Genetic variation characteristics of HA gene of influenza A virus (H3N2) in Guizhou province from 2017 to 2019 / 中国基层医药

Objective:To analyze the genetic variation characteristics of the HA gene of influenza A virus (H3N2) in Guizhou province from 2017 to 2019. Methods:Twenty strains of influenza A virus (H3N2) were randomly selected from 10 network laboratories in Guizhou province for RNA extraction. Reverse transcriptase-polymerase chain reaction and sequencing were performed. The products were analyzed using bioinformatics software.Results:The nucleotide homology of the HA gene of the 20 strains was 97.7%-100%, which was highly homologous to the vaccine strains A/Hong-Kong/4801/2014 recommended by WHO in 2017 and A/Singapore-INFIMH/16-0019/2016 recommended by WHO in 2018, but they were significantly different from the vaccine strain A/Kansas/14/2017 recommended by WHO in 2019. Genetic analysis showed that the 20 strains were divided into two branches, and the strains that were prevalent in 2019 were located in different branches, with marked genetic differences. Key site analysis showed mutations in antigenic determinants A, B, C, and E and mutations in the anterior and posterior walls of receptor binding sites. Key site analysis also showed that there was an increase in the number of glycosylation sites compared with the vaccine strains prevalent in the same year. Genetic distance, antigen sites, and glycosylation sites were slightly different between virus strains prevalent in 2017-2018 and virus strains prevalent in 2019. Conclusion:The HA gene of the influenza A virus subtype H3N2 in Guizhou province from 2017 to 2019 showed heterogeneity and gene mutation, especially in 2019. Therefore, close monitoring of the genetic evolution of the influenza A virus subtype H3N2 is necessary.

Rapid identification of homology of carbapenem-resistant Escherichia coli by FTIR / 中华检验医学杂志

Objective:Evaluate the application of Fourier transform infrared spectroscopy in the identification of homology of carbapenem-resistant Escherichia coli(CREC). Methods:A total of 26 carbapenem-resistant Escherichia coli strains were isolated from 9 provinces in China in 2018. The 900-1 200 cm -1 was selected as a spectral region for the Euclidean distance calculating and average linkage clustering between all isolates.The single nucleotide polymorphism (SNP) was analyzed by whole genome sequencing (WGS). Results:Twenty-six CREC strains were divided into 14 infrared spectros copy(IR) types by FTIR. The same IR type belonged to the same sequence type type.Compared with cluster analysis based on WGS, the consistency of FTIR cluster analysis was 92.3% (24/26).Conclusions:FTIR presented excellent performance in identification of homology of CREC.Besides, with the advantages of simple operation and rapid acquisition of results, FTIR may be a useful tool in clinical labs.

Investigation on hemolysis, resistance and homology of Staphylococcus cohnii urealyticum / 中华检验医学杂志

Objective@#To investigate the characteristics of hemolysis, resistance and homology of Staphylococcus cohnii urealyticum.@*Methods@#A retrospective study was carried out on thirteen clinical strains of Staphylococcus cohnii urealyticum. They were re-identified by MALDI-TOF MS. Their colony and hemolytic characteristics on blood agar plates were observed. The co-hemolysis between Staphylococcus cohnii urealyticum and Staphylococcus aureus was demonstrated. The hemolysin genes and drug resistance genes were detected by PCR. Pulsed field gel electrophoresis and mass spectrometry were used to analyze the homology of strains. The susceptibility of strains to antimicrobial agents was detected by agar dilution.@*Results@#The confirmed 13 strains of Staphylococcus cohnii urealyticum showed various levels of hemolysis and had enhanced synergistic hemolysis with Staphylococcus aureus. All strains were susceptible to vancomycin and tigecycline. There were 12 strains which carried mecA gene, 7 strains carried cfr gene, 7 strains carried ermC gene. The 13 strains were divided into 3 groups by MALDI-TOF MS, and 6 types by pulsed field gel electrophoresis.@*Conclusions@#Clinical strains of Staphylococcus cohnii urealyticum demonstrated various levels of hemolysis which could be enhanced by Staphylococcus aureus. Although they carried different drug resistance genes, they were all susceptible to vancomycin and tigecycline.

