secondary metabolite synthesized by non-ribosomal peptide synthetase (NRPS) that inhibits the growth of various gram-positive bacteria, including methicillin-resistant S. aureus (MRSA),[2] suggesting its potential as an antibiotic. To date, 28 complete genome sequences and 11 partial-assembly genome sequences of S. lugdunensis have been published and uploaded to the GenBank database (https://www.ncbi.nlm.nih.gov/genome/browse/#!/prokaryotes/2548/, January 18, 2022). However, there are limited data on the genome sequences of S. lugdunensis from mainland China, and the effects of geographical origin on genetic variations in S. lugdunensis remain unknown. We analyzed six clinical strains of S. lugdunensis isolated from Beijing, Wuhan, and Fujian, China [Supplementary Table 1, https://links.lww.com/CM9/B273]. The minimum inhibitory concentrations (MICs) of antibiotics were evaluated using the VITEK2 Compact system (bioMerieux, Inc., Durham, USA). Cefoxitin disc dilution (cefoxitin DD), broth microdilution for oxacillin, and oxacillin salt agar methods were used as reference methods for assessing methicillin resistance. The complete genomes of the six S. lugdunensis strains were obtained by next-generation sequencing and Oxford Nanopore sequencing, and then compared with genomes available in the GenBank database. We further characterized the resistome and secondary metabolism gene clusters of these staphylococcal cassette chromosome mec (strains using computational approaches. We identified SCCmec) elements of methicillin-resistant S. lugdunensis (MRSL) and performed collinearity analysis of these strains.[3] Comparisons were performed for the obtained nucleotide sequences of the lug operon with those in the GenBank database using Blastx and Blastp tools against the proteins of the operon. We further explored the relationships of genetic variations of the lug operon with geographical origins and the clonal complex (CC). The detailed methods are reported in the Supplementary Materials, https://links.lww.com/CM9/B273. The genome sizes of the six strains ranged from 2.59 to 2.71 Mbp, with a GC content of 33.7% to 33.9% [Supplementary Figure 1, https://links.lww.com/CM9/B273]. All strains contained 2405 to 2523 coding sequences, with 60 to 61 tRNAs, 16 to 19 rRNAs, and 51 to 53 sRNAs. Two to three plasmids were identified in five strains (except RMLUG5). Multilocus sequence typing revealed sequence type (ST)3 (RMLUG1, RMLUG3, RMLUG6), ST27 (RMLUG2), ST34 (RMLUG4), and ST6 (RMLUG5). In antimicrobial susceptibility tests by VITEK2, three of the six strains were resistant to cefoxitin and oxacillin, as confirmed by the oxacillin broth microdilution method and oxacillin salt agar screening. Cefoxitin DD tests showed that strains RMLUG1 and RMLUG6 were susceptible to cefoxitin, although near the breakpoint [Supplementary Table 2, https://links.lww.com/CM9/B273]. The three MRSL strains were susceptible to antibacterial agents showing activity against MRSA, such as linezolid, vancomycin, and teicoplanin [Supplementary Table 3, https://links.lww.com/CM9/B273]). Notably, the methicillin resistance gene mecA was identified in the three MRSL strains (RMLUG1, RMLUG3, and RMLUG6) and in one methicillin-susceptible S. lugdunensis (MSSL) strain (RMLUG2). The SCCmec elements were V(5C2) (RMLUG1, RMLUG2, and RMLUG6) and IVi (2B) (RMLUG3). Only the ccr class 9 (ccrC2 allele 1) gene was identified in the MSSL strain RMLUG4, which is a composite of the SCCmec element. Supplementary Figure 2, https://links.lww.com/CM9/B273 illustrates the SCCmec structure of the six strains. Strains RMLUG1 and RMLUG6 were consistent with SCCmec type V from S. aureus strain WIS [Supplementary Figure 2A, https://links.lww.com/CM9/B273]. Compared with SCCmec type IVi in S. aureus strain JCSC6668, strain RMLUG3 contained a 1014 bp deletion of the gene encoding ISSep1-like transposase [Supplementary Figure 2B, https://links.lww.com/CM9/B273]. The ST27 strain RMLUG2 contained a complete SCCmec type V, including a type mecA class C2 complex and ccrC1 complex, but in a SCCmec type VII-like order: orfX-J3-ccr-J2-mec-J1. Moreover, the IS431 upstream of mecA had the opposite orientation to that downstream, in