A rare urinary tract infection of multidrug-resistant Chryseobacterium urinae sp. nov. isolated from a diabetic, non-catheterized patient

Chryseobacterium demonstrates a diverse environmental presence and a significant pathogenic potential across various ecosystems. This clinical case showcases a rare instance of bacterial infection in a 75-year-old male with untreated diabetes and recurrent urinary tract infections (UTIs). The patient presented symptoms of abdominal pain, burning urination, fever, and an elevated eosinophil count. A subsequent urine culture identified a Chryseobacterium-related bacterium as the causative agent, exhibiting sensitivity to piperacillin/tazobactam, trimethoprim/sulfamethoxazole, and nitrofurantoin, which led to successful treatment using oral nitrofurantoin. Analysis of the 16S rRNA gene sequence of APV-1T revealed a close relationship of 98.2% similarity to Chryseobacterium gambrini strain 5-1St1aT (AM232810). Furthermore, comparative genome analysis, incorporating Average Nucleotide Identity (ANI), Digital DNA-DNA Hybridization (dDDH) values, and comprehensive phylogenetic assessments utilizing 16S rRNA gene sequences, core genes, and amino acid sequences of core proteins, highlighted the unique phylogenetic positioning of APV-1T within the Chryseobacterium genus. Distinct carbon utilization and assimilation patterns, along with major fatty acid content, set APV-1T apart from C. gambrini strain 5-1St1aT. These findings, encompassing phenotypic, genotypic, and chemotaxonomic characteristics, strongly support the proposal of a novel species named Chryseobacterium urinae sp. nov., with APV-1T designated as the type strain (= MCC 50690 = JCM 36476). Despite its successful treatment, the strain displayed resistance to multiple antibiotics. Genomic analysis further unveiled core-conserved genes, strain-specific clusters, and genes associated with antibiotic resistance and virulence. This report underscores the vital importance of elucidating susceptibility patterns of rare pathogens like Chryseobacterium, particularly in immunocompromised individuals. It advocates for further analyses to understand the functional significance of identified genes and their implications in treatment and pathogenesis.

CSMD1 rs10503253 increases schizophrenia risk in a Tunisian population-group

OBJECTIVES

Schizophrenia is a complex and chronic neuropsychiatric disorder. Recent genome-wide association studies have identified several at risk genetic variants, including two single nucleotide polymorphisms, namely the rs10503253 and the rs1270942 respectively located in the CSMD1 and the CFB loci. The present case-control study was designed to assess potential associations between the two variants and the risk of developing schizophrenia and disease severity. Further we demonstrate the relationship between these variants and clinical characteristics in a population-group from Tunisia.

PATIENTS AND METHODS

In total, 216 patients diagnosed with schizophrenia along with176 healthy controls were included in this case-control study. The molecular analysis of the two polymorphisms was performed using tetra the Primer Amplification Refractory Mutation System-Polymerase Chain method. The statistical analysis was done using Compare V2.1 software, and correlations between genetic results and clinical characteristics were examined by Kruskal-Wallis testing.

RESULTS

The frequency of the rs10503253A allele was found significantly higher among patients with schizophrenia as compared to healthy controls and associated with high negative PANSS scores. While no association was found concerning the implication of the rs1270942 variant in schizophrenia risk, a positive correlation with high positive PANSS scores was further observed.

CONCLUSION

The present finding confirms the previously reported association between the Cub and Sushi multiple Domain 1 rs10503253A allele and the risk to develop schizophrenia and identified the rs1270942 variant as a potential disease risk modifier. Such observations may be important for the definition of the susceptible immunogenetic background in North African individuals at risk to develop mental disorders.

Complete genome sequence of marine filamentous bacterium, Saprospira grandis strain WHT

Here, we report the complete genome sequence of a type strain of the genus Saprospira, Saprospira grandis strain WHT. The genome consists of one circular chromosome and plasmid comprising 4,250,550 bp and 53,161 bp with GC content of 46.6% and 46.8%, respectively.

Analysis of molecular characteristics of CAMP-negative Streptococcus agalactiae strains

Background

Streptococcus agalactiae can produce CAMP factor, which can promote the β-hemolysin activity of Staphylococcus aureus, forming an arrow-shaped hemolysis enhancement zone at the intersection of the two bacterial species on a blood agar plate. This characteristic feature of Streptococcus agalactiae has led to the widespread use of the CAMP test as an identification method.