Virulence gene detection and homology analysis of Klebsiella pneumoniae inducing liver abscess / 临床肝胆病杂志

ObjectiveTo investigate the serotype and virulence genes of Klebsiella pneumoniae capsule for in-hospital liver abscess, as well as the homology of these strains. MethodsA total of 26 non-repetitive strains of Klebsiella pneumoniae isolated from the patients with liver abscess in The First Affiliated Hospital of Jiamusi University from October 2018 to October 2019 were collected. These strains were identified to be Klebsiella pneumonia by Vitek-2 Compact automatic microbiological analyzer. The string test was performed for these strains; PCR was used to determine the major capsular serotypes and related virulence genes; multi-locus sequence typing was used to analyze the homology of the strains. The Fisher’s exact test was used for comparison of categorical data between groups. ResultsThe positive rate of all 26 strains of Klebsiella pneumoniae was 100% in the string test, with 17 strains of K1 type, 5 strains of K2 type, 1 strain of K5 type, 1 strain of K57 type, and 2 strains with unknown serotype. The virulence genes rmpA, aero, and ureA had a positive rate of 100% (26/26); uge and mrkD had a positive rate of 96.2% (25/26); fimH had a positive rate of 80.8% (21/26); iucB had a positive rate of 73.1% (19/26); wcaG, magA, and kfu had a positive rate of 65.4% (17/26); allS had a positive rate of 61.5% (16/26); kpn had a positive rate of 30.8% (8/26); iroNB had a positive rate of 7.7% (2/26). The cf29a gene was not detected; wcaG, magA, and allS were only detected in K1 serotype; uge was not detected in K57 serotype. Multi-locus sequence typing found 17 trains with ST23 type, 3 strains with ST86 type, 2 strains with ST65 type, 2 strains with ST1934 type, 1 strain with ST485 type, and 1 strain with ST592 type. ConclusionK1 and K2 serotypes are the main serotypes in the strains in this experiment, and ST23 type is the main sequence type for infection in our hospital.

Homology analysis of Carbapenems-resistant klebsiella pneumoniae by MALDI-TOF MS / 中华检验医学杂志

Objective@#To evaluate the ability of matrix-assisted laser desorption/ionization-time of flight mass spectrometry(MALDI-TOF MS) in the homology analysis of Carbapenems-resistant klebsiella pneumonia.@*Methods@#Twenty-one non-duplicated strains of Carbapenems-resistant klebsiella pneumoniae were isolated from Shandong Provincial Hospital affiliated to Shandong University during April 2011 and October 2013 in this study. Twenty isolates were from neonatal unit and one from cardiac surgery. The homology analysis of Carbapenems-resistant klebsiella pneumoniae was performed with pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and MALDI-TOF MS respectively.@*Results@#The result of PFGE was consistent with MLST. The twenty-one CRKPN strains were divided into three groups by MALDI-TOF MS according to their relationship, 18 of them belonged to II group, and the homology was higher than 75%. From the analysis of protein mass spectra of 18 strains, the protein peaks were roughly the same. Thus, it was concluded that their relationship was close, and the results were basically consistent with the results of PFGE and MLST. The H13 strain with low homology (<60%) was different from the above strains, especially in the molecular weight 4365, 5381 and 6289.The PFGE analysis showed that the homology between H13 and other strains was 61%, and the MLST classification result was ST54.@*Conclusions@#MALDI-TOF MS can be used to identify CRKPN accurately and analyze its homology analysis more conveniently than other methods in clinical laboratory. MALDI-TOF MS has the potential to be used as an easy and rapid epidemiology typing tool for nosocomial infection investigation caused by drug-resistant bacteria.(Chin J Lab Med, 2018, 41: 589-595)

Facial cutaneous phaeohyphomycosis caused by Microsphaeropsis arundinis: a case report / 中华皮肤科杂志

