Kinetic parameters for KPC-15 and KPC-2 enzymes.

<p>Kinetic parameters for KPC-15 and KPC-2 enzymes.</p

The susceptibility for strains of <i>E. coli</i> J53Az^R, Kp1241, Kp1769, and transconjugants (J53Az^R-Kp1241 and J53Az^R-Kp1769).

<p>Clinical breakpoints of MICs for the antimicrobial agents see the reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111491#pone.0111491-CLSI1" target="_blank">[25]</a>.</p><p>The susceptibility for strains of <i>E. coli</i> J53Az^R, Kp1241, Kp1769, and transconjugants (J53Az^R-Kp1241 and J53Az^R-Kp1769).</p

Phenotypic and Enzymatic Comparative Analysis of the KPC Variants, KPC-2 and Its Recently Discovered Variant KPC-15

<div><p>Sixteen different variants (KPC-2 to KPC-17) in the KPC family have been reported, and most current studies are focusing on KPC-2 and KPC-3. The KPC-15 variant, which isolated from <i>Klebsiella pneumoniae</i> in a Chinese hospital, was a recently discovered KPC enzyme. To compare the characteristics of KPC-15 and KPC-2, the variants were determined by susceptibility testing, PCR amplification and sequencing, and study of kinetic parameters. The strain harboring the KPC-15 showed resistance to 18 conventional antimicrobial agents, especially to cabapenem antibiotics, and the strain involving the KPC-2 also indicated resistance to cabapenem antibiotics, but both strains were susceptible to polymyxin B and colistin. The conjugation experiments showed that the changes of MIC values to the antibiotics were due to the transferred plasmids. The differences of amino acids were characterised at sites of 119 leucine and 146 lysine with KPC-15 and KPC-2. The minimum evolution tree indicated the KPC alleles evolution, and showed that the KPC-15 appeared to be homogenous with KPC-4 closely. Steady-state kinetic parameters showed the catalytic efficiency of KPC-15 was higher than that of KPC-2 for all tested antibiotics in this study. The catalytic efficiency of KPC-15 caused resistance to β-lactam antibiotics was higher than that of KPC-2. Meanwhile, an evolutionary transformation changed KPC from an efficient carbapenemase to its variants (KPC-15) with better ceftazidimase catalytic efficiency, and the old antibiotics polymyxin B and colistin might play a role in the therapy for multi-resistant strains.</p></div

Minimum Evolution tree of amino acid sequences for KPC-2 to KPC-17.

<p>KPC-15 carbapenemase was our newly discovered and appeared to be homogenous with KPC-4 closely. The amino acid sequences of KPCs based on the data of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111491#pone-0111491-g001" target="_blank">Figure 1</a>. This comparison was designed and analysed using MEGA 5.05 software.</p

Sequences of primers utilised to determine the <i>bla</i>_KPC genetic environment in this study.

<p>Sequences of primers utilised to determine the <i>bla</i>_KPC genetic environment in this study.</p

Table_3_The causal effect of triglyceride and high blood pressure on IgA nephropathy: a Mendelian randomization study.XLSX

