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Investigating the genetic and developmental characteristics, infection transmission attributes, and epidemiological trends of pathogens using genomic data represents the foundation for pathogen surveillance and is a crucial prerequisite for guaranteeing global health security. To meet the analytical demands of research relating to pathogen prevention and control, we designed a secure visualization system capable of pathogen genome assembly, annotation, species identification, sequence typing, antibiotic resistance and virulence analysis, genomic mobile element and transferable resistance gene annotation, and phylogenetic tree reconstruction. For highly pathogenic organisms requiring complete data protection, we have developed a secure computing tool that utilizes a trusted execution environment, is combined with blockchain and privacy computing technologies, and is specifically designed for nucleotide basic local alignment search tool (BLASTn) comparison analysis. This technological advancement offers scientific support for in-depth investigations into pathogen transmission and epidemiological mechanisms, environmental adaptability, evolutionary trends, and immune evasion mechanisms, as well as the identification of new or emerging pathogen strains. This, in turn, aids efforts in infectious disease prevention, treatment, and research.

Abstract Cronobacter sakazakii clonal complex 4 (CC4) is strongly associated with neonatal meningitis. However, C. sakazakii CC4‐specific pathogenicity traits have not been determined. In this study, the comparative genomic analysis of 144 genomes of C. sakazakii CC4 strains and 376 non‐CC4 C. sakazakii strains was undertaken. Twenty‐four CC4 strains were previously undescribed clinical and nonclinical strains that had been collected from various regions in China (2006–2017). The remaining genomes were of multiple sequence types of C. sakazakii strains, which had been isolated worldwide (1973–2021). The pan‐genome of C. sakazakii comprised 32,332 genes, of which 2.58% (832 genes) constituted the core genome. More C. sakazakii CC4 strains have a complete cusABCFR efflux system with a significant difference compared with non‐CC4 strains, and the ibeB‐homologous cusC gene in the cusABCFR efflux system is probably associated with the invasion of human brain microvascular endothelial cells (BMEC). In addition, the isolates with K2:CA2 capsule or type IV pili‐associated genes associated with neonatal meningitis were statistically more present in CC4 strains than non‐CC4 strains (p

ABSTRACT Antibiotic resistance has become a worldwide public health and biosafety problem. The clinical efficacy of colistin was jeopardized by the report of the first mobile colistin resistance (mcr) gene, and subsequently, the mcr-gene family of mcr-1 to mcr-10 has been identified. Cronobacter is an emerging foodborne opportunistic pathogen, which can cause neonatal meningitis, bacteremia, and necrotizing enterocolitis (NEC) by contaminating food. However, the entire picture of foodborne Cronobacter carriage of the mcr genes is not known. Here, we investigated the mcr genes of Cronobacter isolates (N = 877) by whole-genome sequencing. We found 133 of 877 previously undescribed Cronobacter isolates carrying mcr genes. Further genomic analysis revealed that these mcr genes mainly belonged to the mcr-9 and mcr-10. Genomic analysis of the flanking structures of mcr genes revealed that two core flanking structures were prevalent in foodborne Cronobacter isolates, and the flanking structure carrying IS1R was found for the first time in this study. These findings suggest that foodborne Cronobacter isolates carrying the mcr genes already pose a threat to human health. IMPORTANCE Cronobacter is an emerging foodborne opportunistic pathogen, which can cause neonatal meningitis, bacteremia, and NEC by contaminating food. However, the entire picture of foodborne Cronobacter carriage of the mcr genes is not known. Here, we investigated the mcr genes of Cronobacter isolates by whole-genome sequencing and found 133 previously undescribed Cronobacter isolates carrying mcr genes. Further genomic analysis revealed that these mcr genes mainly belonged to the mcr-9 and mcr-10. Genomic analysis of the flanking structures of mcr genes revealed that two core flanking structures were prevalent in foodborne Cronobacter isolates, and the flanking structure carrying IS1R was found for the first time in this study.

As the central flow channel for fluid seepage through rock layers, the visible fracture system (VFS) significantly affects geoenergy extraction for petroleum, natural gas, geothermal resources, and greenhouse gas sequestration. In this work, we propose a new mode of VFS in coal seams, including hydraulic fractures, exogenetic fractures, interlayer fractures, gas-expanding fractures, and cleats. The development characteristics of VFSs in coal seams are analyzed, including containing their geometry, orientation, scale, distribution, and connection between each other. Furthermore, the implications of the VFS for fluid (gas and water) and solid (coal fines) flow through coal seams are discussed. The development of the VFS determines the effective flow conductivity, affecting the flow of gas, water, and coal fines. Additionally, as the reservoir pressure transfer channel, the VFS significantly influences depressurization with reservoir depletion, determining the extension of the methane desorption range. The exogenetic fractures and interlayer fractures dominate the expansion of the primary hydraulic fractures, and gas-expanding and cleats usually control the branch of hydraulic fractures. Furthermore, we find that the daily production rate distribution of most CBM wells presents a particular banded, L-shaped, or T-shaped pattern. It is thought that the VFS dominates the productivity of CBM in coal seams. The field production data also provide evidence that the occurrence of the VFS makes the CBM reservoir heterogeneous. This study presents a recommended framework involving the characteristics of the VFS and its influences on CBM production.