A 55-year-old male patient presented with plaques on the face for more than 20 years,and no immunodeficiency diseases were diagnosed.Skin examination showed large areas of pink plaques on the nose,bilateral cheeks and upper oral lips with slight desquamation,verrucous hyperplasia on the dorsal area of the nose,and a bean-sized verrucous protuberance on the tip of the nose.Histopathological examination of the skin lesions revealed pseudoepitheliomatous hyperplasia in the epidermis and hyphae-like structures in the stratum corneum.Moreover,there was diffuse infiltration of inflammatory cells in the dermis,which mainly included neutrophils,lymphocytes,histiocytes and multinucleated giant cells.Periodic acid-Schiff (PAS)-positive spore-like structures were observed in the multinucleated giant cells.Culture of the lesional tissues on Sabouraud dextrose agar (SDA) medium showed grey-brown villous colonies.Microculture on the potato dextrose agar (PDA) medium yielded dark septate hyphae and pycnidia filled with a large number of spores.Microsphaeropsis arundinis was identified by fungal molecular biological techniques.The patient was diagnosed with cutaneous phaeohyphomycosis caused by Microsphaeropsis arundinis.The patient was treated with CO2 laser for the removal of verrucous protuberance on the tip of the nose,and oral itraconazole capsules at a dose of 200 mg twice a day.After 3-month treatment,the skin lesions subsided and the drug was withdrew.During 6-month follow-up,no relapse occurred.

Relationship between vitiligo and Hashimoto's thyroiditis / Relação entre vitiligo e tireoidite de Hashimoto

Introduction: vitiligo is a multifactorial acquired depigmenting disorder, characterized by a spontaneous loss of functional melanocytes from the epidermis. Vitiligo and Hashimoto's thyroiditis (HT) often occur in association and seem to be characterized by an autoimmune process. The vitiligo associated with HT suggests genetic homologies between them. Objective: to identify protein sequence homology between melanocyte protein (Pmel) and thyroid peroxidase (TPO), using bioinformatics tools, to propose an initial mechanism which could explain the production of cross-reacting autoantibodies to melanocyte and TPO. Methods: we performed a comparison between Pmel and TPO amino acids (AA) sequences, available on the National Center for Biotechnology Information (NCBI) database by BLAST (Basic Local Alignment Search Tool) in order to find local homology regions between the AA sequences. Results: the homology sequence between the Pmel and TPO ranged from 21.0 % (19 identical residues out of 90 AA in the sequence) to 55.0% (6 identical residues out of 11 AA in the sequence). The identical alignments presented relatively high E values due to presence of short alignment. Conclusion: bioinformatics data suggest a possible pathological link between Pmel and TPO. Sequence homology between Pmel and TPO may present a molecular mimicry suggesting the possibility of antigen crossover between Pmel and TPO that might represent an immunological basis for vitiligo associated with HT.

Introdução: o vitiligo é uma doença de despimentação adquirida multifatorial, caracterizada por uma perda espontânea de melanócitos funcionais da epiderme. Vitiligo e tiroidite de Hashimoto (TH) ocorrem frequentemente em associação e parecem ser caracterizados por um processo autoimune. O vitiligo associado à TH sugere homologias genéticas entre eles. Objetivo: identificar homologia das sequências de proteína entre a proteína do melanócito (Pmel) e peroxidase da tiróide (TPO), usando ferramentas de bioinformática, para propor um mecanismo inicial que poderia explicar a produção de autoanticorpos de reação cruzada entre o melanócito e a TPO. Metodologia: foi realizada uma comparação entre a sequência de aminoácidos (AA) da Pmel e da TPO, disponível no banco de dados Basic Local Alignment Search Tool (BLAST) do National Center for Biotechnology Information (NCBI), a fim de encontrar regiões de homologia locais entre as sequências de AA. Resultados: a sequência de homologia entre a Pmel e a TPO variou de 21,0% (19 resíduos idênticos na sequência de cada 90 AA na sequência) a 55,0% (6 resíduos idênticos na sequência de 11 AA). Os alinhamentos idênticos apresentaram valores relativamente altos (E) devido à presença de alinhamentos curtos. Conclusão: os dados de Bioinformática sugerem uma possível ligação patológica entre Pmel e a TPO. A sequência de homologia entre Pmel e a TPO pode apresentar um mimetismo molecular sugerindo a possibilidade de cruzamento entre antígeno da Pmel e da TPO que pode representar uma base imunológica para a associação entre o vitiligo e a TH.