BackgroundIt has been reported that high blood pressure (HBP) and triglyceride (TG) are considered risk factors in immunoglobulin A nephropathy (IgAN). This study aimed to explore the causalities between HBP and TG, and IgAN on the basis of Mendelian randomization (MR) analysis.MethodsFirstly, the genome-wide association study (GWAS) summary data of IgAN (GCST90018866) and two exposure factors, TG (ukb-d-30870_raw) and HBP (ukb-a-437), were sourced from the GWAS Catalog and Integrative Epidemiology Unit (IEU) OpenGWAS databases, respectively. In this study, five methods were utilized to perform MR analysis after picking out single nucleotide polymorphisms (SNPs) as instrumental variables, including MR-Egger, weighted median, simple mode, weighted mode, and inverse variance weighted (IVW), followed by the sensitivity analysis containing the heterogeneity, horizontal pleiotropy test and leave-one-out (LOO) analysis. Finally, the enrichment analysis and interaction network construction of genes corresponding to SNPs of HBP and TG were performed.ResultsThe univariate MR results revealed that HBP and TG regarded as risk factors were causally related to IgAN [TG: p = 0.046, odds ratio (OR) = 1.065, 95% confidence interval (CI) = 1.001–1.133; HBP: p = 7.09 × 10−7, OR = 1.970, 95% CI = 1.507–2.575] based on random-effect IVM method, of which TG had a weaker impact. The reliability of these univariate MR results was certified by the sensitivity analysis, in which there was no horizontal pleiotropy and exaggerated influence of each SNP. Furthermore, HBP was markedly causally related to IgAN (p = 0.000512) with the help of multivariate MR analysis, rather than TG (p = 0.332). Therefore, when HBP and TG occur simultaneously, HBP is a direct influencing factor on IgAN. Ultimately, a total of 208 and 153 genes separately corresponding to SNPs of TG and HBP were included in enrichment analysis, and thereinto, genes relevant to TG were mainly enriched in lipid homeostasis and cholesterol metabolism, while genes concerned with HBP played their roles in regulation of cell growth, aldosterone synthesis and secretion and so forth.ConclusionTG and HBP as risk factors were causally connected with IgAN, of which HBP was strongly related to the onset of IgAN, providing more reliable evidence for further exploring the relationship between TG and HBP and IgAN.</p

Promoter elements of the <i>bla</i>_KPC-15 and <i>bla</i>_TEM genes in 8.997 kb-length nucleotide sequence.

<p>The sequence provided the upstream and downstream regions of <i>bla</i>_KPC-15 structural genes. The <i>tnpA</i> gene, which was upstream of the <i>bla</i>_KPC-15 (3,020 bp) gene, was homologous to a putative IS<i>Kpn8</i> transposon, and the downstream region of the <i>bla</i>_KPC-15 gene (1,320 bp) was homologous to a putative IS<i>Kpn6</i>-like transposon. The nucleotides upstream of the <i>bla</i>_KPC-15 and <i>bla</i>_TEM-12 gene translational start codons were shown in the box. The putative −10 promoter elements of the <i>bla</i>_KPC-15 gene were shown as <i>gattaa</i>, labeled as −10 below, and there were no obvious −35 promoter elements to be discovered in the promoter region. The putative −10 and −35 promoter elements of the <i>bla</i>_TEM-12 gene were shown as <i>tataac</i> and <i>ttattg</i>, labeled as −10 and −35 below the promoter region. The start sites of transcription were indicated as G by +1 residue. RBS was the abbreviation of the ribosome binding site.</p

Comparison of amino acid sequence alignments of KPC carbapenemases.

<p>KPC-15 was recently identified as a carbapenemase in <i>Klebsiella pneumonae</i> from the Taizhou Municipal Hospital of China. The data within parentheses are GenBank accession numbers.</p

Data_Sheet_4_The causal effect of triglyceride and high blood pressure on IgA nephropathy: a Mendelian randomization study.CSV

