Molecular evolution of carbapenemases KPC-12 and molecular docking analysis of β-lactams / 中华临床感染病杂志

Objective To analyze molecular evolution of carbapenemase KPC-12 and its binding free energies with β-lactams.Methods Class A beta-lactamases were divided into 2 clusters:those with carbapenemase activities and those without.Minimum Evolution method in MEGA4.1 software was used to analyze molecular evolution of class A beta-lactamases with carbapenemase activity,including KPC-2 to KPC-13,SFC-1,SME-1,IMI-1,NMC-A,and class A beta-lactamases without carbapenemase activity,including TEM-1,SHV-1.Then,tertiary structure of KPC-12 was predicted by homology modeling as reported in SWISS-MODEL database depending on tertiary structure of KPC-2.Moreover,DOCK module in ArgusLab 4.1 software was used to perform molecular docking of KPC-12 to 10 kinds of beta-lactams substrates,and the binding free energies (△ G) were calculated.Results Molecular evolution between KPC-12 and KPC-2 was the closest.The top three decline in binding free energies of β-lactams were penicillin G sodium salt (△G =-8.45149 kcal/mol),ertapenem (△G =-8.36383 kcal/mol) and ampicillin (△G =-8.19326 kcal/mol),while the last two decline in binding free energies of β-lactams were aztreonam (△G =-6.50614 kca]/mol) and clavulanic acid (△G =-6.88533 kcal/mol).Conclusion Carbapenemase KPC-12 has high catalytic activities to penicillin G sodium salt,ertapenem and ampicillin,while has low catalytic activities to aztreonam and clavulanic acid.

The relationship between distribution of different subtypes of human immunodeficiency virus-1 and the transmission routes in Shenzhen / 中华传染病杂志

ObjectiveTo investigate the distribution of human immunodeficiency virus-1 (HIV-1)subtypes and the relationship with transmission routes in Shenzhen city. MethodsThe epidemiological survey was conducted in 429 subjects with HIV-1 infection.Vein blood was collected and prepared with anticoagulation.Thereafter,the viral nucleic acid was extracted and subsequently amplified for HIV-1 env,gag genes by reverse transcription nested polymerase chain reaction. The viral sequences were analyzed using Mega software and compared with those in HIV database. The HIV-1 subtypes were confirmed and evolutionary tree was established. The gene discrete rate of different subtypes was calculated.ResultsFour hundred qualified samples were identified as CRF01_AE (n=207),CRF07_BC (n=115),CRF08 _BC (n=14),CRF02_AG (n=1),B (n=49) and C(n=14),respectively.CRF01_AE was the predominant subtype that was detected in the subjects with different transmission routes,such as homosexual contact,heterosexual contact,intravenous drug use and hospital-acquired infection. Among these,sexual contact was the most common route.There were nine cases infected with subtype B HIV-1 in 10 case who were blood borne. The gene discrete rate was more significant in subtype B HIV-1 compared to the other subtypes.According to the evolutionary tree analysis,the viruses under the same subtype formed the relatively independent clusters by different transmission routes. But some overlaps were observed as well. Conclusions Tbere are many HIV-1subtypes in HIV-1 infected subjects in Shenzhen, while the recombinant viruses present as the predominant form.Transmission routes are various with sexual contact as the most common route.Every subset distributes unevenly and forms its own characteristic.Overlap can be observed among the gene distribution of different HIV-1 subtypes.

Molecular evolution and binding free energy analysis of substrates of cephalosporinase ADC-57 / 中华临床感染病杂志

Objective To analyze molecular evolution and binding free energies of cephalosporinase ADC-57.Methods Minimum Evolution method in MEGA 5.0 was used to analyze molecular evolution of cephalosporinase ADC-57 and other 19 kinds of beta-lactamases.Tertiary structure of ADC-57 was predicted by homology modeling referring to tertiary structure of CMY-2.The molecular docking of ADC-57 to 11kinds of beta-lactams substrates was performed using DOCK module in ArgusLab 4.1and the binding free energies (△G) was calculated.Results ADC-57,CMY-2,DHA-1,ADC-7,ADC-56 were all belong to class C beta-lactamase,and molecular evolution between ADC-57 and ADC-56 was closest.The top three antibiotics with declining binding free energy of beta-lactams were ertapenem,cefoxitin and ceftazidine,while the last two were clavulanic acid and aztreonam.Conclusions Catalytic activities of cephalosporinase ADC-57 to ertapenem,cefoxitin and ceftazidine are high,while to clavulanic acid and aztreonam are low. Hydrolytic activities of enzyme to beta-lactams (substrates) can be analyzed by molecular docking.