Sequence similarity between thyroid self-protein and hepatitis c virus polyprotein: possible triggering mechanism of autoimmune thyroiditis / Similaridade de sequências entre auto-proteínas da tireoide e poliproteínas do vírus da hepatite C: possível mecanismo de desencadeamento da tireoidite auto-imune

ABSTRACT Background - Exposure to viral antigens that share amino acid sequence similar with self- antigens might trigger autoimmune diseases in genetically predisposed individuals, and the molecular mimicry theory suggests that epitope mimicry between the virus and human proteins can activate autoimmune disease. Objective - The purpose of this study is to explore the possible sequence similarity between the amino acid sequences of thyroid self-protein and hepatitis C virus proteins, using databanks of proteins and immunogenic peptides, to explain autoimmune thyroid disease. Methods - Were performed the comparisons between the amino acid sequence of the hepatitis C virus polyprotein and thyroid self-protein human, available in the database of National Center for Biotechnology Information on Basic Local Alignment Search Tool. Results - The sequence similarity was related each hepatitis C virus genotype to each thyroid antigen. The similarities between the thyroid and the viral peptides ranged from 21.0 % (31 identical residues out of 147 amino acid in the sequence) to 71.0% (5 identical residues out of 7 amino acid in the sequence). Conclusion - Bioinformatics data, suggest a possible pathogenic link between hepatitis C virus and autoimmune thyroid disease. Through of molecular mimicry is observed that sequences similarities between viral polyproteins and self-proteins thyroid could be a mechanism of induction of crossover immune response to self-antigens, with a breakdown of self-tolerance, resulting in autoimmune thyroid disease.

RESUMO Contexto - A exposição a antígenos virais que compartilham sequência de aminoácidos semelhantes a auto-antígenos pode provocar doenças auto-imunes em indivíduos predispostos geneticamente, e a teoria do mimetismo molecular sugere que o mimetismo entre epítopos de vírus e proteínas humanas pode ativar doenças auto-imunes. Objetivo - O objetivo deste estudo foi explorar a possível semelhança entre as sequências de aminoácidos de auto-proteinas da tireóide e proteínas do vírus da hepatite C, utilizando bancos de dados de proteínas e peptídeos imunogênicos, para explicar a doença auto-imune da tireóide. Métodos - Foram realizadas comparações entre as sequências de aminoácidos de poliproteínas do vírus da hepatite C e auto-proteinas da tireóide humana, disponível na base de dados do National Center for Biotechnology Information no Basic Local Alignment Search Tool. Resultados - A semelhança de sequências foi relacionada para cada genótipo de vírus da hepatite C e proteínas da tireóide. As semelhanças entre proteínas da tireóide e os peptídeos virais variaram de 21,0% (31 resíduos idênticos da sequência de 147 aminoácidos) a 71,0% (cinco resíduos idênticos da sequência de 7 aminoácidos). Conclusão - Dados de bioinformática sugerem uma possível ligação entre vírus da hepatite C e doença auto-imune da tireóide. Através de mimetismo molecular observa-se que as semelhanças entre as sequências de poliproteínas virais e auto-proteínas da tireóide pode ser um mecanismo de indução de resposta imune resultando em doença auto-imune da tireóide.

Análisis filogenético de secuencias suramericanas del gen ns1 del serotipo dengue-2, relacionadas con sangrado clínico severo / Phylogenetic analysis of South American sequences of the nonstructural protein-1 (ns1) of dengue serotype 2 associated with severe clinical bleeding

Objetivo Comparar secuencias de nucleótidos y de aminoácidos de la proteína no estructural 1-NS1 de cepas DENV-2, aisladas de pacientes febriles de diferentes países suramericanos, que cursaron cuadros clínicos con severidad o sin ella. Materiales y Métodos El análisis filogenético fue realizado a partir de 28 secuencias moleculares completas (1 056 pb) del gen NS1 del serotipo DENV-2. Se realizó un análisis filogenético bayesiano utilizando el software MrBayes v.3.2.0, con el modelo SYM+G y un análisis filogenético con el método Neighbor-Joining con el modelo Jukes-Cantor. Además, las secuencias de aminoácidos fueron alineadas y comparadas entre sí, mediante el programa Clustal W incluido en el software MEGA v. 5.2. Resultados En las secuencias de aminoácidos asociadas a sangrado, la sustitución más frecuente fue isoleucina→ treonina, en la posición 93. Estas secuencias presentaron un mayor porcentaje (94,6 %) de homología de aminoácidos de la proteína NS1 en comparación con el porcentaje de homología (74 %) de los aislamientos DENV-2 no asociados a sangrado. Se identificaron cinco clados que agrupan la mayoría de las secuencias analizadas (19/24; 79,2 %) con valores de probabilidad posterior mayores o iguales al 58 %. Siete (87,5 %) secuencias asociadas a sangrado se relacionan filogenéticamente dentro de los clados 4 y 5, con valores de probabilidad posterior del 58 % y 97 %, respectivamente. Conclusión No se encontraron características filogenéticas ni tampoco diferencias entre las secuencias de aminoácidos de la proteína NS1-DENV-2 estudiadas, que pudieran ser relacionadas, de manera directa, con la severidad de la enfermedad.(AU)