Non-small cell lung cancer (NSCLC) is a common lung disorder. In this study, we applied bioinformatics methods to analyze and investigate the role of the NFIX gene in NSCLC. Hsa_circ_0049657 is derived from the NFIX gene, this research aimed to verify the potential role of hsa_circ_0049657 in the development of NSCLC. The results suggested that NFIX was downregulated in most cancers. In addition, the NFIX expression in lung adenocarcinoma (LUAD) was associated with the clinicopathological stage. In LUAD, NFIX expression was associated with the degree of infiltration of most immune cells. The expression levels of hsa_circ_0049657 were significantly lower in cancerous tissues than in paracancerous tissues. Moreover, the results showed that hsa_circ_0049657 expression was downregulated in NSCLC cells. After overexpression of hsa_circ_0049657, the proliferation and migration ability of NSCLC cells were significantly inhibited and the level of apoptosis was increased. We could suppress the proliferation and invasion abilities and promote apoptosis of NSCLC cells by up-regulating hsa_circ_0049657, which might be a potential biomarker for NSCLC.

Background Cyclocytidine hydrochloride (HCl) has been reported to inhibit DNA synthesis by affecting DNA polymerase. Here, we tested the antiviral effect of cyclocytidine on hepatitis B virus (HBV) DNA synthesis, which is reliant on DNA polymerase activity. Materials and Methods Cyclocytidine HCl was treated to HBV-producing HepAD38 cells or added to an endogenous polymerase reaction, and HBV DNA was detected by Southern blot. Results Treatment of 20 µM cyclocytidine HCl significantly decreased the production of relaxed circular (rc) DNA in HepAD38 cells and block rcDNA synthesis in endogenous polymerase reaction (EPR), a cell free assay, possibly by inhibiting the HBV DNA polymerase activity. Conclusion Cyclocytidine HCl could inhibit the synthesis of HBV rcDNA, the precursor of covalently closed circular DNA, and this result provides a case for the usage of “old” drugs for “new” applications.

Abstract Background Long non-coding RNAs became the hot spots in the carcinogenesis of various tumors. This case-control study evaluated the association between the rs2151280 in lncRNA CDKN2B-AS1 and lung cancer risk. Methods This study included 507 lung cancer patients and 542 healthy individuals. Odds ratios and their 95% confidence intervals were calculated by unconditional logistic regression analysis to evaluate the association between the rs2151280 and lung cancer risk. Results Compared with individuals carrying TT genotype, individuals carrying CC genotype of rs2151280 had a decreased risk of lung cancer (OR = 0.640, 95%CI = 0.421–0.972, P = 0.036). In the recessive model, rs2151280 CC genotype was observed to reduce the risk of lung cancer (OR = 0.684). C allele was associated with non-small cell lung cancer risk (OR = 0.674). The rs2151280 was significantly associated with lung adenocarcinoma risk (CCvsTT: OR = 0.567, 95%CI = 0.333–0.965, P = 0.037; CCvsTC+TT: OR = 0.543, 95%CI 0.330–0.893, P = 0.016, respectively). However, there was no significant association between rs2151280 and lung squamous cell carcinoma risk in five models. The quantitative analysis suggested that there were no significant interactions of rs2151280 with smoking exposure to lung cancer susceptibility. Conclusions This hospital-based case-control study suggested that CDKN2B-AS1 rs2151280 T>C was associated with the risk of lung cancer.

Abstract Background Long non-coding RNA (lncRNA) H19 is a hot spot in tumor development, progression and metastasis. This study assessed the association between H19 genetic polymorphisms and the susceptibility of lung cancer. Methods The case-control study was conducted to evaluate the association between four selected single nucleotide polymorphisms (rs217727, rs2107425, rs2735469 and rs17658052) in H19 gene and the risk of lung cancer. There were 556 female never smoking lung cancer patients and 395 cancer-free controls. Unconditional logistic regression analysis was used to analyze the associations between four SNPs and lung cancer risks by calculating the odds ratios and their 95% confidence intervals. The gene-environment interactions were assessed on both additive and multiplicative scales. Results Compared with carriers carrying homozygous CC genotype, there was a statistically significant increased risk of lung cancer for carriers of the rs2107425 TT genotype (odds ratio = 1.599, 95%CI = 1.106–2.313, P = 0.013). In both dominant and recessive models, significant associations were found between rs2107425 and lung cancer risk, and the corresponding odds ratios were 1.346 (1.022–1.774) and 1.400 (1.011–1.937), with P values 0.035 and 0.043, respectively. There was no significant correlation between lung cancer risk and rs2735469, rs217727 and rs17658052. Interaction analysis showed that their combined effects had a greater impact on lung cancer than individual effects of polymorphism and cooking smoke exposure. However, further analysis showed that the both additive model and the multiplicative model were not statistically significant. Conclusion The polymorphism rs2107425 in H19 gene was associated with the risk of lung cancer among female who never smokes in Shenyang, China.

