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Background To investigate the combined effect of red blood cell distribution width(RDW) and inflammatory biomarkers on in-hospital outcomes of acute ischemic stroke(AIS) patients with thrombolysis. Methods and Results 417 AIS patients with thrombolysis were included. The participants were divided into four groups according to the cut-off of white blood cell (WBC) or C reactive protein(CRP) and RDW: LWLR, LWHR, HWLR, and HWHR; or LCLR, LCHR, HCLR, and HCHR(L-low, H-high, W-WBC, C-CRP, R-RDW). Logistic regression models were used to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) of in-hospital pneumonia and functional outcome across the four subgroups. Patients with higher RDW and inflammatory biomarkers levels have the highest risk of in-hospital outcomes. Compared with patients in LWLR group, the ORs (95% CIs) of those in HWHR group were 12.16 (4.21–35.14) and 9.31 (3.19–27.17) for in-hospital pneumonia and functional outcome. The ORs (95% CIs) of those in HCHR group were 6.93 (2.70-17.78) and 3.38(1.10-10.39) for in-hospital pneumonia and functional outcome, compared with patients in LCLR group. Simultaneously adding RDW and WBC or CRP to the basic model with established risk factors significantly improved risk discrimination and reclassification for pneumonia and functional outcome (all P

SARS-CoV and SARS-CoV-2 have been thought to originate from bats. In this study, we screened pharyngeal and anal swabs from 13,064 bats collected between 2016 and 2021 at 703 locations across China for sarbecoviruses, covering almost all known southern hotspots, and found 146 new bat sarbecoviruses. Phylogenetic analyses of all available sarbecoviruses show that there are three different lineages, L1 as SARS-CoV related CoVs (SARSr-CoVs), L2 as SARS-CoV-2 related CoVs (SC2r-CoVs), and novel L-R (recombinants of L1 and L2) present in R. pusillus bats, in the mainland of China. Among the 146 sequences, only 4 are L-Rs. Importantly, none belongs in the L2 lineage, indicating that circulation of SC2r-CoVs in China might be very limited. All remaining 142 sequences belong in the L1 lineage, of which YN2020B-G shares the highest overall sequence identity with SARS-CoV (95.8%). The observation suggests endemic circulations of SARSr-CoVs, but not SC2r-CoVs, in bats in China. Geographic analysis of the collection sites in this study, together with all published reports, indicates that SC2r-CoVs may be mainly present in bats of Southeast Asia including the southern border of Yunnan province but absent in all other regions within China. In contrast, SARSr-CoVs appear to have broader geographic distribution, with the highest genetic diversity and sequence identity to human sarbecoviruses along the southwest border of China. Our data provide the rationale for further extensive surveys in broader geographical regions within, and beyond, Southeast Asia in order to find the most recent ancestors of human sarbecoviruses.

The effect of emergency department length of stay (EDLOS) on outcomes of patients with acute ischemic stroke (AIS) remains largely unexamined. We aimed to investigate the association between EDLOS and outcomes in AIS patients.618 AIS patients were enrolled. Baseline demographics, vascular risk factors, ED admission information, hyperacute treatment of AIS and stroke severity were collected. Stroke progression was defined as any new neurological symptoms/signs or any neurological worsening within 7 days after stroke onset and poor prognosis was defined as modified Rankin Scale(mRS) scores2 at 30 day. The effect of EDLOS on stroke progression and prognosis was assessed.The median EDLOS was 2.5 h (1.4-6.9 h). On multivariable linear regression, presentation month between Apr. and Jun., admission at the ED between 7 am to 3 pm(P = 0.036), transferring to stroke unit, receiving endovascular interventional treatment, onset on holidays, and progressive stroke were associated with shorter EDLOS(all P 0.05). A shorter EDLOS was significantly associated with an increased risk of stroke progression (P = 0.007). Patients with the lowest EDLOS (≤1.35 h) were 2-3 fold more likely to have stroke progression, compared with those with the highest EDLOS (6.93 h) (OR, 2.52; 95% CI, 1.29-4.93; P = 0.043). However, no significant association between EDLOS and stroke prognosis was revealed.In AIS patients, shorter EDLOS was associated with the increased risk of stroke progression, possibly reflecting prioritized admission of more severely affected patients at high risk of stroke progression. EDLOS alone might be an insufficient indicator of stroke care in the ED.

Objective To screen out potential biomarkers by analyzing fundamental nutrients in the bronchoalveolar lavage fluid (BALF) before confirming the lung cancer. Methods In this study, 44 patients were enrolled with clinical information. The concentrations of 23 amino acids and 35 carnitines in their BALF were detected with the high-performance liquid chromatography–mass spectrometry (HPLC–MS). Combined with clinicopathological diagnosis, the patients were divided into the lung cancer group (grades I & II and III & IV) and the non-cancer group for standard statistical analysis. Results The partial least squares-discriminant analysis (PLS-DA), the Shapiro–Wilk test, and the Bonferroni correction results showed that the serine concentration was higher and the butane-diacyl-carnitine (C4DC) concentration was lower in the lung cancer group, further showing the same changing trend continuously through the non-cancer stage, grades I & II stage and grades III & IV stage. Those two potential biomarkers have been identified. Conclusion The HPLC–MS target detection in clinic for nutrient concentration levels is a promising technique to find the changing concentration of serine and C4DC in BALF, which provides an economical and practical way for early warning of lung cancer.