contrast with the structure of SCCmec type VII, suggesting a novel SCCmec type V variant [Supplementary Figure 2C, https://links.lww.com/CM9/B273]. The SCCmec elements of RMLUG4 did not carry the mecA gene but contained ccr class 9 (ccrC2) and determinants of resistance to heavy metals such as arsenic and copper. According to SCCmec classification,[4] this element is described as an SCC element, which was designated SCCRMLUG4 [Supplementary Figure 2D, https://links.lww.com/CM9/B273]. MIC tests and genomic analysis indicated that strain RMLUG2 carried the mecA gene but did not exhibit oxacillin resistance. No mutation of the mecA gene was observed among the MRSL strains. C to T substitution was identified at position –33 (i.e., 33 bp upstream of the start codon) within the mecA promoter in strain RMLUG2, which also occurred in RMLUG1 and RMLUG6. A comparison of the sequences of FemXAB family genes between strain RMLUG2 and the MRSL strain JICS135 revealed several mutations in femX (eg, R176K and D341E) and femB (eg, D245N and D259Y). The femX and femB genes of strains RMLUG1, RMLUG3, and RMLUG6 matched those of strain JICS135. A comparison of the genomes of the six strains to 14 lug operon genes (lugJ to lugM; Supplementary Table 4, https://links.lww.com/CM9/B273) identified the complete lug operon in all strains except RMLUG2, which only contained lugM. There was a nonsense mutation (g.308T > A) in lugM in strain RMLUG2. Six frameshift mutations were identified in all strains in the genes encoding NRPS enzymes. All frameshift mutations resulted from the deletion of one or two nucleotides, leading to premature termination codons. Additionally, an 18 bp deletion was identified at the beginning of the putative regulator lugR gene in our five strains. An insertion segment, g.67_68insATTTTATACAGGAAGAAG, was identified in lugZ of strains RMLUG4 and RMLUG5. Among all strains, 34 of the 39 genomes in the GenBank database contained 14 complete lug genes, two of which belonged to the same type of strain (NCTC12217) despite different assembly levels from different laboratories. Similar to strain RMLUG2, strains VCU150, VISLISI_25, and C_33 harbored only lugM, but had missense mutations instead of the nonsense mutation. Further analysis of the 38 strains indicated missense mutations in 12 of 14 genes (excluding lugI and lugD), making this the most common mutation type. Missense mutations were detected in lugJ (g.394G > A) in all CC1 isolates. Interestingly, missense mutations were found in lugE (g.331A > G) in 32 of the 38 S. lugdunensis strains, but were not present in any ST1 strain, except strain HKU09-01. Missense mutations in lugG (g.551C > T) were present in all CC6 isolates. In addition, genetic variations in the lug operon were independent of geographical origin. In the current study, the MIC tests and genomic analysis indicated discordance between genotype and phenotype, similar to the findings of Kao et al[5] There are several possible reasons for this discrepancy. First, the heterogeneity of the mecA gene can suppress methicillin resistance. Gargis et al[6] reported that a frameshift mutation in mecA and lack of the full mecA promoter sequence can cause susceptibility to oxacillin and cefoxitin, respectively. Additionally, Chen et al[7] reported that the –33C to T substitution within the mecA promoter can lower the oxacillin MIC, whereas this mutation was identified in strains RMLUG2(MSSL), RMLUG1(MRSL), and RMLUG6(MRSL). Second, mutations in auxiliary genes may contribute to decreased resistance to methicillin. Giannouli et al[8] reported that the accumulation of amino acid changes in FemXAB family proteins may affect cell wall synthesis, leading to atypical oxacillin responsiveness. Several mutations were detected in the femX, femA, and femB genes between strain RMLUG2 and S. lugdunensis JICS135, which might account for the lowered MIC. Moreover, we identified CC-dependent genetic variations of the 14 lug genes, indicating that the lug operon may not be conserved in the S. lugdunensis genome. Lebeurre et al[9] detected significant genetic variations independent of CCs in the lug locus. However, they only searched against genes encoding four NRPS enzymes (lugA, lugB, lugC, and lugD) and one regulator gene (lugR), with the results being somewhat consistent with our findings. Our results indicated that not all S. lugdunensis isolates harbor the lug operon. Four strains containing only lugM varied in clinical source and geographical location; thus, no link was evident between S. lugdunensis lug polymorphisms and geographical origin. There were some limitations to this study. First, we only described the phenotypes and genotypes of the six strains, which could not establish a causal relation. Functional studies are needed to investigate the activity of resistance genes and the lug operon. Second, the GenBank data may be biased because some sequences were obtained only by third-generation sequencing without assembling sequence fragments obtained by other methods. Thus, the accuracy of the sequences should be taken into account. In particular, some nucleotides need to be corrected to confirm the mutations of the lug operon in the future. Overall, our findings revealed variations in the genomes of S. lugdunensis strains isolated from different cities in China. We report novel SCCmec and SCCRMLUG4 elements, suggesting the need for additional studies on this species. Comparative analysis of the lug operon for all available genomes demonstrated CC-dependent genetic variations; however, further research is needed to elucidate the relationships between genotypes and phenotypes. Data availability The complete genome sequences have been deposited at GenBank under the accessions CP084480-CP084483 (RMLUG1), CP084434-CP084436 (RMLUG2), CP084437-CP084439 (RMLUG3), CP084440-CP084442 (RMLUG4), CP084443 (RMLUG5), and CP084444-CP084446 (RMLUG6). Acknowledgments The authors thank Pengcheng Du (Beijing YuanShengKangTai (ProtoDNA) Genetech Co Ltd.) for the technical help in Oxford Nanopore sequencing. We would like to thank Jing Wu for the collection of patient characteristics. We would like to thank Dr. Ronghua Liu (Microbiology Laboratory of Linfen Central Hospital, Linfen, Shaanxi, China) for antibiotic susceptibility test. Funding This work was supported by grants from the National Science and Technology Major Project of China (No. 2017ZX10103004-006) and the National Key Research and Development Programme of China (No. 2016YFC0903800). Conflicts of interest None.

ABSTRACT The carbapenem-resistant Klebsiella pneumoniae (CRKP) strain GX34 was recovered from the respiratory tract of an elderly male with severe pneumonia, and only susceptible to amikacin, tigecycline, and colistin. Complete genome suggested that it belonged to K51-ST16 and harbored plasmid-encoded NDM-4 and OXA-181, located on IncFIB plasmid GX34p1_NDM-4 and ColKP3/IncX3 plasmid GX34p4_OXA-181, respectively. A series of transconjugants generated in the plasmid conjugation assays, including Escherichia coli J53-N1 (harboring a self-transmissible and bla NDM-1 -producing plasmid Eco-N-1-p), J53-N2 (harboring a bla NDM-4 -producing plasmid and a helper plasmid GX34p5), and J53-O (harboring a bla OXA-181 -producing plasmid), could be stably inherited after 10 days of serial passage and no significant biological fitness costs were detected. Furthermore, we first reported the bla NDM-1 gene, derived from bla NDM-4 mutation (460C>A) under meropenem pressure, could be in vitro transferred into a self-conjugative, recombined plasmid Eco-N-1-p of J53-N1. Eco-N-1-p was mainly recombined by GX34p4_OXA-181 (40,449 bp, 75.16%) and GX34p1_NDM-4 (8,553 bp, 15.89%), in which IS 26 and IS 5-like probably played a major role. Eco-N-1-p could be transferred into the conjugation recipient K. pneumoniae KP54 and make the latter sacrifice fitness. The retention rates of bla NDM-1 remained high stability (>80% after 200 generations). The comparative genomic analysis of GX34 and those carrying bla NDM-4 or bla OXA-181 genes retrieved from the NCBI RefSeq database showed all bla NDM-4 (26/26, 100.00%) and bla OXA-181 (13/13, 100.00%) were surrounded by IS 26 . The immediate environment of bla NDM-4 and bla OXA-181 in GX34 and some retrieved strains shared identical features, hinting at their possible dissemination. Effective measures should be taken to monitor the spread of this clone.