We compared several identification methods for Aeromonas genus members, including traditional biochemical testing, multiplex-PCR amplification, mass spectrometry identification, whole-genome sequencing, multilocus phylogenetic analysis (MLPA), and rpoD, gyrA, and rpoD-gyrA gene sequencing. Isolates (n = 62) belonging to the Aeromonas genus, which were came from the bacterial bank in the laboratory, were used to assess the identification accuracy of the different methods. Whole-genome sequencing showed that the Aeromonas spp. isolates comprised A. caviae (n = 21), A. veronii (n = 18), A. dhakensis (n = 8), A. hydrophila (n = 7), A. jandaei (n = 5), A. enteropelogenes (n = 2), and A. media (n = 1). Using the whole-genome sequencing results as the standard, the consistency of the other methods was compared with them. The results were 46.77% (29/62) for biochemical identification, 83.87% (52/62) for mass spectrometric identification, 67.74% (42/62) for multiplex-PCR, 100% (62/62) for MLPA typing, 72.58% for gyrA, and 59.68% for rpoD and gyrA-rpoD. MLPA was the most consistent, followed by mass spectrometry. Therefore, in the public health laboratory, both MLPA and whole-genome sequencing methods can be used to identify various Aeromonas species. However, rapid and relatively accurate mass spectrometry is recommended for clinical lab.

Lung cancer is a leading cause of cancer death all around the world. Long non-coding RNAs (lncRNAs) have been confirmed to be involved in carcinogenesis of malignancies. However, the molecular mechanism of most lncRNAs in various kinds of cancers remains unclear. LncRNA HOTAIR and HNRNPA1 are reported to play an oncogenic role in non-small cell lung cancer, and the overexpression of HNRNPA1 is shown to promote the proliferation of lung adenocarcinoma cells. In our study, we find that the overexpression of HOTAIR could promote the proliferation and overexpression of miR-149-5p could inhibit the proliferation of lung cancer cells. Flow cytometric analysis determines that overexpression of miR-149-5p induces cell cycle arrest in the G0/G1 phases, whereas overexpression of HOTAIR decreases the proportion of G0/G1phase cells. Also, overexpression of HOTAIR promotes the migration and invasion ability of lung cancer cells, confirmed by the wound-healing and transwell assays, which are suppressed by overexpression of miR-149-5p. Furthermore, the dual-luciferase reporter assay indicates that miR-149-5p could bind both HOTAIR and the 3′UTR of HNRNPA1. In summary, we find that HOTAIR can regulate HNRNPA1 expression through a ceRNA mechanism by sequester miR-149-5p, which post-transcriptionally targets HNRNPA1, thus promoting lung cancer progression.

Cronobacter spp. can cause systemic infections, such as meningitis, sepsis, and necrotizing enterocolitis, in immunocompromised patients, especially neonates. Although some virulence factors have been reported previously, the pathogenesis of Cronobacter remains unclear. In this study, we compared genome sequences from different Cronobacter species, sequence types, and sources, with the virulence genes in the virulence factor database. The results showed that Cronobacter has species specificity for these virulence genes. Additionally, two gene clusters, including sfp encoding fimbriae and hly encoding hemolysin, were discovered. Through cell adhesion, cytotoxicity, and hemolysis assays, we found that the isolates possessing the two gene clusters had higher cytotoxicity and stronger hemolysis capacity than those of other isolates in this study. Moreover, analysis of type VI secretion system (T6SS) cluster and putative fimbria gene clusters of Cronobacter revealed that T6SS have species specificity and isolates with high cytotoxicity possessed more complete T6SS cluster construction than that of the rest. In conclusion, the two novel gene clusters and T6SS cluster were involved in the mechanism underlying the cytotoxicity of Cronobacter.

Abstract Background The aberrant regulation of MALAT1 has been indicated to be involved in various carcinogenic pathways contributing to the tumourigenesis and progression of cancers. The current meta-analysis summarized the research advances of MALAT1 functions and analyzed its prognostic value among multiple types of cancers. Methods Eligible studies were identified through retrieving the PubMed, Web of Science, and CNKI databases, up to Mar 1, 2018. 28 studies of 5436 patients and 36 studies of 3325 patients were enrolled in the meta-analysis to evaluate the association of MALAT1 expression with survival outcomes and clinical parameters. Results The results demonstrated that over-expression of MALAT1 may predict lymph node metastasis (pooled OR = 2.335, 95% CI 1.606–3.395, P = 0.000) and distant metastasis (pooled OR = 2.456, 95% CI 1.407–4.286, P = 0.002). Moreover, MALAT1 was also related with tumour size (pooled OR = 1.875, 95% CI 1.257–2.795, P = 0.002) and TNM stage (pooled OR = 2.034, 95% CI 1.111–3.724, P = 0.021). Additionally, elevated MALAT1 expression could predict poor OS (pooled HR = 2.298, 95% CI 1.953–2.704, P = 0.000), DFS (pooled HR = 2.036, 95% CI 1.240–3.342, P = 0.005), RFS (pooled HR = 2.491, 95% CI 1.505–4.123, P = 0.000), DSS (pooled HR = 2.098, 95% CI 1.372–3.211, P = 0.001) and PFS (pooled HR = 1.842, 95% CI 1.138–2.983, P = 0.013) in multivariate model. Importantly, subgroup analyses disclosed that increased MALAT1 expression had a poor OS among different cancer types (Estrogen-dependent cancer: pooled HR = 2.656, 95% CI 1.560–4.523; urological cancer: pooled HR = 1.952, 95% CI 1.189–3.204; glioma: pooled HR = 2.315, 95% CI 1.643–3.263; digestive cancer: pooled HR = 2.451, 95% CI 1.862–3.227). Conclusions The present findings demonstrated that MALAT1 may be a novel biomarker for predicting survival outcome, lymph node metastasis and distant metastasis.