BackgroundIt has been reported that high blood pressure (HBP) and triglyceride (TG) are considered risk factors in immunoglobulin A nephropathy (IgAN). This study aimed to explore the causalities between HBP and TG, and IgAN on the basis of Mendelian randomization (MR) analysis.MethodsFirstly, the genome-wide association study (GWAS) summary data of IgAN (GCST90018866) and two exposure factors, TG (ukb-d-30870_raw) and HBP (ukb-a-437), were sourced from the GWAS Catalog and Integrative Epidemiology Unit (IEU) OpenGWAS databases, respectively. In this study, five methods were utilized to perform MR analysis after picking out single nucleotide polymorphisms (SNPs) as instrumental variables, including MR-Egger, weighted median, simple mode, weighted mode, and inverse variance weighted (IVW), followed by the sensitivity analysis containing the heterogeneity, horizontal pleiotropy test and leave-one-out (LOO) analysis. Finally, the enrichment analysis and interaction network construction of genes corresponding to SNPs of HBP and TG were performed.ResultsThe univariate MR results revealed that HBP and TG regarded as risk factors were causally related to IgAN [TG: p = 0.046, odds ratio (OR) = 1.065, 95% confidence interval (CI) = 1.001–1.133; HBP: p = 7.09 × 10−7, OR = 1.970, 95% CI = 1.507–2.575] based on random-effect IVM method, of which TG had a weaker impact. The reliability of these univariate MR results was certified by the sensitivity analysis, in which there was no horizontal pleiotropy and exaggerated influence of each SNP. Furthermore, HBP was markedly causally related to IgAN (p = 0.000512) with the help of multivariate MR analysis, rather than TG (p = 0.332). Therefore, when HBP and TG occur simultaneously, HBP is a direct influencing factor on IgAN. Ultimately, a total of 208 and 153 genes separately corresponding to SNPs of TG and HBP were included in enrichment analysis, and thereinto, genes relevant to TG were mainly enriched in lipid homeostasis and cholesterol metabolism, while genes concerned with HBP played their roles in regulation of cell growth, aldosterone synthesis and secretion and so forth.ConclusionTG and HBP as risk factors were causally connected with IgAN, of which HBP was strongly related to the onset of IgAN, providing more reliable evidence for further exploring the relationship between TG and HBP and IgAN.</p

Data_Sheet_5_The causal effect of triglyceride and high blood pressure on IgA nephropathy: a Mendelian randomization study.CSV

BackgroundIt has been reported that high blood pressure (HBP) and triglyceride (TG) are considered risk factors in immunoglobulin A nephropathy (IgAN). This study aimed to explore the causalities between HBP and TG, and IgAN on the basis of Mendelian randomization (MR) analysis.MethodsFirstly, the genome-wide association study (GWAS) summary data of IgAN (GCST90018866) and two exposure factors, TG (ukb-d-30870_raw) and HBP (ukb-a-437), were sourced from the GWAS Catalog and Integrative Epidemiology Unit (IEU) OpenGWAS databases, respectively. In this study, five methods were utilized to perform MR analysis after picking out single nucleotide polymorphisms (SNPs) as instrumental variables, including MR-Egger, weighted median, simple mode, weighted mode, and inverse variance weighted (IVW), followed by the sensitivity analysis containing the heterogeneity, horizontal pleiotropy test and leave-one-out (LOO) analysis. Finally, the enrichment analysis and interaction network construction of genes corresponding to SNPs of HBP and TG were performed.ResultsThe univariate MR results revealed that HBP and TG regarded as risk factors were causally related to IgAN [TG: p = 0.046, odds ratio (OR) = 1.065, 95% confidence interval (CI) = 1.001–1.133; HBP: p = 7.09 × 10−7, OR = 1.970, 95% CI = 1.507–2.575] based on random-effect IVM method, of which TG had a weaker impact. The reliability of these univariate MR results was certified by the sensitivity analysis, in which there was no horizontal pleiotropy and exaggerated influence of each SNP. Furthermore, HBP was markedly causally related to IgAN (p = 0.000512) with the help of multivariate MR analysis, rather than TG (p = 0.332). Therefore, when HBP and TG occur simultaneously, HBP is a direct influencing factor on IgAN. Ultimately, a total of 208 and 153 genes separately corresponding to SNPs of TG and HBP were included in enrichment analysis, and thereinto, genes relevant to TG were mainly enriched in lipid homeostasis and cholesterol metabolism, while genes concerned with HBP played their roles in regulation of cell growth, aldosterone synthesis and secretion and so forth.ConclusionTG and HBP as risk factors were causally connected with IgAN, of which HBP was strongly related to the onset of IgAN, providing more reliable evidence for further exploring the relationship between TG and HBP and IgAN.</p