Methods

Vaginal/rectal swabs, collected from women at 35-37  weeks of pregnancy, were first inoculated into a selective enrichment broth media, then subcultured onto GBS chromogenic agar and 5% sheep blood agar sequentially. The VITEK-2 automatic identification system and MALDI-TOF MS were initially employed for identification, followed by the CAMP test. CAMP-negative strains underwent 16S rDNA and cfb gene sequence analysis, as well as bacterial multilocus sequence typing.

Results

A total of 190 strains were isolated, with 15 identified as CAMP-negative. Further 16S rDNA gene sequence analysis confirmed that all 15 strains were Streptococcus agalactiae. The MLST typing assay revealed that these 15 strains were of the ST862 type. The cfb gene was amplified and electrophoresed, but no specific fragments were found, indicating that these strains lack the CAMP factor due to cfb gene deletion. Antibiotic susceptibility tests demonstrated no resistance to penicillin, ampicillin, vancomycin and linezolid among the GBS strains. However, there are significant differences in resistance rates to tetracycline.

Conclusion

This study found that 7.9% of GBS strains isolated from the vagina/rectum of pregnant women were CAMP-negative, suggesting that the CAMP test method or primers targeting the cfb gene should not be used as the sole presumptive test for GBS identification.

Targeted genotyping of COVID-19 patients reveals a signature of complement C3 and factor B coding SNPs associated with severe infection

We have attempted to explore further the involvement of complement components in the host COVID-19 (Coronavirus disease-19) immune responses by targeted genotyping of COVID-19 adult patients and analysis for missense coding Single Nucleotide Polymorphisms (coding SNPs) of genes encoding Alternative pathway (AP) components. We have identified a small group of common coding SNPs in Survivors and Deceased individuals, present in either relatively similar frequencies (CFH and CFI SNPs) or with stark differences in their relative abundance (C3 and CFB SNPs). In addition, we have identified several sporadic, potentially protective, coding SNPs of C3, CFB, CFD, CFH, CFHR1 and CFI in Survivors. No coding SNPs were detected for CD46 and CD55. Our demographic analysis indicated that the C3 rs1047286 or rs2230199 coding SNPs were present in 60 % of all the Deceased patients (n = 25) (the rs2230199 in 67 % of all Deceased Males) and in 31 % of all the Survivors (n = 105, p = 0.012) (the rs2230199 in 25 % of all Survivor Males). When we analysed these two major study groups using the presence of the C3 rs1047286 or rs2230199 SNPs as potential biomarkers, we noticed the complete absence of the protective CFB rs12614 and rs641153 coding SNPs from Deceased Males compared to Females (p = 0.0023). We propose that in these individuals, C3 carrying the R102G and CFB lacking the R32W or the R32Q amino acid substitutions, may contribute to enhanced association dynamics of the C3bBb AP pre-convertase complex assembly, thus enabling the exploitation of the activation of the Complement Alternative pathway (AP) by SARS-CoV-2.

Experimental study and theoretical analysis on fluidized activation of coal gasification fly ash from an industrial CFB gasifier

The gasification fly ash (GFA), a bulk industrial solid waste from coal gasification process, urgently needs to be effectively disposed. In order to use the GFA as porous carbon materials, fluidized activation experiments of the GFA from an industrial circulating fluidized bed (CFB) gasifier were conducted in a bench-scale CFB test rig, as well as steam activation experiments of GFA in a vertical tube furnace and theoretical analysis on the activation process. Due to the ultrafine particle size, the GFA faces a fluidization problem and auxiliary particles are needed to stabilize its fluidization. In the fluidized activation, the pore structure of GFA particles becomes developed in a seconds-level time (about 1.5 s). The specific surface area (S_BET) of activated GFA increases with temperature, maximally increasing by 48.9 % and reaching 204 m²/g. Steam activation experiments show that the GFA has an activation potential of 362 m²/g (S_BET) and the pore structure evolution of GFA can be quantified by carbon conversion ratio. Based on this, the fluidized activation of GFA is found in the stage of pore development. By appropriately increasing the carbon conversion ratio (below 40 %), the fluidized activation effect of GFA is expected to be improved. Theoretical analysis indicates for the GFA the features of ultra-fine particle size and well-developed pore structure greatly enhance the diffusion rate of active component into the particles. Under the strong diffusion effect, increasing temperature is a critical means to realize the rapid and effective activation of GFA in a finite time.