Cigarette smoke is a major preventable risk factor of ischemic stroke. Cigarette smoke induces a significant increase in circulating leukocytes. However, it remains unclear to what extent and by what mechanisms smoke priming influences stroke severity. Here we report that exposure to cigarette smoke exacerbated ischemic brain injury in mice subjected to transient middle cerebral artery occlusion (MCAO). The augmentation of neurodeficits and brain infarction was accompanied by increased production of pro-inflammatory factors and brain infiltration of neutrophils and monocytes. Prior to brain ischemia, exposure to cigarette smoke induced mobilization of peripheral neutrophils, and monocytes. Furthermore, the detrimental effects of smoke priming on ischemic brain injury were abolished either by pharmacological inhibition of the recruitment of neutrophils and monocytes or by blockade of the NLRP3 inflammasome, an effector protein of neutrophils and monocytes. Our findings suggest that cigarette smoke-induced mobilization of peripheral neutrophils and monocytes augments ischemic brain injury.

Objective: Preeclampsia is a common complication of pregnancy that is characterized by high blood pressure. Preeclampsia can have both negative maternal and fetal effects, including impaired fetal development from reduced placental perfusion. Because umbilical vessels provide fetal blood supply, morphological changes in these vessels can critically affect fetal function. This study investigated morphological and structural changes in umbilical veins from 17 controls and 19 preeclampsia cases. Methods: 36 umbilical cords were collected, and take umbilical cord of placental, middle, and fetal segment to H&E and orange G staining. Microscope images were obtained by digital microscope, and wall thickness, lumen diameter, wall-luminal ratio and tunica media thickness, Area of smooth muscle, area of nuclei, nuclei density, and nuclear area density of smooth muscle in tunica media were tested by Image-pro Plus. Results: Lumen diameter of umbilical veins gradually decreased, while wall thickness, tunica media thickness, and wall-luminal ratio gradually increased, from placental to fetal segments of umbilical veins. Area of smooth muscle, area of nuclei, nuclei density, and nuclear area density did not significantly differ from placental to fetal segments of umbilical veins. Compared to controls, (1) Preeclampsia cases had a smaller lumen diameter and greater wall thickness, tunica media thickness, wall-luminal ratio; (2) Preeclampsia cases had higher nuclei density and nuclear area density, and had no difference in area of smooth muscle and area of nuclei. In fetal segments of umbilical veins from preeclampsia cases, correlation analysis showed that wall-luminal ratio negatively correlated with gestation age, birth weight, and Apgar score. Conclusions: These results indicate that umbilical vein of preeclampsia cases has a thickened tunica media from smooth muscle proliferation, which may be an adapted reaction to hypertension. Altogether, this study demonstrates that morphological changes in umbilical veins adversely affect fetal development in preeclampsia cases.

Abstract Background Long non-coding RNAs play pivotal roles in the carcinogenesis of multiple types of cancers. This study is firstly to evaluate influence of rs4848320 and rs1110839 polymorphisms in long non-coding RNA AC016683.6 on the susceptibility of lung cancer. Methods The present study was a hospital-based case–control study with 434 lung cancer patients and 593 cancer-free controls. Genotyping of the two SNPs detected by Taqman® allelic discrimination method. Results There were no statistically significant associations between rs4848320 and rs1110839 polymorphisms in AC016683.6 and risk of lung cancer in overall population. However, in the smoking population, rs4848320 and rs1110839 polymorphisms significantly increased the risk of lung cancer in dominant and homozygous models (Rs4848320: P = 0.029; Rs1110839: P = 0.034), respectively. In male population, rs1110839 genetic variant was related to the risk of lung cancer in all genetic models (GG vs. TT: P = 0.008; Dominant model: P = 0.029; Recessive model: P = 0.027) rather than heterozygous model. The crossover analyses provided rs4848320 and rs1110839 risk genotypes carriers combined with smoking exposure 2.218-fold, 1.755-fold increased risk of lung cancer (Rs4848320: P = 0.005; Rs1110839: P = 0.017). Additionally, there were significantly positive multiplicative interaction of rs4848320 polymorphism with smoking status, with adjusted OR of 2.244 (1.162–4.334), but rs1110839 polymorphism did not exist. Conclusions Rs4848320 and rs1110839 polymorphisms may be associated with lung cancer susceptibility. Interaction of rs4848320 risk genotypes with smoking exposure may strengthen the risk effect on lung cancer.