The prognostic significance of combination of white blood cell (WBC) and D-dimer on acute ischemic stroke (AIS) remains to be explored. We aimed to investigate the combined effect of WBC and D-dimer levels on in-hospital outcomes of AIS patients.801 AIS patients were included. Patients were divided into four groups according to the cut-point identified by receiver operating characteristic (ROC) curve of D-dimer (1.105 μg/L) and WBC (7.05 × 109/L): LWLD (low WBC count and low D-dimer), LWHD (low WBC count and high D-dimer), HWLD (high WBC count and low D-dimer), and HWHD (high WBC count and high D-dimer). HWHD group had the highest cumulative incidence of in-hospital mortality (hazard ratio, 5.79; 95%CI, 1.71-19.58, P = 0.006). Patients in HWHD group were 4.14 fold more likely to have in-hospital pneumonia (odds ratio, 4.14; 95%CI, 2.09-8.21; P 0.001), compared with those in LWLD group. The area under curve (AUC) of the combination of WBC and D-dimer levels for in-hospital mortality and pneumonia was larger than that of WBC and D-dimer alone (0.920 vs. 0.900 vs. 0.915; 0.831 vs. 0.829 vs. 0.807).The combination of WBC count and D-dimer levels at admission was independently associated with in-hospital outcomes of AIS patients. The addition of WBC to D-dimer levels had a tendency to improve the predictive power for in-hospital mortality and pneumonia.

Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 have been thought to originate from bat, but whether the cross-species transmission occurred directly from bat to human or through an intermediate host remains elusive. In this study, we performed CoV screening of 102 samples collected from animal-selling stalls of Wuhan Huanan Market (WHM) and pharyngeal and anal swabs from13,064 bats collected at 703 locations across China, covering almost all known southern hotspots for sarbecovirus, between 2016 and 2021. This is the first systematic survey of bat CoV in China during the outbreak of Corona Virus Disease 2019. We found four non-sarbeco CoVs in samples of WHM, and 142 SARS-CoV related CoVs (SARSr-CoV) and 4 recombinant CoVs in bats, of which YN2020B-G share the highest sequence identity with SARS-CoV among all known bat CoVs, suggesting endemic SARSr-CoVs in bats in China. However, we did not find any SARS-CoV-2 related CoVs (SC2r-CoV) in any samples, including specimens collected from the only two domestic places where RaTG13 and RmYN02 were previously reported (the Tongguan caves and the karst caves around the Xishuangbanna Tropical Botanical Garden), indicating that SC2r-CoVs might not actively circulate among bats in China. Phylogenetic analysis showed that there are three different lineages of sarbecoviruses, L1 (SARSr-CoV), L2 (SC2r-CoV), and L-R (a novel CoV lineage from L1 and L2 recombination), in China. Of note, L-R CoVs are only found in R. pusillus. Further macroscopical analysis of the genetic diversity, host specificity for colonization and accidental infection, and geographical characteristics of available CoVs in database revealed the presence of a general geographical distribution pattern for bat sarbecoviruses, with the highest genetic diversity and sequence homology to SARS-CoV or SARS-CoV-2 along the southwest border of China, the least in the northwest of China. Considering the receptor binding motifs for spike gene of sarbecoviruses in Indochina Peninsula show the greatest diversity, our data provide the rationale that extensive surveys in further south and southwest to or of China might be needed for finding closer ancestors of SARS-CoV and SARS-CoV-2.

The study aims to develop a hierarchical framework for sustainable tourism considering socio-economic, socio-environmental and eco-efficiency aspects (coordinated triple bottom line). However, development of this hierarchical framework development must consider linguistic preferences and the interrelationships between the aspects and the criteria. Hence, the vague set is used to address linguistic preferences, and the interrelationships are presented with the decision-making and trial evaluation laboratory technique. Interpretive structural modeling is used to develop the sustainable tourism hierarchical framework. The results reveal that (1) socio-economics has a greater influence and (2) eco-efficiency performance does not reach the expected level because tourism firms encounter conflicts in balancing economic growth and environmental impact. This proposed hierarchical framework aims to guide the tourism industry toward sustainability. This study also proposes rewarding employees for promoting eco-processes, creating new eco-commercial links with the public and adopting an eco-organization to increase competitiveness and profitability for the practitioners.

Summary Background: An improved understanding of the gut microbiota could lead to better strategies for the diagnosis, therapy and prophylaxis of tuberculosis (TB). The impact of both Mycobacterium tuberculosis (Mtb) infection and anti-TB treatment on the gut microbiota has rarely been studied. Methods: We characterized the diversity and composition of the gut microbiota in pulmonary TB patients as well as the effects of anti-TB drugs on the gut microbiota. Results: Pulmonary Mtb infection led to a minor decrease in the α diversity of the gut microbiota when compared to healthy controls, which mainly resulted from changes in the relative abundance of the members of genus Bacteroides. Anti-TB therapy caused a rapid, significant alteration in the community structure. The relative abundance of members of genus Clostridiales of the phylum Firmicutes significantly decreased during anti-TB treatment, while many members of genus Bacteroides, including Bacteroides OTU230 and Bacteroides fragilis, were among the taxa that increased. OTU8 and OTU2972 assigned to family Erysipelotrichaceae of the phylum Firmicutes showed a dramatic increase 1 week after the start of therapy, while the other members of this family decreased. Conclusions: Pulmonary TB and anti-TB treatment caused a distinct dysbiosis of the gut microbiota. Our study contributes valuable information implying potential links between the gut microbiota and TB.