Application of post-combustion ultra-low NOx emissions technology on coal slime solid waste circulating fluidized bed boilers

In order to achieve thermal treatment of coal slime and depth control of NO_x, a 75 t/h circulating fluidized bed (CFB) boiler arranging post-combustion air is constructed. In the experiment, the combustion atmosphere and the ratio of primary air and secondary air are adjusted to decrease the NO_x emissions below 50 mg/m³ (dry basis at 6% O₂). Compared with conventional CFB combustion, the post-combustion technology decreases the NO_x emissions from 92.9 to 65.4 mg/m³ by adjusting the combustion atmosphere. Then, the primary air volume is adjusted to decrease the NO_x emissions further. On the one hand, decreasing primary air volume contributes to inhibiting the NO_x generation in the dense phase. On the other hand, it is proved that the combination of the cyclone and a post-combustion chamber plays a crucial role in the de-NO_x process of post-combustion technology. More char particles are brought to the cyclone as the primary air volume decreases. The NO_x reduction in the cyclone and the post-combustion chamber is promoted. Finally, the NO_x emissions are decreased to 42.6 mg/m³ when the ratio of primary air and secondary air is 50.0%. In addition, the SO₂ emissions and the combustion efficiency during the ultra-low NO_x condition are 23.2 mg/m³ and 98.3%, respectively.

Experimental and computational modeling for signature and biomarker discovery of renal cell carcinoma progression

BACKGROUND

Renal Cell Carcinoma (RCC) is difficult to treat with 5-year survival rate of 10% in metastatic patients. Main reasons of therapy failure are lack of validated biomarkers and scarce knowledge of the biological processes occurring during RCC progression. Thus, the investigation of mechanisms regulating RCC progression is fundamental to improve RCC therapy.

METHODS

In order to identify molecular markers and gene processes involved in the steps of RCC progression, we generated several cell lines of higher aggressiveness by serially passaging mouse renal cancer RENCA cells in mice and, concomitantly, performed functional genomics analysis of the cells. Multiple cell lines depicting the major steps of tumor progression (including primary tumor growth, survival in the blood circulation and metastatic spread) were generated and analyzed by large-scale transcriptome, genome and methylome analyses. Furthermore, we performed clinical correlations of our datasets. Finally we conducted a computational analysis for predicting the time to relapse based on our molecular data.

RESULTS

Through in vivo passaging, RENCA cells showed increased aggressiveness by reducing mice survival, enhancing primary tumor growth and lung metastases formation. In addition, transcriptome and methylome analyses showed distinct clustering of the cell lines without genomic variation. Distinct signatures of tumor aggressiveness were revealed and validated in different patient cohorts. In particular, we identified SAA2 and CFB as soluble prognostic and predictive biomarkers of the therapeutic response. Machine learning and mathematical modeling confirmed the importance of CFB and SAA2 together, which had the highest impact on distant metastasis-free survival. From these data sets, a computational model predicting tumor progression and relapse was developed and validated. These results are of great translational significance.

CONCLUSION

A combination of experimental and mathematical modeling was able to generate meaningful data for the prediction of the clinical evolution of RCC.

A non-synonymous variant rs12614 of complement factor B associated with risk of chronic hepatitis B in a Korean population

Background

Hepatitis B is known to cause several forms of liver diseases including chronic hepatitis B (CHB), and hepatocellular carcinoma. Previous genome-wide association study of CHB risk has demonstrated that rs12614 of complement factor B (CFB) was significantly associated with CHB risk. In this study, fine-mapping study of previously reported GWAS single nucleotide polymorphism (SNP; CFB rs12614) was performed to validate genetic effect of rs12614 on CHB susceptibility and identify possible additional causal variants around rs12614 in a Korean population. This association study was conducted in order to identify genetic effects of CFB single nucleotide polymorphisms (SNPs) and to identify additional independent CHB susceptible causal markers within a Korean population.

Methods

A total of 10 CFB genetic polymorphisms were selected and genotyped in 1716 study subjects comprised of 955 CHB patients and 761 population controls.

Results

A non-synonymous variant, rs12614 (Arg32Trp) in exon2 of CFB, had significant associations with risk of CHB (odds ratio = 0.43, P = 5.91 × 10^− 10). Additional linkage disequilibrium and conditional analysis confirmed that rs12614 had independent genetic effect on CHB susceptibility with previously identified CHB markers. The genetic risk scores (GRSs) were calculated and the CHB patients had higher GRSs than the population controls. Moreover, OR was found to increase significantly with cumulative GRS.