Objectives: To conduct a one-year pathogen surveillance of acute diarrheal disease based on outpatient clinics in township hospitals in rural Hongta District of Yunnan Province, China. Methods: Fecal specimens of acute diarrhea cases and relevant epidemiological information were collected. Salmonella, Shigella, Vibrio, Aeromonas, Plesiomonas shigelloides and diarrheogenic Escherichia coli (DEC) were examined. Results: Among the 797 stool specimens sampled, 198 samples (24.8%) were positive in pathogen isolation, and 223 strains were isolated. The order of isolation rates from high to low were DEC, Aeromonas, P. shigelloides, Salmonella, Shigella and Vibrio. The overall positive rate in middle school students and preschool children was relatively high; while the overall positive rate of less than 1-year-old infants and above 55 years olds was relatively low. The isolates were analyzed by pulsed-field gel electrophoresis (PFGE). Some cases had the same or very close onset time, and the isolates had similar PFGE patterns, suggesting a possible outbreak once occurred but was not detected by the current infectious disease reporting system. Conclusions: Pathogen infection and transmission in rapidly urbanized rural areas is a serious issue. There is a great need for a more sensitive and accurate mode of monitoring, reporting and outbreak identification of diarrheal disease. Keywords: Diarrheal disease, Diarrheogenic pathogen, Molecular typing, Surveillance, Bacterial pathogen

Abstract Background An increasing number of publications are drawing attention to the associations between six common polymorphisms in HOX transcript anti-sense RNA (HOTAIR) and the risk of cancers, while these results have been controversial and inconsistent. We conducted an up-to-date meta-analysis to pool eligible studies and to further explore the possible relationships between HOTAIR polymorphisms (rs920778, rs7958904, rs12826786, 4,759,314, rs874945, and rs1899663) and cancer risk. Methods A systematic retrieval was conducted up to 1 July 2017 in the PubMed, Web of Science, and CNKI databases. Eighteen eligible publications including 45 case-control studies with 58,601subjects were enrolled for assessing the associations between the 6 polymorphisms in HOTAIR and cancer risk. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were analyzed to reveal the polymorphisms and susceptibility to cancer. All the statistical analyses were performed using STATA 11.0 software. Results The pooled analyses detected significant associations between the rs920778 polymorphism and increased susceptibility to cancer in recessive, dominant, allelic, homozygous, and heterozygous models. For the rs7958904 polymorphism, we obtained the polymorphism significantly decreased susceptibility to overall cancer risk among five genetic models rather than recessive and homozygous models. For the rs12826786 polymorphism, we identified it significantly increased susceptibility to cancer risk in all genetic models rather than heterozygous models. However, no significant association was found between the rs1899663, rs874945, and rs4759314 polymorphisms and susceptibility of cancer. Conclusion These findings of the meta-analysis suggest that HOTAIR polymorphism may contribute to cancer susceptibility.

Streptococcus suis sequence type 7 emerged and caused 2 of the largest human infection outbreaks in China in 1998 and 2005. To determine the major risk factors and source of the infections, we analyzed whole genomes of 95 outbreak-associated isolates, identified 160 single nucleotide polymorphisms, and classified them into 6 clades. Molecular clock analysis revealed that clade 1 (responsible for the 1998 outbreak) emerged in October 1997. Clades 2–6 (responsible for the 2005 outbreak) emerged separately during February 2002–August 2004. A total of 41 lineages of S. suis emerged by the end of 2004 and rapidly expanded to 68 genome types through single base mutations when the outbreak occurred in June 2005. We identified 32 identical isolates and classified them into 8 groups, which were distributed in a large geographic area with no transmission link. These findings suggest that persons were infected in parallel in respective geographic sites.

Abstract Background Recently, accumulating evidence have revealed that circular RNA (circRNA) was deregulated in multiple types of cancer, suggesting that circRNA might serve as a novel candidate biomarker of cancer diagnosis. However, inconsistent results have become an obstacle in applying circRNAs to clinical practice. The aim of this study is to evaluate diagnostic value of circRNAs among cancers. Methods A literature search was systematically performed among PubMed, Sciencedirect, Cochrane Library, Web of Science, Wanfang, and Chinese National Knowledge Infrastructure databases up to February 15, 2019. The pooled sensitivity (SEN), specificity (SPE), positive likelihood ratios, negative likelihood ratios, diagnostic odds ratio, and area under the SROC curve (AUC) were applied to evaluate diagnostic performance of circRNAs. Results In total, the study included 64 studies with single circRNA and 13 studies with combined circRNAs. Overall, the study presented that a single circRNA had moderate diagnostic value, with a SEN of 0.75, a SPE of 0.76, and an AUC of 0.82. The plasma circRNAs had higher diagnostic accuracy than tissue (AUC: 0.87, 95% confidence interval [CI]: 0.83–0.89 for plasma/serum subgroup; AUC: 0.79, 95% CI: 0.75–0.82 for tissue subgroup). Furthermore, the combined circRNAs had good diagnostic efficacy for GC, with a SEN of 0.89, a SPE of 0.94, and an AUC of 0.97, respectively. Conclusion This study confirmed that circRNAs may be candidate biomarkers for cancer diagnosis. In particular, diagnosis of combined circRNAs will be a new alternative applied to clinical research and practice for cancer.