Identification of a suspected Klebsiella variicola strain isolated from a patient with severe septic shock / 中华传染病杂志

Objective To identify a suspected Klebsiella variicola strain isolated from a patient with severe septic shock. Methods Sequences of rpoB, gyrA, mdh, infB, phoE and nifH genes were obtained from the clinical isolated suspected Klebsiella variicola strain, and used for constructing phylogenectic trees. Characteristics of phylogenetic trees were used to distinguish Klebsiella variicola from Klebsiella pneumoniae. Results All target gene sequences from this clinical isolated strain constantly formed a cluster with their counterparts from other Klebsiella variicola strains. These clusters were readily differentiated from Klebsiella pneumoniae clusters. Conclusions The clinical isolated strain belongs to Klebsiella variicola class and can cause septic shock. From genetic perspective, Klebsiella variicola is distinctly different from Klebsiella pneumoniae, most of which can be isolated from normal healthy people.

Molecular evolution and binding free energy analysis on substrates of KPC carbapenemases / 中华临床感染病杂志

Objective To analyze molecular evolution and binding free energies in substrates of KPC-2,KPC-5 and KPC-10 carbapenemases.Methods Minimum Evolution method in MEGA 4.1 was used to analyze molecular evolution of KPC-2,KPC-5 and KPC-10 carbapenemases,Dock module in ArgusLab 4.1 was used to perform molecular docking of these 3 carbapenemases to 10 kinds of β-lactams substrates,and calculate binding free energies(△G).Results Ambler Class A β-lactamases with carbapenemase activities were grouped in the same cluster and had good conservation,while ordinary Ambler Class A β-lactamases without carbapenemase activities were groupod in the other cluster.Binding free energies of KPC-2,KPC-5 and KPC-10 carbapenemases were lower to carbapenem antibiotics than the thirdgeneration cephalosporins,while binding free energies to aztreonam and clavulanic acid were of comparatively higher levels.Conclusion Catalytic activities of KPC to carbapenem antibiotics are higher than those to the third-generation cephalosporins,but the activities to aztreonam and clavulanic acid are low.

Evolutionary analysis of neuraminidase gene of novel influenza virus A/H1N1 in 2009 pandemic in Guangdong Province / 中华传染病杂志

Objective To analyze the genetic characterization(evolution, antigenicity, enzyme activity sites and glycosylation sites)of the neuraminidase(NA)gene of the novel influenza virus A/H1N1 in 2009 pandemic in Guangdong Province. Methods The viral RNA was extracted from 69 isolates of influenza virus A/H1N1 from patients in 2009 pandemic in Guangdong Province. NA gene fragments were amplified by reverse transcription polymerase chain reaction (RT-PCR) and sequenced. The other 52 NA gene sequences of influenza virus A in different years and different regions were retrieved from GenBank. The analysis of evolution and amino acid sequences were analyzed by MEGA 4.0 software. Results The homology of 2009 novel H1N1 influenza viruses in Guangdong and avian H5N1 influenza virus strains was high(＞85 % ). The amino acid distributions of potential antigenic sites were identical. The enzyme activity sites of NA genes of all virus strains were strictly conserved, which had eight glycosylation sites. But there were amino acid substitutions in 5 glycosylation sites, while it was identical with the 2001 avian H5N1 influenza virus. Conclusion The NA genes of 2009 novel H1N1 influenza viruses in Guangdong are high homologous with avian H5N1 influenza virus and the viral specific binding sites of neuraminidase inhibitor are not changed.