Background Infiltration of the lower respiratory tract (LRT) microenvironment could be significantly associated with respiratory diseases. However, alterations in the LRT microbiome and metabolome in infectious and inflammatory respiratory diseases and their correlation with inflammation still need to be explored. Methods Bronchoalveolar lavage samples from 44 community-acquired pneumonia (CAP) patients, 29 connective tissue disease-associated interstitial disease (CTD-ILD) patients, and 30 healthy volunteers were used to detect microbiota and metabolites through 16S rRNA gene sequencing and untargeted high-performance liquid chromatography with mass spectrometry. Results The composition of the LRT microbial communities and metabolites differed in disease states. CAP patients showed a significantly low abundance and both diseases presented a depletion of some genera of the phylum Bacteroidetes, including Prevotella, Porphyromonas, and health-associated metabolites, such as sphingosine (d16:1), which were negatively correlated with infectious indicators. In contrast, Bacillus and Mycoplasma were both enriched in the disease groups. Streptococcus was specifically increased in CTD-ILD. In addition, co-elevated metabolites such as FA (22:4) and pyruvic acid represented hypoxia and inflammation in the diseases. Significantly increased levels of amino acids and succinate, as well as decreased itaconic acid levels, were observed in CAP patients, whereas CTD-ILD patients showed only a handful of specific metabolic alterations. Functions related to microbial lipid and amino acid metabolism were significantly altered, indicating the possible contributions of microbial metabolism. Dual omics analysis showed a moderate positive correlation between the microbiome and metabolome. The levels of L-isoleucine and L-arginine were negatively correlated with Streptococcus, and itaconic acid positively correlated with Streptococcus. Conclusion In the LRT microenvironment, shared and specific alterations occurred in CAP and CTD-ILD patients, which were associated with inflammatory and immune reactions, which may provide a new direction for future studies aiming to elucidate the mechanism, improve the diagnosis, and develop therapies for different respiratory diseases.

Background Metagenomic next-generation sequencing (mNGS) is an important supplement to conventional tests for pathogen detections of pneumonia. However, mNGS pipelines were limited by irregularities, high proportion of host nucleic acids, and lack of RNA virus detection. Thus, a regulated pipeline based on mNGS for DNA and RNA pathogen detection of pneumonia is essential. Methods We performed a retrospective study of 151 patients with pneumonia. Three conventional tests, culture, loop-mediated isothermal amplification (LAMP) and viral quantitative real-time polymerase chain reaction (qPCR) were conducted according to clinical needs, and all samples were detected using our optimized pipeline based on the mNGS (DNA and RNA) method. The performances of mNGS and three other tests were compared. Human DNA depletion was achieved respectively by MolYsis kit and pre-treatment using saponin and Turbo DNase. Three RNA library preparation methods were used to compare the detection performance of RNA viruses. Results An optimized mNGS workflow was built, which had only 1-working-day turnaround time. The proportion of host DNA in the pre-treated samples decreased from 99 to 90% and microbiome reads achieved an approximately 20-fold enrichment compared with those without host removal. Meanwhile, saponin and Turbo DNase pre-treatment exhibited an advantage for DNA virus detection compared with MolYsis. Besides, our in-house RNA library preparation procedure showed a more robust RNA virus detection ability. Combining three conventional methods, 76 (76/151, 50.3%) cases had no clear causative pathogen, but 24 probable pathogens were successfully detected in 31 (31/76 = 40.8%) unclear cases using mNGS. The agreement of the mNGS with the culture, LAMP, and viral qPCR was 60%, 82%, and 80%, respectively. Compared with all conventional tests, mNGS had a sensitivity of 70.4%, a specificity of 72.7%, and an overall agreement of 71.5%. Conclusions A complete and effective mNGS workflow was built to provide timely DNA and RNA pathogen detection for pneumonia, which could effectively remove the host sequence, had a higher microbial detection rate and a broader spectrum of pathogens (especially for viruses and some pathogens that are difficult to culture). Despite the advantages, there are many challenges in the clinical application of mNGS, and the mNGS report should be interpreted with caution.