Abstract Background MicroRNAs (miRNAs) have been proved to play important roles in the tumorigenesis and development of human gastric cancer (GC). Our study aims to investigate the expression and clinical significance of miR-198 in GC patients. Methods Quantitative real-time polymerase chain reaction (RT-PCR) was performed to evaluate miR-198 levels in 106 pairs of GC specimens and adjacent noncancerous tissues. Then, the associations of miR-198 expression with clinicopathological factors and patient’s survival were determined. Results The expression levels of miR-198 in GC tissues were significantly lower than those in corresponding noncancerous tissues (p

Plague, caused by Yersinia pestis, was classified as a reemerging infectious disease by the World Health Organization. The five human pneumonic plague cases in Yulong County in 2005 gave rise to the discovery of a Yulong plague focus in Yunnan province, China. Thereafter, continuous wild rodent plague (sylvatic plague) was identified as the main plague reservoir of this focus. In this study, the epizootics in Yulong focus were described, and three molecular typing methods, including the different region (DFR) analysis, clustered regularly interspaced short palindromic repeats (CRISPRs), and the multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) (14+12), were used for the molecular typing and source tracing of Y. pestis isolates in the Yulong plague focus. Simultaneously, several isolates from the vicinity of Yunnan were used as controls. The results showed that during the 10-year period from 2006 to 2016, an animal plague epidemic occurred in 6 of those years, and 5 villages underwent an animal plague epidemic within a 30-km2 area of the Yulong plague focus. Searching for dead mice was the most effective monitoring method in this plague focus. No positive sample has been found in 6937 captured live rodents thus far, suggesting that the virulence of strains in the Yulong plague focus is stronger and the survival time of mice is shorter after infection. Strains from Lijiang, Sichuan and Tibet were of the same complex based on a typing analysis of DFR and CRISPR. The genetic relationship of Y. pestis illustrated by MLVA "14+12" demonstrates that Tibet and Sichuan strains evolved from the strains 1.IN2 (Qinghai, 1970 and Tibet, 1976), and Lijiang strains are closer to Batang strains (Batang County in Sichuan province, 2011, Himalaya marmot plague foci) in terms of genetic or phylogenic relationships. In conclusion, we have a deeper understanding of this new plague focus throughout this study, which provides a basis for effective prevention and control.

Vibrio cholerae has caused massive outbreaks and even trans-continental epidemics. In 2008 and 2010, at least 3 remarkable cholera outbreaks occurred in Hainan, Anhui and Jiangsu provinces of China. To address the possible transmissions and the relationships to the 7th pandemic strains of those 3 outbreaks, we sequenced the whole genomes of the outbreak isolates and compared with the global isolates from the 7th pandemic. The three outbreaks in this study were caused by a cluster of V. cholerae in clade 3.B which is parallel to the clade 3.C that was transmitted from Nepal to Haiti and caused an outbreak in 2010. Pan-genome analysis provided additional evolution information on the mobile element and acquired multiple antibiotic resistance genes. We suggested that clade 3.B should be monitored because the multiple antibiotic resistant characteristics of this clade and the 'amplifier' function of China in the global transmission of current Cholera pandemic. We also show that dedicated whole genome sequencing analysis provided more information than the previous techniques and should be applied in the disease surveillance networks.

Streptococcus suis sequence type (ST) 7 has been spreading throughout China. To determine events associated with its emergence, we tested 114 isolates. In all 106 ST7 strains responsible for human outbreaks and sporadic infections, the tetracycline-resistance gene, tetM, was detected on the conjugative transposon Tn916. Horizontal transmission of tetM is suspected.

Both genetic polymorphisms and environmental risk factors play important roles in the development of human chronic diseases including lung cancer. This is the first case-control study of interaction between polymorphisms in pre-miRNA genes and cooking oil fume exposure on the risk of lung cancer.A hospital-based case-control study of 258 cases and 310 controls was conducted. Six polymorphisms in miRNAs were determined by Taqman allelic discrimination method. The gene-environment interactions were assessed on both additive and multiplicative scale. The statistical analyses were performed mostly with SPSS.The combination of the risk genotypes of five miRNA SNPs (miR-146a rs2910164, miR-196a2 rs11614913, miR-608 rs4919510, miR-27a rs895819 and miR-423 rs6505162) with risk factor (cooking oil fume exposure) contributed to a significantly higher risk of lung cancer, and the corresponding ORs (95% confidence intervals) were 1.91(1.04-3.52), 1.94 (1.16-3.25), 2.06 (1.22-3.49), 1.76 (1.03-2.98) and 2.13 (1.29-3.51). The individuals with both risk genotypes of miRNA SNPs and exposure to risk factor (cooking oil fumes) were in a higher risk of lung cancer than persons with only one of the two risk factors (ORs were 1.91, 1.05 and 1.41 for miR-146a rs2910164, ORs were 1.94, 1.23 and 1.34 for miR-196a2 rs11614913, ORs were 2.06, 1.41 and 1.68 for miR-608 rs4919510, ORs were 1.76, 0.82 and 1.07 for miR-27a rs895819, and ORs were 2.13, 1.15 and 1.02 for miR-423 rs6505162, respectively). All the measures of biological interaction indicate that there were not indeed biological interactions between the six SNPs of miRNAs and exposure to cooking oil fumes on an additive scale. Logistic models suggested that the gene-environment interactions were not statistically significant on a multiplicative scale.The interactions between miRNA SNPs and cooking oil fume exposure suggested by ORs of different combination were not statistically significant.