Conclusions

rs12614 showed significant genetic effect on CHB risk within the Korean population. As such rs12614 may be used as a possible causal genetic variant for CHB susceptibility.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12881-020-01177-w.

Alternative complement pathway is activated in the brains of scrapie-infected rodents

Activation of complement system in central nervous system (CNS) of the patients suffering from prion diseases or animal models infected with prion agents experimentally is reported repeatedly, but which pathways are involved in the complement system during prion infection is not well documented. Here, we evaluated the level of complement factor B (CFB), which is the key factor that triggers alterative pathway (AP) of complement in the brain tissues of scrapie-infected mice with various methodologies. We found that the levels of mRNA and protein of CFB significantly increased in the brain tissues of scrapie-infected mice. Morphologically, the increased CFB-specific signal overlapped with the elevated C3 signal in brain sections of scrapie-infected mice, meanwhile overlapped with damaged neurons and activated microglia, but not with the proliferative astrocytes. Additionally, the level of complement factor P (CFP), the key positive regulator of AP, also increased remarkably in the brain tissues of infected mice. The transcriptional levels of CD55 and CD46, two negative regulators of AP, decreased without significance in brain tissues of scrapie-infected mice at the terminal stage. However, the mRNA and protein levels of CFH, another negative regulator of AP, increased. Through the dynamic analyses of the expressions of CFB, CFP, and CFH in brain sections of 139A-infected mice, which were collected at different time-points during incubation period, illustrated time-dependent increase levels of each factor during the incubation period of scrapie infection. Taken together, our data here demonstrate that the AP of complement cascade is activated in the CNS microenvironment during prion infection.

Gasification of algal biomass (Cladophora glomerata L.) with CO2/H2O/O2 in a circulating fluidized bed

Gasification is one of the most important thermochemical routes to produce both synthesis gas (syngas) and chars. The quality of produced syngas wieldy depends on the operating conditions (temperature, residence time, heating rate, and gasifying agent), hydrodynamic properties of gasifier (particle size, minimum fluidization velocity, and gasifier size), and type of feedstock (coal, biomass, oil, and municipal solid wastes). In the present study, simulation of syngas production via circulating fluidized bed (CFB) gasification of algal biomass (Cladophora glomerata L.) at different gasifying agents and particle sizes was carried out, using Aspen Plus simulator. The model which has been validated by using experimental data of the technical literature was used to evaluate the influence of operating conditions on gas composition and performance parameters. The results show that biomass gasification using pure oxygen as the gasification agent has great potential to improve the caloric value of produced gas and performance indicators. It was also found that the produced gas caloric value, syngas yield, and performance parameters (CCE and CGE) increase with reaction temperature but are inversely proportional to the biomass particle size.

Problematic issues of air protection during thermal processes related to the energetic uses of sewage sludge and other waste. Case study: Co-combustion in peaking power plant

Currently, it is necessary to deal with issues related to the emissions as there is a constantly increasing interest in combusting sludge from sewage treatment plants in the boilers for wood. An analysis of the energetic importance of the combustion of sewage sludge has already been carried out, but the effects of various treatments of the sludge are not always clear, e.g. composting and subsequent combustion to the air pollution. Investments in other thermal processes of energetic utilisation of sewage sludge and organic waste are not always successfully implemented. The objective of this paper is to point out some problematic cases for acceptance of thermal processes related to energetic use of waste in terms of the air protection. The other aim is to mention the experience with solutions of such issues in Slovakia. There are mentioned first results of the operational validation experiments during the energy generation in circulating fluidized bed boiler in peaking power plant (Power 110MW) with the addition of the so-called alternative fuel based on wood and sewage sludge to the main fuel - black coal (anthracite). And there has already been achieved the highest share of 12.4%w. (dry matter) of sewage sludge in form of compost in blend with black coal, which is technologically viable. Moreover analyzed the problems of the authorization and operation of the co-combustion of sewage sludge and of combustion of products of various kinds of pyrolysis waste - pyrolysis gas and pyrolysis oil are analyzed.