Background: Tracking the spread of the Neisseria gonorrhoeae strains with decreased susceptibility or resistance to cephalosporins is a major priority for global surveillance programmes. Whole-genome sequencing (WGS) has been widely used by increasing countries in North America, Europe, and Pacific to determine the decreased susceptible or resistance determinants of Neisseria gonorrhoeae, track the spread of these determinants throughout the gonococcal population at national or regional level. However, no studies to date have examined the genomic epidemiology of gonorrhea in Asia where the antimicrobial resistant strains of Neisseria gonorrhoeae appears to have emerged before disseminating the strains globally. Methods: We obtained clinical isolates and data from the China Gonococcal Resistance Surveillance Programme (China-GRSP) from 2012 to 2013. We sequenced the genomes of 435 clinical isolates of Neisseria gonorrhoeae, including 112 (25.6%) isolates with decreased susceptibility to ceftriaxone (Cfx-DS). We assessed the association between antimicrobial resistance genotype and phenotype. We also compared our data with the whole genome data of the isolates from the USA and the UK in the GenBank. Findings: The most prevalent MLST STs in our gonococcal population were MLST ST7827 (n = 74), followed by ST7365 (n = 58), ST1600 (n = 38), ST7367 (n = 35), and ST7363 (n = 29). MLST ST1901 which was reported as the predominant ST in the US was not found in our population. A total of 2512 strains, including additional 2077 published NG strains, were further included for phylogenetic analysis. It generated two distinct lineages - lineage 1 and lineage 2. Analysis of MLST ST1901 in the database indicate that most of MLST ST1901 isolates in the lineage2.6 were Cfx-DS isolates while all isolates in the lineage 2.1 were sensitive to ceftriaxone (77/110 vs. 0/13; p

Background Circular RNAs (circRNAs) are a group of noncoding RNAs that participate in gene expression regulation in various pathways. The essential roles of circRNAs have been revealed in many species. However, knowledge of circRNAs in fungi is still not comprehensive. Results Trichophyton rubrum (T. rubrum) is considered a model organism of human pathogenic filamentous fungi and dermatophytes. In this study, we performed a genome-wide investigation of circRNAs in T. rubrum based on high-throughput sequencing and ultimately identified 4254 circRNAs. Most of these circRNAs were specific to the conidial or mycelial stage, revealing a developmental stage-specific expression pattern. In addition, 940 circRNAs were significantly differentially expressed between the conidial and mycelial stages. PCR experiments conducted on seven randomly selected differentially expressed (DE-) circRNAs confirmed the circularized structures and relative expression levels of these circRNAs. Based on their genome locations, most circRNAs originated from intergenic regions, unlike those in plants and animals. Furthermore, we constructed circRNA-miRNA-mRNA regulatory networks that included 661 DE-circRNAs targeting 140 miRNAs and further regulating 2753 mRNAs. The relative expression levels of two randomly selected circRNA-miRNA-mRNA axes were investigated by qRT-PCR, and the competing endogenous RNA (ceRNA) network theory was validated. Functional enrichment analysis of the target genes suggested that they were significantly involved in posttranscriptional processes and protein synthesis as well as some small-molecule metabolism processes. CircRNAs are relatively more conserved in closely related dermatophytes but rarely conserved in distantly related species. Tru_circ07138_001 is a highly conserved circRNA that was conserved in all ten dermatophytes analyzed in our study and three distantly related species. Its host gene TERG_07138 was also highly conserved in two of these distantly related species Gallus gallus and Caenorhabditis elegans. The specific role of this circRNA deserves further exploration. Conclusions Our study is the first to provide a global profile of circRNAs in T. rubrum as well as dermatophytes. These results could serve as valuable resources for research on circRNA regulatory mechanisms in fungi and reveal new insights for further investigation of the physical characteristics of these significant human fungal pathogens.

Current power grid development-diagnosis management doesn’t analyze the power grid cooperation-scale, development-speed, business-quality, operation-effectiveness and internal policy from comprehensive view. In order to improve management efficiency, this paper modified the evaluation method, built the evaluation index system based on Analytic Network Process (ANP), which took the connection and restriction among index into full consideration. And then took 5 aspect namely Scale, Structure, Safety, Effectiveness and Policy of 220 kV Grid from one province into calculation, obtained the provided the index score. Finally, concluded the advantages and disadvantages of this province 220 kV grid and provided objective and pointed suggestions to the high-quality development of power grid management as an example to other provinces.

The global electronics industry has faced pressure from diversity standards and regulations such as RoHS, WEEE, and REACH, among others. Therefore, electronics firms are striving to implement the triple bottom line (TBL) in their real practices to attain the co-benefits for stakeholders. However, to assess the firms’ performance, there is a lack of a hierarchical structure to consider the interrelationships among these co-benefits. Hence, the objective of this study is to develop a precise TBL structure to assist firms in identifying the key practices to attain the co-benefits. There are three notable results: 1. there are nine aspects of the hierarchical structure, in contrast to the original TBL framework; 2. the hierarchical structure offers precise guidelines for firm practices; and 3. the proposed hybrid method is employed to address the co-benefits the industry seeks to attain. This study provides a theoretical basis for enhancing the understanding of co-benefits and identifies a precise way to guide firms to achieve the co-benefits of the TBL.

The current descriptive cross-sectional study aimed to explore the mediating role of perceived nursing work environment (PNWE) in the relationship between psychological capital (PsyCap) and perceived professional benefits among Chinese nurses. Participants ( N = 351) working in two large general hospitals in Guangdong, China completed self-report questionnaires from March to May 2017. Linear regression analyses and structural equation modeling were performed to explore the mediating effect. PsyCap (particularly for hope and optimism) had a positive effect on perceived professional benefits, and PNWE was a mediator in this relationship among Chinese nurses. A good working environment can be regarded as a mediator variable, increasing staff's competence and sense of belonging to a team. For successful implementation, nurse managers should use effective strategies to increase nurses' confidence and hope while providing a comfortable work environment. [ Journal of Psychosocial Nursing and Mental Health Services, 56 (4), 38–47.]