An outbreak of Streptococcus suis serotype 2 emerged in the summer of 2005 in Sichuan Province, and sporadic infections occurred in 4 additional provinces of China. In total, 99 S. suis strains were isolated and analyzed in this study: 88 isolates from human patients and 11 from diseased pigs. We defined 98 of 99 isolates as pulse type I by using pulsed-field gel electrophoresis analysis of SmaI-digested chromosomal DNA. Furthermore, multilocus sequence typing classified 97 of 98 members of the pulse type I in the same sequence type (ST), ST-7. Isolates of ST-7 were more toxic to peripheral blood mononuclear cells than ST-1 strains. S. suis ST-7, the causative agent, was a single-locus variant of ST-1 with increased virulence. These findings strongly suggest that ST-7 is an emerging, highly virulent S. suis clone that caused the largest S. suis outbreak ever described.

Epidemiologic investigations showed that 2 of 4 patients with severe acute respiratory syndrome (SARS) identified in the winter of 2003–2004 were a waitress at a restaurant in Guangzhou, China, that served palm civets as food and a customer who ate in the restaurant a short distance from animal cages. All 6 palm civets at the restaurant were positive for SARS-associated coronavirus (SARS-CoV). Partial spike (S) gene sequences of SARS-CoV from the 2 patients were identical to 4 of 5 S gene viral sequences from palm civets. Phylogenetic analysis showed that SARS-CoV from palm civets in the restaurant was most closely related to animal isolates. SARS cases at the restaurant were the result of recent interspecies transfer from the putative palm civet reservoir, and not the result of continued circulation of SARS-CoV in the human population.

Streptococcus suis is an important zoonotic pathogen. However, identification of virulent S. suis strains is complicated because of the high diversity of the species. Here we evaluated the genetic difference among S. suis strains using comparative genomic hybridization (CGH) and virulence variation in vivo and in vitro. We showed that different clades differed in their ability to activate TLR2/6 in vitro and their capacity to induce cytokine production in vivo as well as their resistance to phagocytosis and survival in vivo. Our data showed the S. suis strains tested can be classified into three groups having differing levels of virulence: epidemic and highly virulent strains were clustered into clade Ia (epidemic and highly virulent group, E/HV group), virulent strains were clustered into clade Ib (virulent group, V group), and intermediately or weakly virulent strains were clustered into other clades (intermediately or weakly virulent group, I/WV group). Our study provided further insight into the genomic and virulence variation of S. suis.

Cronobacter spp. (Enterobacter sakazakii) is an important pathogen contaminating powdered infant formula (PIF). To describe the genotypic diversity of Cronobacter isolated in China, we identified the isolates using fusA allele sequencing, and subtyped all of the isolates using pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and multiple-locus variable-number tandem-repeat analysis (MLVA). A total of 105 isolates were identified, which included C. sakazakii (58 isolates), C. malonaticus (30 isolates), C. dublinensis (11 isolates), C. turicensis (5 isolates), and C. muytjensii (1 isolate). These isolates were showed to have 85 PFGE-patterns, 71 sequence types (STs), and 55 MLVA-patterns. Comparisons among the three molecular subtyping methods revealed that the PFGE method was the most distinguishable tool in identifying clusters of Cronobacter spp. through DNA fingerprinting, and MLST method came second. However, ESTR-1, ESTR-2, ESTR-3, and ESTR-4 were not effective loci for subtyping Cronobacter spp. such that the MLVA method requires further improvement.

An Escherichia coli O157:H7 outbreak in China in 1999 caused 177 deaths due to hemolytic uremic syndrome. Sixteen outbreak associated isolates were found to belong to a new clone, sequence type 96 (ST96), based on multilocus sequence typing of 15 housekeeping genes. Whole genome sequencing of an outbreak isolate, Xuzhou21, showed that the isolate is phylogenetically closely related to the Japan 1996 outbreak isolate Sakai, both of which share the most recent common ancestor with the US outbreak isolate EDL933. The levels of IL-6 and IL-8 of peripheral blood mononuclear cells induced by Xuzhou21 and Sakai were significantly higher than that induced by EDL933. Xuzhou21 also induced a significantly higher level of IL-8 than Sakai while both induced similar levels of IL-6. The expression level of Shiga toxin 2 in Xuzhou21 induced by mitomycin C was 68.6 times of that under non-inducing conditions, twice of that induced in Sakai (32.7 times) and 15 times higher than that induced in EDL933 (4.5 times). Our study shows that ST96 is a novel clone and provided significant new insights into the evolution of virulence of E. coli O157:H7.