Selective kinetics of HIV-1 non-nucleoside reverse transcriptase inhibitor drug resistanace-associated mutations in AIDS patients receiving highly active anti-retrovirul therapy / 中华检验医学杂志

Objective To elucidate the molecular evolutional characteristics of HIV-1 non-nucleoside reverse transcriptase inhibitor (NNRTI) drug resistance-associated mutations in AIDS patients receiving highly active antiretroviral therapy (HAART).Methods Four AIDS patients receiving HAART with good adherence within a HlV-1 drug resistance cohort from a rural region in central China were selected,who possessed susceptible virus at the beginning of treatment and gradually came to produce resistance to NNRTIs during the process of antiretroviral therapy (ART),reverse transcriptase (RT) genes from each patient's peripheral blood samples (from 3 to 30 months after withdrawal) were cloned and sequenced in succession.Results To sequenced total 855 clones and obtained the HIV-1 NNRTI drug resistance-asseciated mutations patterns of the four patients: (1)G190A often appeared with F227 L and had the tendency of accumulating P236V during the process of treatmenL (2)Y188C always presented alone and sometimes it concured with P236V.(3) YI81C frequently concured with VI79D or KIO3N and the combination varies from patient to patient.(4)K103N often combined with Y181C or M230L Conclusions The molecular evolutional characteristics of HIV-1 NNRTI drug resistance-asseciated mutations in the 4 AIDS patients are summarized.They showed different pathways on HIV-1 NNRTI drug resistance-associated mutations and those mutations detected early tend to be predominant strains.

Tumorigenic theories and clinical prevention and treatment of tumor / 肿瘤研究与临床

Nowadays,with the sharply increasing morbidity and stable high mortality,tumor has become the greatest threaten for human health and life.After taking a view of preservations,diagnoses and treatments on tumor, oncologists considered the cure rate had not improved evidently in patients with advanced tumor in the past several decades even though the total cure rate and survival rate had increased.Facing the puzzle,people should evaluate original tumorigenic theories again.A review about it was presented here.

The evolution and dissemination of macrolide-resistance Streptococcus pneumoniae in Shanghai / 中华检验医学杂志

Objective To determine the genetic background and evolutional route of macrolideresistance Streptococcus pneumoniae(MRSP)strains in Shanghai.Methods Forty-seven MRSP clinical isolates were genotyped by pulse field gel electrophoresis(PFGE)to detect the donal relationship of therm.Serotyping and muhilocus sequence typing(MIST)on 6 multi-resistant strains wag used to investigate the evolutional relationship between serum types and international epidemic strain among MRSP strains in Shanghai.Results There were 2 epidemical clones(type A 45%,type B 17%)in MRSP clinical isolates containing both the ermB and the mefE genes in Shanghai.MIST analysis showed that all 6 multi-resistant strains whose PFGE pattern was A type belonging to Asia clonal complex-CC236(Taiwan19F-14 clone).There was a novel ST-ST2116,which might derived from CC236 due to the recombination with alldic change.Conclusion,The high prevalence of erythromycin-resistant Streptococcus pneumoniae containing both the ermB and the mere genes in Shanghai is partly due to the clonal spread of a few mtdtidrng-resistant clones.

Evolutionary trend of the novel A/H1N1 influenza virus in 2009 and the major problems concerning prevention and control of this pandemic / 解放军医学杂志

Objective Eight functional fragments of the novel A/H1N1 influenza pandemic virus in 2009 had their own evolutionary characteristics.Among them,the hemagglutinin(HA),the major antigenic gene,was originated from swine influenza virus epidemics in North America.The HA gene,polymerase genes(PB2,PB1 and PA),nucleoprotein gene(NP) and nonstructural protein gene(NS) of the virus strain isolated in Iowa of US in 2005 shared close homology(identities more than 90%) with the corresponding sequences of the novel A/H1N1 influenza pandemic virus in 2009.The Iowa strain might be an intermediate step of the evolutionary process of this novel A/H1N1 influenza virus.The evolutionary process of the novel A/H1N1 influenza might be realized in pigs re-assorted with the neuraminidase(NA) gene from European swine H1N1 influenza virus and matrix proteins(M1 and M2) genes from European H3N2 swine influenza virus.The present paper presented possible evolutionary processes of the novel A/H1N1 influenza pandemic virus in 2009,and pointed out several relevant scientific points which should be emphasized in the prevention and control of the epidemics of the novel A/H1N1 influenza in near future.