Tuberculosis (TB) is one of the leading causes of death worldwide, especially in developing countries. Neonatal BCG vaccination occurs in various regions, but the level of protection varies in different populations. Recently, Mycobacterium vaccae is found to be an immunomodulating therapeutic agent that could confer a significant level of protection against TB. It is the only vaccine in a phase III trial from WHO to assess its efficacy and safety in preventing TB disease in people with latent TB infection. However, the mechanism of immunotherapy of M. vaccae remains poorly understood. In this study, the full genome of M. vaccae was obtained by next-generation sequencing technology, and a proteogenomic approach was successfully applied to further perform genome annotation using high resolution and high accuracy MS data. A total of 3,387 proteins (22,508 unique peptides) were identified, and 581 proteins annotated as hypothetical proteins in the genome database were confirmed. Furthermore, 38 novel protein products not annotated at the genome level were detected and validated. Additionally, the translational start sites of 445 proteins were confirmed, and 98 proteins were validated through extension of their translational start sites based on N terminus-derived peptides. The physicochemical characteristics of the identified proteins were determined. Thirty-five immunogenic proteins of M. vaccae were identified by immunoproteomic analysis, and 20 of them were selected to be expressed and validated by Western blot for immunoreactivity to serum from patients infected with M. tuberculosis. The results revealed that eight of them showed strong specific reactive signals on the immunoblots. Furthermore, cellular immune response was further examined and one protein displayed a higher cellular immune level in pulmonary TB patients. Twelve identified immunogenic proteins have orthologous in H37Rv and BCG. This is the first study to obtain the full genome and annotation of M. vaccae using a proteogenomic approach, and some immunogenic proteins that were validated by immunoproteomic analysis could contribute to the understanding of the mechanism of M. vaccae immunotherapy.

Anelloviruses comprise a group of non-enveloped circular single-stranded DNA viruses with genomes of 2–4 kb. Anelloviruses were first reported in 1997 in a Japanese patient with post-transfusion he...

An improved understanding of the lung microbiome may lead to better strategies to diagnose, treat, and prevent pulmonary tuberculosis (PTB). However, the characteristics of the lung microbiomes of patients with TB remain largely undefined. In this study, 163 bronchoalveolar lavage (BAL) samples were collected from 163 sputum-negative suspected PTB patients. Furthermore, 12 paired BAL samples were obtained from 12 Mycobacterium tuberculosis-positive (MTB+) patients before and after negative conversion following a two-month anti-TB treatment. The V3-V4 region of the 16S ribosomal RNA (rRNA) gene was used to characterize the microbial composition of the lungs. The results showed that the prevalence of MTB in the BAL samples was 42.9% (70/163) among the sputum-negative patients. The α-diversity of lung microbiota was significantly less diverse in MTB+ patients compared with Mycobacterium tuberculosis-negative (MTB-) patients. There was a significant difference in β-diversity between MTB+ and MTB- patients. MTB+ patients were enriched with Anoxybacillus, while MTB- patients were enriched with Prevotella, Alloprevotella, Veillonella, and Gemella. There was no significant difference between the Anoxybacillus detection rates of MTB+ and MTB- patients. The paired comparison between the BAL samples from MTB+ patients and their negative conversion showed that BAL negative-conversion microbiota had a higher α-diversity. In conclusion, distinct features of airway microbiota could be identified between samples from patients with and without MTB. Our results imply links between lung microbiota and different clinical groups of active PTB.

Hantaviruses (HVs) and arenaviruses (AreVs) of rodent origin are important causative agents of human diseases. Many types of rodent HVs (e.g., Hantaan virus, HTNV; Seoul virus, SEOV; and Puumala vi...

Enterovirus 71 (EV71) causes outbreaks of hand, foot and mouth disease (HFMD), primarily in the Asia-Pacific area, that are often associated with complications of severe to fatal neurological symptoms. There are currently no anti-viral therapies or vaccines available for the treatment of EV71 infection. Illustrating human antibody responses neutralizing EV71 infection could potentially provide valuable information for the development of effective therapies and vaccines. Here, we constructed a comprehensive phage display library based on peripheral blood of eight EV71-infected donors and identified 27 EV71-specific human antibodies, of which four have neutralizing activity in in vitro experiments. Deep sequencing analysis of the antibody heavy chains at the transcript level of another three independent EV71-infected donors and three controls demonstrates that heavy chains of the EV71-specific antibodies are conserved among EV71-infected individuals but absent in controls, suggesting convergent evolution of human antibodies against EV71.

Background Pre-hospital delay was a critical factor affecting stroke patients receiving intravenous thrombolytic therapy. The aim of this study was to explore the factors associated with pre-hospital delay and thrombolysis in China. Methods Patient data were obtained from emergency department (ED), and the factors of patient pre-hospital delay were recorded through a well-designed form. Results A total of 630 patients were eventually included in the study. 317 patients were admitted to the ED during the thrombolysis time window, and only 105 patients received intravenous thrombolytic therapy. In the univariate analysis, transportation (OR: 0.15; 95% CI: 0.44 - 0.518; p = 0.001), atrial fibrillation (OR: 0.555; 95% CI: 0.372-0.828; p = 0.004) and response of symptoms (OR: 0.002; 95% CI: 0.000-0.013; p = 0.000) were associated with early arrival. Speech disturbances (OR: 2.095; 95% CI: 1.294-3.391; p = 0.002), smoking (OR: 2.563; 95% CI: 1.527-4.304; p = 0.000), alcohol consumption (OR: 2.155; 95% CI: 1.159-4.005; p = 0.014) and referral presentation (OR: 2.837; 95% CI: 1.584-5.082; p = 0.000) were associated with thrombolysis. In the logistic regression analysis, direct visiting to the hospital after onset and rushing to emergency after onset were independent predictor of early arrival of AIS and intravenous thrombolytic. Conclusions The pre-hospital delay of acute ischemic stroke in China was still serious. Strengthening the ability to identify stroke-related symptoms and establishing a mutual referral medical support service model between lower and upper hospitals may effectively shorten the pre-hospital delay of stroke patients.