Background: Community-acquired pneumonia (CAP) is often accompanied by changes in lipid metabolism. This study aimed to examine the changes in serum phospholipids (PLs) that may be useful for early disease stratification and as potential therapeutic targets in patients with CAP. Methods: Serum samples from 58 patients hospitalized with CAP and 11 control samples were collected during admission between January 2017 and October 2018. Targeted lipidomic analysis was used to determine the concentrations of phosphatidylcholine (PC), lysophosphatidylcholine (LPC), phosphatidylethanolamine (PE), and lysophosphatidylethanolamine (LPE). The Gene Expression Omnibus (GEO) database was used to evaluate the gene expression levels of key enzymes in the Lands cycle, and quantitative real-time polymerase chain reaction (qRT-PCR) was used for further verification. Results: A significant decrease in LPC levels and an increase in PE levels, PC/LPC and PE/LPE ratios were observed in patients with CAP (P<0.05). The area under the curve (AUC) of PE serum concentrations combined with CURB-65 scores (confusion, uremia, respiratory rate, blood pressure, and age >= 65 years) was 0.848 for discriminating disease severity, which was significantly higher than the discriminating disease severity of CURB-65 (P<0.05). The efficiency of predicting 30-day mortality using PC, LPC, or PC/LPC ratio combined with CURB-65 scores (AUC =0.811, AUC =0.854, AUC =0.838, respectively) was better than CURB-65 alone (P<0.05). Gene expression analysis revealed the upregulation of LPC acyltransferase 2. Conclusions: LPC or PE serum levels as well as PC/LPC ratios combined with CURB-65 are effective biomarkers for predicting the disease severity and 30-day mortality of patients with CAP. Further investigations of phospholipid metabolism will improve our understanding and treatment of CAP.

Despite progress in intensive care, the morbidity and mortality of patients with community-acquired pneumonia (CAP) remains high. Furthermore, the predictive and prognostic utility of resistin-like molecule beta (RELM-β) in patients with CAP is uncertain. This study investigated the role of RELM-β in patients with CAP and evaluated its correlation with disease severity and the risk of death. A prospective, multicenter study was conducted in 2017, and admission serum levels of RELM-β were detected using quantitative enzyme-linked immunosorbent assay. A total of 114 and 112 patients with severe CAP (SCAP) and non-severe CAP (NSCAP) were enrolled, respectively, with 15 healthy controls. Patients with SCAP, especially non-survivors, had significantly higher levels of serum RELM-β than patients with NSCAP. RELM-β levels positively correlated with severity scores and consistently predicted SCAP in patients with CAP (area under the curve = 0.794). Increased levels of RELM-β were closely related to the severity and prognosis of patients with CAP. The accuracy of 30-day mortality predictions of CURB-65 (confusion, urea, respiratory rate, blood pressure, and age ≥ 65 years) can be significantly improved when combined with RELM-β levels. The level of RELM-β can assist clinicians in risk stratification of patients with CAP in early stages.