Multilocus sequence typing (MLST) based on six loci was used to analyze the relationship of 58 Candida tropicalis isolates from individual patients in a general hospital in Beijing, China. A total of 52 diploid sequence types (DSTs) were generated by the MLST, all of which were new to the central database. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrograms were constructed, which showed that the 58 isolates were distributed robustly and 6 main groups were clustered regardless of the specimen source and medical department. The minimum spanning tree (MST) of the 58 isolates (52 DSTs) and all 401 isolates (268 DSTs) in the C. tropicalis central database (http://pubmlst.org/ctropicalis/) indicated that the isolates in this study clustered in three relative pure clonal complexes, and 2 clustered with isolates from Taiwan, Belgium, Brazil, and the US. This study presents the first MLST analysis of C. tropicalis isolates from Mainland China, which may be useful for further studies on the similarity, genetic relationship, and molecular epidemiology of C. tropicalis strains worldwide.

Citrobacter freundii is an infrequent but established cause of diarrhea in humans. However, little is known of its genetic diversity and potential for virulence. We analyzed 26 isolates, including 12 from human diarrheal patients, 2 from human fecal samples of unknown diarrheal status, and 12 from animals, insects, and other sources. Pulsed field gel electrophoresis using XbaI allowed us to divide the 26 isolates into 20 pulse types, while multi-locus sequence typing using 7 housekeeping genes allowed us to divide the 26 isolates into 6 sequence types (STs) with the majority belonging to 4 STs. We analyzed adhesion and cytotoxicity to HEp-2 cells in these 26 strains. All were found to adhere to HEp-2 cells. One strain, CF74, which had been isolated from a goat, showed the strongest aggregative adhesion pattern. Lactate dehydrogenase (LDH) released from HEp-2 cells was evaluated as a measure of cytotoxicity, averaging 7.46%. Strain CF74 induced the highest level of LDH, 24.3%, and caused >50% cell rounding, detachment, and death. We named strain CF74 "cytotoxic and aggregative C. freundii." Genome sequencing of CF74 revealed that it had acquired 7 genomic islands, including 2 fimbriae islands and a type VI secretion system island, all of which are potential virulence factors. Our results show that aggregative adherence and cytotoxicity play an important role in the pathogenesis of C. freundii.

The predominant bioserotypes of pathogenic Yersinia enterocolitica in China are 2/O: 9 and 3/O: 3; no pathogenic O: 8 strains have been found to date. Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA) based on seven loci was able to distinguish 104 genotypes among 218 pathogenic Y. enterocolitica isolates in China and from abroad, showing a high resolution. The major pathogenic serogroups in China, O: 3 and O: 9, were divided into two clusters based on MLVA genotyping. The different distribution of Y. enterocolitica MLVA genotypes maybe due to the recent dissemination of specific clones of 2/O: 9 and 3/O: 3 strains in China. MLVA was a helpful tool for bacterial pathogen surveillance and investigation of pathogenic Y. enterocolitica outbreaks.

Vibrio cholerae is commonly found in estuarine water systems. Toxigenic O1 and O139 V. cholerae strains have caused cholera epidemics and pandemics, whereas the nontoxigenic strains within these serogroups only occasionally lead to disease. To understand the differences in the genome and clonality between the toxigenic and nontoxigenic strains of V. cholerae serogroups O1 and O139, we employed a whole genome PCR scanning (WGPScanning) method, an rrn operon-mediated fragment rearrangement analysis and comparative genomic hybridization (CGH) to analyze the genome structure of different strains. WGPScanning in conjunction with CGH revealed that the genomic contents of the toxigenic strains were conservative, except for a few indels located mainly in mobile elements. Minor nucleotide variation in orthologous genes appeared to be the major difference between the toxigenic strains. rrn operon-mediated rearrangements were infrequent in El Tor toxigenic strains tested using I-CeuI digested pulsed-field gel electrophoresis (PFGE) analysis and PCR analysis based on flanking sequence of rrn operons. Using these methods, we found that the genomic structures of toxigenic El Tor and O139 strains were syntenic. The nontoxigenic strains exhibited more extensive sequence variations, but toxin coregulated pilus positive (TCP+) strains had a similar structure. TCP+ nontoxigenic strains could be subdivided into multiple lineages according to the TCP type, suggesting the existence of complex intermediates in the evolution of toxigenic strains. The data indicate that toxigenic O1 El Tor and O139 strains were derived from a single lineage of intermediates from complex clones in the environment. The nontoxigenic strains with non-El Tor type TCP may yet evolve into new epidemic clones after attaining toxigenic attributes.

Spliced hepatitis B virus (HBV) RNA has been reported to affect the viral life cycle and progression of liver disease. As much as 30% of HBV RNA are spliced in infected cells, and some can be reverse transcribed to spliced DNA. To date, only a small number of spliced DNA have been identified and the majority require further investigation. This study aimed to identify the types of spliced DNA from the sera of a chronic hepatitis B patient. HBV DNA was isolated from the serum, and both full-length and spliced DNA were amplified by PCR. The amplified PCR products were then subcloned and sequenced using a Sanger sequence analysis. As a result, 19 types of spliced DNA were identified, 11 of which were assumed to be putative novel spliced DNA. These spliced DNA were doubly spliced with varied splice donor sites and splice acceptor sites. In addition to the frequently detected HBV SP1, SP2, and SP4, we also identified 11 putative novel spliced DNA in the serum. These findings indicate the complexity of HBV RNA splicing during viral life cycle. [ABSTRACT FROM AUTHOR]