Whole-genome sequencing was used to analyze the profiles of isoniazid (INH) resistance-related mutations among 188 multidrug-resistant strains of Mycobacterium tuberculosis (MDR-TB) and mono-INH-resistant isolates collected in a recent Chinese national survey. Mutations were detected in 18 structural genes and two promoter regions in 96.8% of 188 resistant isolates. There were high mutation frequencies in katG, the inhA promoter, and ahpC-oxyR regulator regions in INH-resistant isolates with frequencies of 86.2%, 19.6%, and 18.6%, respectively. Moreover, a high diversity of mutations was identified as 102 mutants contained various types of single or combined gene mutations in the INH-resistant group of isolates. The cumulative frequencies of katG 315 or inhA-P/inhA mutations was 68.1% (128/188) for the INH-resistant isolates. Of these isolates, 46 isolates (24.5% of 188) exhibited a high level of resistance. A high level of resistance was also observed in 21 isolates (11.2% of 188) with single ahpC-oxyR mutations or a combination of ahpC-oxyR and katG non-315 mutations. The remaining 17 mutations occurred sporadically and emerged in isolates with combined katG mutations. Such development of INH resistance is likely due to an accumulation of mutations under the pressure of drug selection. Thus, these findings provided insights on the levels of INH resistance and its correlation with the combinatorial mutation effect resulting from less frequent genes (inhA and/or ahpC). Such knowledge of other genes (apart from katG) in high-level resistance will aid in developing better strategies for the diagnosis and management of TB.

Background Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encephalitis viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. Results We used next-generation sequencing metagenomic analysis to survey for a range of mammalian viral families in rodents and other small animals of the orders Rodentia, Lagomorpha, and Soricomorpha in China. We sampled 3,055 small animals from 20 provinces and then outlined the spectra of mammalian viruses within these individuals and the basic ecological and genetic characteristics of novel rodent and shrew viruses among the viral spectra. Further analysis revealed that host taxonomy plays a primary role and geographical location plays a secondary role in determining viral diversity. Many viruses were reported for the first time with distinct evolutionary lineages, and viruses related to known human or animal pathogens were identified. Phylogram comparison between viruses and hosts indicated that host shifts commonly happened in many different species during viral evolutionary history. Conclusions These results expand our understanding of the viromes of rodents and insectivores in China and suggest that there is high diversity of viruses awaiting discovery in these species in Asia. These findings, combined with our previous bat virome data, greatly increase our knowledge of the viral community in wildlife in a densely populated country in an emerging disease hotspot. Electronic supplementary material The online version of this article (10.1186/s40168-018-0554-9) contains supplementary material, which is available to authorized users.

The global epidemic of drug-resistant tuberculosis is a catastrophic example of how antimicrobial resistance is undermining the public health gains made possible by combination drug therapy. Recent evidence points to unappreciated bacterial factors that accelerate the emergence of drug resistance. In a genome-wide association study of Mycobacterium tuberculosis isolates from China, we find mutations in the gene encoding the transcription factor prpR enriched in drug-resistant strains. prpR mutations confer conditional drug tolerance to three of the most effective classes of antibiotics by altering propionyl-CoA metabolism. prpR-mediated drug tolerance is carbon-source dependent, and while readily detectable during infection of human macrophages, is not captured by standard susceptibility testing. These data define a previously unrecognized and clinically prevalent class of M. tuberculosis variants that undermine antibiotic efficacy and drive drug resistance.

This study aimed to validate the Chinese version of the Functional Oral Intake Scale (FOIS) score in acute stroke patients with dysphagia. A sample of 128 consecutive patients with acute stroke, admitted to Department of Neurology from April to October in 2016, completed the FOIS. The interrater reliability, criterion validity, discriminant validity, cross validation, and the sensitivity of FOIS scale were evaluated. Results showed that rater agreements were excellent for FOIS (Kw = 0.881, plt; 0.001). A highly negative correlation between FOIS and WST (water swallow test) was detected (r = -0.937, plt; 0.001). There was significant difference for FOIS level of patients with different evaluation outcomes (χsup2/sup= 126.551, plt; 0.001). The FOIS evaluation results were significantly correlated with two physiological measures of swallowing. The Chinese version of the FOIS score is a reliable scale for evaluating the level of oral feeding function in patients with acute stroke.

Figure S1. Arenavirus G. Phylogenetic tree showing the relationships (amino acid) between arenaviruses in the G polymerase. The viruses found in this study are labeled in red font. Figure S2. Arenavirus N. Phylogenetic tree showing the relationships (amino acid) between arenaviruses in the N polymerase. The viruses found in this study are labeled in red font. Figure S3. Phylogenetic tree showing the relationships (amino acid) between arteriviruses in the pp1a proteins. The viruses found in this study are labeled in red font. Figure S4. Genomic organization of the Rat-arterivirus-1/Ningxia2015 and Rat-arterivirus/Jilin2014. Figure S5. phylogenetic tree based on the polyproteins of TBEV. The viruses found in this study are labeled in red font. Figure S6. Phylogenetic tree based on the complete Spike (S) proteins of CoVs. The viruses found in this study are labeled in red font. Figure S7. Phylogenetic treebased on the L proteins of ParaVs. The viruses found in this study are labeled in red font. Figure S8. Phylogenetic tree based on the polyproteins of Noroviruses. The viruses found in this study are labeled in red font. Figure S9. Phylogenetic tree based on diverse sequences of partial amino acid of the polymerases of AdVs. The viruses found in this study are labeled in red font. Figure S10. The phylogenetic relationships between CoVs and their hosts. Figure S11. The phylogenetic relationships between PicoVs and their hosts. Figure S12. The phylogenetic relationships between AstVs and their hosts. Figure S13. The phylogenetic relationships between CVs and their hosts. Figure S14. The phylogenetic relationships between ParVs and their hosts. (DOCX 5298 kb)