Association of the C2-CFB locus with non-infectious uveitis, specifically predisposed to Vogt-Koyanagi-Harada disease

Complement component 2 (C2) and factor B (CFB) are regulators of complement system and involved in the alternative pathway, which have been identified to be associated with multiple immune-related diseases. This study aimed to investigate the association of these genes with non-infectious intermediate and posterior uveitis. A total of 260 Chinese non-infectious uveitis patients were recruited, including 97 patients with Vogt-Koyanagi-Harada disease (VKH), 70 patients with intermediate uveitis (IU) and 93 patients with Behçet's disease (BD). Two hundred and ninety-three normal control subjects were also recruited. Five SNPs across the C2/CFB region were selected and genotyped using TaqMan SNP Genotyping Assays. Association analysis was adjusted for gender and stratified by different subtypes. The CFB SNP rs1048709 was significantly associated with non-infectious uveitis [P corr = 0.01, OR 1.49 (allele model) and P corr = 0.04, OR 1.58 (dominant model), respectively], and similar association was also detected between rs1048709 and female uveitis patients (P corr = 0.01, OR 1.70 and P corr = 0.049, OR 184, respectively). Moreover, subgroup analyses showed that CFB-rs1048709 was specifically associated with VKH, where significantly higher frequencies of A allele and AA homozygosity were observed in VKH patients compared with controls (P corr = 0.025 and P corr = 0.035, respectively), whereas none of these five SNPs was associated with IU or BD. In addition, a haplotype block across CFB (GTG) was significantly predisposed to uveitis with protective effect (OR 0.66, P corr = 0.048). Our results revealed a significant association of CFB with non-infectious uveitis, particularly predisposed to VKH disease. Genetic differences for uveitis could be gender-specific.

Short-term efficacy of calcium fructoborate on subjects with knee discomfort: a comparative, double-blind, placebo-controlled clinical study

Calcium fructoborate (CFB) at a dose of 110 mg twice per day was previously reported to improve knee discomfort during the first 14 days of treatment. In this study, 60 participants with self-reported knee discomfort were randomized into two groups receiving CFB or placebo. Initial levels of knee discomfort were evaluated by Western Ontario and McMaster Universities Arthritis Index (WOMAC) and McGill Pain Questionnaire (MPQ) scores at the beginning of the study and also at 7 and 14 days after treatment. Results showed that supplementation with CFB significantly improved knee discomfort in the study subjects; significant reductions of mean within-subject change in WOMAC and MPQ scores were observed for the CFB group compared to the placebo group at both 7 and 14 days after treatment. Estimated treatment differences for the MPQ score were -5.8 (P=0.0009) and -8.9 (P<0.0001) at Day 7 and 14, respectively. Estimated differences for the WOMAC score were -5.3 (P=0.06) and -13.73 (P<0.0001) at Day 7 and 14, respectively. Negative values indicate greater reductions in reported discomfort. On both Day 7 and Day 14, the trend was toward greater improvement in the CFB group. The placebo group did not exhibit any change in the WOMAC and MPQ scores. In conclusion, supplementation with 110 mg CFB twice per day was associated with improving knee discomfort during the 2 weeks of intake.

Analysis of changes in hepatic gene expression in a murine model of tolerance to acetaminophen hepatotoxicity (autoprotection)

Pretreatment of mice with a low hepatotoxic dose of acetaminophen (APAP) results in resistance to a subsequent, higher dose of APAP. This mouse model, termed APAP autoprotection was used here to identify differentially expressed genes and cellular pathways that could contribute to this development of resistance to hepatotoxicity. Male C57BL/6J mice were pretreated with APAP (400mg/kg) and then challenged 48h later with 600mg APAP/kg. Livers were obtained 4 or 24h later and total hepatic RNA was isolated and hybridized to Affymetrix Mouse Genome MU430_2 GeneChip. Statistically significant genes were determined and gene expression changes were also interrogated using the Causal Reasoning Engine (CRE). Extensive literature review narrowed our focus to methionine adenosyl transferase-1 alpha (MAT1A), nuclear factor (erythroid-derived 2)-like 2 (Nrf2), flavin-containing monooxygenase 3 (Fmo3) and galectin-3 (Lgals3). Down-regulation of MAT1A could lead to decreases in S-adenosylmethionine (SAMe), which is known to protect against APAP toxicity. Nrf2 activation is expected to play a role in protective adaptation. Up-regulation of Lgals3, one of the genes supporting the Nrf2 hypothesis, can lead to suppression of apoptosis and reduced mitochondrial dysfunction. Fmo3 induction suggests the involvement of an enzyme not known to metabolize APAP in the development of tolerance to APAP toxicity. Subsequent quantitative RT-PCR and immunochemical analysis confirmed the differential expression of some of these genes in the APAP autoprotection model. In conclusion, our genomics strategy identified cellular pathways that might further explain the molecular basis for APAP autoprotection.