This study aimed to characterize the lipidomic responses to community-acquired pneumonia (CAP) and provide new insight into the underlying mechanisms of pathogenesis and potential avenues for diagnostic and therapeutic treatments. This study was performed from January 2017 to October 2018. Lipidomic profiles were generated using ultra high-performance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) platform. Spearman’s rank correlation test and multiple linear regression analysis were applied to explore the correlation between changes in the relative abundance of lipids and clinical parameters. Kaplan–Meier methods were used to build 30-day survival curves. From the UHPLC-MS/MS results, a total of 509 and 195 lipid species were detected in the positive and negative ionization mode respectively. Positive ionization covered six lipid classes (glycerol-phospholipids, glycerolipids, sphingolipids, sterol-lipids, prenol-lipids, and fatty acid), whilst negative ionization covered three (glycerol-phospholipids, sphingolipids, fatty acid). Four lipids were selected as targets: PC (16:0_18:1), PC (18:2_20:4), PC (36:4), and PC (38:6). The relative increase of the areas under the curves for all four lipids were superior to the pneumonia severity index and CURB-65 (confusion, urea, respiratory rate, blood pressure, and age ≥65 years old) for discriminating severe CAP from CAP. Decreasing relative levels of PC (18:2_20:4), PC (38:6), and PC (36:4) were negatively related to fraction of inspiration O2; Changes in the relative abundance of PC (16:0_18:1) and PC (18:2_20:4) had significantly linear relationship with procalcitonin. Patients with an elevated level of PC (16:0_18:1) had significantly longer duration of hospital stays. As the relative abundance of PC (18:2_20:4), PC (36:4), and PC (38:6) decreased, the length of hospitalization days and 30-day mortality rate increased significantly (all log-rank p<0.05). Therefore, using the UHPLC-MS/MS platform’s serum lipidomic approach can help reveal changes in lipid abundance during CAP and establish lipid profiles related to disease severity.

Community-acquired pneumonia (CAP) is a respiratory disease frequently requiring hospital admission, and a significant cause of death worldwide. This study aimed to investigate the prognostic value of clinical indicators. A prospective, multi-center study was conducted (January 2017–December 2018) where patient demographic and clinical data were recorded (N = 366). The 30-day mortality rate was 5.46%. Cox Regression analyses showed that serum albumin (ALB) and respiratory rate (RR) were independent prognostic variables for 30-day survival in patients with CAP. Albumin negatively correlated with the Pneumonia Severity Index (PSI) and CURB-65 scores using Pearson and Spearman tests. Survival curves showed that a RR >24 breaths/min or ALB ≤30 g/L were associated with a significantly higher risk of mortality. The area-under-the-curve (AUC) for predicting 30-day mortality in patients with CAP was 0.762, 0.763, 0.790, and 0.784 for ALB, RR, PSI, and CURB-65, respectively. The AUC for the prediction of 30-day mortality using ALB combined with PSI, CURB-65 scores, and RR was 0.822 (95% CI 0.731–0.912), 0.847 (95% CI 0.755–0.938), and 0.847 (95% CI 0.738–0.955), respectively. Albumin and RR were found to be reliable prognostic factors for CAP. This combination showed equal predictive value when compared to adding ALB assessment to PSI and CURB-65 scores, which could improve their prognostic accuracy.

Polymorphisms of the catechol-O-methyl transferase (COMT) or monoamine oxidase B (MAO-B) genes may affect the occurrence of dyskinesia in Parkinson’s disease (PD) patients. However, the findings are inconsistent. Thus, we performed a meta-analysis to assess whether COMT and MAO-B genetic variants are associated with an increased incidence of levodopa-induced dyskinesia (LID) in PD patients. A literature search of PubMed, Embase, and Cochrane Library was conducted to identify relevant studies published up to January 2021. The strength of the association between the polymorphisms and LID susceptibility was estimated by odds ratio (OR) and associated 95% confidence interval (CI). The pooled ORs were assessed in different genetic models. Ten studies involving 2385 PD patients were included in the meta-analysis. Analysis of pooled ORs and 95% CIs suggested that the AA genotype of COMT(rs4680) was associated with LID (OR = 1.39, 95%CI: 1.02–1.89, P = 0.039) in the recessive model, and this correlation was more obvious in Brazilian samples in the analysis stratified by ethnicity. For the AG genotype of MAO-B(rs1799836), the pooled OR was 1.66 (95% CI: 1.04–2.65, P = 0.03) in patients with LID versus those without LID in the heterozygote model. Our meta-analysis implicates the AA genotype of the COMT rs4680 polymorphism as potentially increasing the risk of LID in a recessive genetic model for PD patients. Furthermore, the AG genotype of the MAO-B rs1799836 polymorphism may influence the prevalence of LID in PD patients in the heterozygote model. However, further well-designed studies with larger PD patient cohorts are required to validate these results after adjusting for confounding factors.