Infections caused by dermatophytes, Trichophyton rubrum in particular, are among the most common diseases in humans. In this study, we present a proteogenomic analysis of T. rubrum based on whole-genome proteomics and RNA-Seq studies. We confirmed 4291 expressed proteins in T. rubrum and validated their annotated gene structures based on 35 874 supporting peptides. In addition, we identified 323 novel peptides (not present in the current annotated protein database of T. rubrum) that can be used to enhance current T. rubrum annotations. A total of 104 predicted genes supported by novel peptides were identified, and 127 gene models suggested by the novel peptides that conflicted with existing annotations were manually assigned based on transcriptomic evidence. RNA-Seq confirmed the validity of 95% of the total peptides. Our study provides evidence that confirms and improves the genome annotation of T. rubrum and represents the first survey of T. rubrum genome annotations based on experimental evidence. Additionally, our integrated proteomics and multisourced transcriptomics approach provides stronger evidence for annotation refinement than proteomic data alone, which helps to address the dilemma of one-hit wonders (uncertainties supported by only one peptide).

Objectives: To observe the effectiveness of different targeted temperature management (TTM) methods in patients with acute cerebral infarction (ACI) and explore the most feasible cooling strategies for ACI. Methods: We retrospectively analyzed the effectiveness of different TTM strategies for ACI patients treated in the Neuointensive Care Unit of South Hospital of Southern Medical University from June 1, 2012 to May 31, 2015. Patients were divided into four groups according to the presence or absence of fever and the cooling method: control group (n=63, normal body temperature), group A (ibuprofen alone, n=53), group B (ice bag alone, n=49), and group AB (ibuprofen + ice bag, n=62). We measured rectal temperature at admission and 1 h, 2 h, 4 h, 6 h, 12 h, 48 h and 72 h after admission in the control group. In groups A, B, and AB, we measured rectal temperature immediately after cooling and 1 h, 2 h, 4 h, 6 h, 12 h, 48 h, and 72 h after cooling. Results: Body temperature showed no significant difference immediately after cooling among groups A, B, and AB (P>0.05); however, cooling effectiveness was significantly different at multiple time points after cooling (P

Received 10 August 2012; returned 4 October 2012; revised 6 February 2013; accepted 11 February 2013Objectives: This study examined the phenomenon of heteroresistance in Mycobacterium tuberculosis clinicalisolates obtained from retreated patients in Beijing, China between 2006 and 2011.Methods: The iPLEX Gold assay platform was used to determine the prevalence of heteroresistance to inject-able second-line drugs (amikacin, kanamycin and capreomycin) in resistant isolates.Results: Heteroresistance was identified in 10.9% of 220 phenotypic amikacin-resistant isolates.Conclusions: Heteroresistance was related mainly to the short duration and repeated use of amikacin andcapreomycin during retreatment. These findings further our understanding of the evolution of resistance to in-jectable drugs used for tuberculosis treatment and help guide the rational use of injectable drugs duringtherapy.Keywords: heteroresistance, MDR-TB, aminoglycoside antibiotics, molecular typing

Rodents are important reservoir hosts of many important zoonotic viruses. The family Picornaviridae contains clinically important pathogens that infect humans and animals, and increasing numbers of rodent picornaviruses have recently been associated with zoonoses. We collected 574 pharyngeal and anal swab specimens from 287 rodents of 10 different species from eight representative regions of China from October 2013 to July 2015. Seven representative sequences identified from six rodent species were amplified as full genomes and classified into four lineages. Three lineage 1 viruses belonged to a novel genus of picornaviruses and was more closely related to Hepatovirus than to others genera of picornaviruses based on aa homology. Lineage 2, lineage 3, and lineage 4 viruses belonged to the genera Rosavirus, Hunnivirus, and Enterovirus, respectively, representing new species. According to both phylogenetic and identity analyses, Lineage 2 viruses had a close relationship with rosavirus 2 which was recovered from the feces of a child in Gambia and Lineage 3 viruses had a close relationship with domestic animal Hunnivirus. Lineage 4 viruses provide the first evidence of these enteroviruses and their evolution in rodent hosts in China.

Studies have demonstrated that {\textasciitilde}60\%-80\% of emerging infectious diseases (EIDs) in humans originated from wild life. Bats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals. However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. The purpose of this study was to survey the ecological and biological diversities of viruses residing in these bat species, to investigate the presence of potential bat-borne zoonotic viruses and to evaluate the impacts of these viruses on public health. The data obtained in this study revealed an overview of the viral community present in these bat samples. Many novel bat viruses were reported for the first time and some bat viruses closely related to known human or animal pathogens were identified. This genetic evidence provides new clues in the search for the origin or evolution pattern of certain viruses, such as coronaviruses and noroviruses. These data offer meaningful ecological information for predicting and tracing wildlife-originated EIDs.

Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in Escherichia coli and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in Shigella flexneri, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the ΔpldA mutant strain. Furthermore, the ΔpldA mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.

Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in Escherichia coli and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in Shigella flexneri, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the ΔpldA mutant strain. Furthermore, the ΔpldA mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.

Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in Escherichia coli and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in Shigella flexneri, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the ΔpldA mutant strain. Furthermore, the ΔpldA mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support PldA, which is widespread across Gram-negative bacteria, as an important factor for the bacterial life cycle, particularly in human pathogens.

The presence of heteroresistance was represented by 23% of 235 fluoroquinolone (FQ)-resistant Mycobacterium tuberculosis isolates in Beijing, China, from 2008 to 2010. The main mechanism of FQ heteroresistance is due to the segregation of a single M. tuberculosis strain in patients; the majority of isolates with multidrug-resistant tuberculosis contained a mixture of bacterial subpopulations consisting of various mutant types, suggesting that the improper use of FQ is the major cause of FQ resistance.

Background Recent outbreaks of severe pneumonia or acute respiratory distress syndrome have attracted much public interest. Rapid and accurate diagnosis of the causative agent is key for an adequate response to suspected outbreaks. Objectives We report a case that highlights the potential of semiconductor sequencing to rapidly determine the novel virus genome sequences. Study design We have developed a method for rapid de novo assembly of the novel influenza A H7N9 virus genome directly from the tracheal aspirate of a patient using semiconductor sequencer without culture and prior sequence information. Further, characteristic amino acids were analyzed and phylogenetic analysis were done for key genes of the influenza A virus. Results Deep sequencing yielded 435,239 reads assigned to H7N9 viruses, with an average length of 172 bp, accounting for 18.6% of total reads (2,339,680). Complete genome of the virus was obtained by de novo assembly method within 2 days. Genomic average depth of coverage of the Ion Torrent PGM was up to 5679 fold. Selected characteristic amino acids were observed, and phylogenetic analyses showed that the novel H7 virus was genetically close to 2011 duck H7N3 viruses in Zhejiang. The novel N9 sequences were most closely related to gene sequences of N9 derived from ducks H11N9 in 2011 in Jiangxi and H2N9 sequences from Hong Kong in 2010, in China, and therefore they may share a common ancestor. Conclusions The sequence-independent semiconductor sequencing is a powerful tool to investigate outbreak of a novel pathogen.

The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence indicates that Shigella, as well as enteroinvasive Escherichia coli, are derived from multiple origins of E.coli and form a single pathovar. Nevertheless, Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella boydii is restricted to the Indian subcontinent, while Shigella flexneri and Shigella sonnei are prevalent in developing and developed countries respectively. To begin to explain these distinctive epidemiological and pathological features at the genome level, we have carried out comparative genomics on four representative strains. Each of the Shigella genomes includes a virulence plasmid that encodes conserved primary virulence determinants. The Shigella chromosomes share most of their genes with that of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300 approximately 700 copies of insertion sequence (IS) elements, and numerous deletions, insertions, translocations and inversions. There is extensive diversity of putative virulence genes, mostly acquired via bacteriophage-mediated lateral gene transfer. Hence, via convergent evolution involving gain and loss of functions, through bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements and formation of pseudogenes, the Shigella spp. became highly specific human pathogens with variable epidemiological and pathological features.

To clarify the evolutionary relationships among betavoronaviruses that infect bats, we analyzed samples collected during 2010–2011 from 14 insectivorous bat species in China. We identified complete genomes of 2 novel betacoronaviruses in Rhinolophus pusillus and Chaerephon plicata bats, which showed close genetic relationships with severe acute respiratory syndrome coronaviruses.

Rapid determination of full genomes of influenza A viruses from clinical samples is vital to outbreak preparedness. We benchmarked Ion Torrent PGM and Illumina MiSeq to the standard Sanger sequencing on two real clinical samples and demonstrated their performance for full-genome determination and polymorphism identification.

Serogroup A meningococcal strains have been involved in several pandemics and a series of epidemics worldwide in the past. Determination of the genome sequence of the prevalent genotype strain will help us understand the genetic background of the evolutionary and epidemiological properties of these bacteria. We sequenced the complete genome of Neisseria meningitidis NMA510612, a clinical isolate from a patient with meningococcal meningitis.

To the Editor: Middle East respiratory syndrome coronavirus (MERS-CoV), a novel lineage C betacoronavirus, was first described in September 2012, and by April 16, 2014, the virus had caused 238 infections and 92 deaths in humans worldwide (1). Antibodies against MERS-CoV in dromedary camels were recently reported (2), as was the full genome of MERS-CoV from dromedary camels (3). Finding the natural reservoir of MERS-CoV is fundamental to our ability to control transmission of this virus to humans (4). We report a novel lineage C betacoronavirus identified from Vespertilio superans bats in China. The full-length genome of this betacoronavirus showed close genetic relationship with MERS-CoV. Together with other evidence of MERS-CoV–related viruses in bats (5–8), our findings suggest that bats might be the natural reservoirs of MERS-related CoVs. In June 2013, we collected anal swab samples from 32 V. superans bats from southwestern China. A small proportion of each sample was pooled (without barcoding) and processed by using virus particle–protected nucleic acid purification and sequence-independent PCR for next-generation sequencing analysis with the Illumina (Solexa) Genome Analyzer II (Illumina, San Diego, CA, USA). Redundant reads were filtered, as described (9), from the raw sequencing reads generated by the genome analyzer and then aligned with the nonredundant protein database of the National Center for Biotechnology Information (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) by using BLAST (http://blast.ncbi.nlm.nih.gov). The taxonomy of these aligned reads was parsed by using MEGAN 4 (http://ab.inf.uni-tuebingen.de/software/megan/). On the basis of the BLAST results, 8,751,354 sequence reads 81 nt in length were aligned with the protein sequences of the nonredundant protein database: 72,084 of the reads were uniquely matched with virus proteins. Of these 72,084 reads, 32,365 were assigned to the family Coronaviridae, primarily to lineage C of the genus Betacoronavirus, and found to share 60%–97% aa identity with MERS-CoV. The MERS-CoV–related reads were extracted and assembled by using SeqMan software from the Lasergene 7.1.0 program (DNASTAR, Madison, WI, USA), resulting in a draft CoV genome. Reverse transcription PCR selective for the partial RNA-dependent RNA polymerase (RdRp) gene of this novel lineage C betacoronavirus suggested that 5 of the 32 samples (≈16%) were positive for the novel betacoronavirus, and the PCR amplicons shared >98% nt identity with each other. Using a set of overlapped nested PCRs and the rapid amplification of cDNA ends method, we determined the full-length genome of 1 strain of this V. superans bat–derived betacoronavirus (referred to as BtVs-BetaCoV/SC2013, GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"KJ473821","term_id":"627792518","term_text":"KJ473821"}}KJ473821). The betacoronavirus strain had a genome length of 30,413 nt, excluding the 3′ poly (A) tails, and a G+C content of 43.1%. Pairwise genome sequence alignment, conducted by the EMBOSS Needle software (http://www.ebi.ac.uk/Tools/psa/emboss_needle/) with default parameters, suggested that the genome sequence of BtVs-BetaCoV/SC2013 showed 75.7% nt identity with that of human MERS-CoV (hCoV-MERS); this shared identity is higher than that for other lineage C betacoronaviruses (from bats and hedgehogs) with full genomes available. hCoV-MERS showed 69.9% nt identity with bat CoV (BtCoV) HKU4-1, 70.1% nt identity with BtCoV-HKU5-1, and 69.6% nt identity with hedgehog CoV EriCoV-2012–174. Compared with those lineage C betacoronaviruses, which had an 816-bp partial RdRp sequence fragment available, BtVs-BetaCoV/SC2013 shared 96.7 % aa identity with hCoV-MERS. Pipistrellus BtCoVs found in Europe (BtCoV-8-724, BtCoV-8-691, BtCoV-UKR-G17) shared 98.2 % aa identity with hCoV-MERS, and Eptesicus BtCoV found in Italy (BtCoV-ITA26/384/2012) and other lineage C betacoronaviruses shared 96.3 % aa and

To serologically and genetically characterize other serogroups (except A, B, and C) of Neisseria meningitidis isolates in China, we collected 56 strains of other serogroups, identified by serogroup typing and multilocus sequence typing (MLST). All of them are non-invasive isolates. The serogroups of the 56 Chinese isolates were W135 (11 isolates), Y (4), X (15), 29E (15), D (1), H (4), I (3), K (2), and non-groupable (1). By MLST, 34 different sequence types (STs) were identified, 28 of which were not found in the MLST database as of July 2006 and seemed to be unique to China. Statistical analysis of the MLST results revealed that, although the Chinese isolates seemed to be genetically divergent, they could be classified into 5 major clonal groups and other minor groups. Among these isolates, none of the well-documented ST complexes found worldwide was present.

An epidemic caused by influenza A (H7N9) virus was recently reported in China. Deep sequencing revealed the full genome of the virus obtained directly from a patient’s sputum without virus culture. The full genome showed substantial sequence heterogeneity and large differences compared with that from embryonated chicken eggs.

Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in Escherichia coli and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in Shigella flexneri , termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the ΔpldA mutant strain. Furthermore, the ΔpldA mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support that PldA, which is widespread across Gram-negative bacteria, is an important factor for the bacterial life cycle, particularly in human pathogens.

Characterization of expression profile of organisms in response to antimicrobials provides important information on the potential mechanism of action of the drugs. The special expression signature can be used to predict whether other drugs act on the same target. Here, the common response of Shigella flexneri to two inhibitors of RNA polymerase was examined using gene expression profiling. Consistent with similar effects of the two drugs, the gene expression profiles indicated that responses of the bacteria to these drugs were roughly the same, with 225 genes affected commonly. Of them, 88 were induced and 137 were repressed. Real-time PCR was performed for selected genes to verify the microarray results. Analysis of the expression data revealed that more than 30% of the plasmid-encoded genes on the array were up-regulated by the antibiotics including virF regulon, other virulence-related genes, and genes responsible for plasmid replication, maintenance, and transfer. In addition, some chromosome-encoded genes involved in virulence and genes acquired from horizontal transfer were also significantly up-regulated. However, the expression of genes encoding the beta-subunit of RNA polymerase was increased moderately. The repressed genes include those that code for products associated with the ribosome, citrate cycle, glycolysis, thiamine biosynthesis, purine metabolism, fructose metabolism, mannose metabolism, and cold shock proteins. This study demonstrates that the two antibiotics induce rapid cessation of RNA synthesis resulting in inhibition of translation components. It also indicates that the production of virulence factors involved in intercellular dissemination, tissue invasion and inflammatory destruction may be enhanced through derepressing horizontal transfer genes by the drugs.

Mycobacterium abscessus ( M. abscessus) is a non-tuberculous mycobacterium and an important emerging pathogen causing skin, soft tissue and pulmonary infections. The case of a 59-year-old man with a history of pulmonary tuberculosis (TB) and current pulmonary infection due to M. abscessus, complicated with pneumocardial disease and bronchiectasis, is described. Zhiel—Neelsen stain and acid Lowenstein—Jensen culture were both positive for acid-fast bacillus. The patient was initially misdiagnosed and ineffectively treated for pulmonary TB. Antimycobacterial susceptibility tests found the isolate to be resistant to four first-line and seven second-line antituberculosis drugs. The isolate was finally identified as M. abscessus using 16S ribosomal RNA and hsp65 and rpoB gene sequence analysis. Species of mycobacterium should be included in the differential diagnosis when patients do not respond to standard antituberculosis therapy. Molecular methods are useful for rapid and species-specific identification.

Bacillus cereus strain Q1 was isolated from a deep-subsurface oil reservoir in the Daqing oil field in northeastern China. This strain is able to produce biosurfactants and to survive in extreme environments. Here we report the finished and annotated genome sequence of this organism.