Objective The objective of this in silico study was to compare nucleotide and amino acids DENV-2-NS1 sequences isolated from febrile patients, with and without disease severity, from different South American countries. Matherials and Methods A bayesian MCMC phylogenetic analysis was carried out using 28 complete sequences of the gene NS1 of the DENV-2 serotype (1 056 bp), using MrBayes v.3.2.0 software, with the model SYM+G (2.5 million generations). We also carried out a phylogenetic analysis with Neighbor-Joining method (Jukes-Cantor model). In addition, the amino acids sequences were aligned and compared with each other, using Clustal W included in MEGA v.5.2 software. Results In the amino acids sequences associated with bleeding, the most frequent substitution was isoleucine → threonine at posicion 93. These sequences showed a high percentage (94.6 %) of amino acid homology in comparison with the percentage of amino acids homology (74 %) of DENV-2 isolates not associated with bleeding. Five clades were identified that group the vast majority of the DENV-2-NS1 sequences analyzed (19/24; 79.2 %) with posterior probability values greater than or equal to 58 %. Seven sequences (87.5 %) associated with bleeding were phylogenetically related within clades 4 and 5, the posterior probability values were 58 % and 97 %, respectively. Conclusion Neither phylogenetic characteristics nor differences between amino acids of the DENV-2-NS1 sequences studied were found that could be associated directly with severity of the disease.(AU)

Reduced antibiotics sensitivity of Acinetobaoter baumannii induced by meropenem in vitro and related mechanism / 中华临床感染病杂志

Objective To investigate the mechanism related to reduced antibiotic sensitivity of Acinetobacter baumannii inducted by meropenem in vitro.Methods Three strains of clinically isolated carbapenems-sensitive Acinetobacter baumannii were induced by meropenem in vitro, and the mutant strains (MS1, MS2 and MS3) were obtained.Minimal inhibitory concentrations (MICs) of antimicrobial agents to strains before and after induction were determined by automatic drug sensitivity analyzer .The homology of strains was analyzed by Enterobacterial repetitive intergenic consensus -polymerase chain reaction ( ERIC-PCR).Modified Hodge test and EDTA-Na2-double disk synergy test were used to detect carbapenemase and metallo-β-lactamase (MBL), respectively.Main carbapenemase genes were detected by PCR and followed by DNA sequencing.Expressions of adeB and outer membrane proteins in strains before and after induction were detected with fluorescence quantitative PCR and SDS -polyacrylamide gel electrophoresis , respectively.t test was used for data analysis .Results The sensitivity of mutant Acinetobacter baumannii strains to meropenem and most antibiotics was reduced , except to imipenem, amikacin and polymyxin; and the reduced sensitivity to meropenem in MS2 and MS3 was of genetic stability.ERIC-PCR showed 100%homology between the mutant strains and parental strains .Both carbapenemase and metallo -β-lactamase were negative in mutant strains and parental strains , and only OXA-51 gene was found.The expressions of adeB gene in mutant strains were 24.26 ±0.91, while those in parental strains were 22.81 ±0.38, and the difference was not significant (t =2.534, P >0.05).Outer membrane protein with molecular weight 54 000 was missing in MS1, while that with molecular weight 47 000 was missing in MS2 and MS3.Conclusion Reduced antibiotics sensitivity in meropenem -induced Acinetobacter baumannii may be correlated with the deficiency of outer membrane protein with molecular weight 47 000.

Surveillance and genetic characteristics of echovirus 6 strains isolated from environmental sewage and aseptic encephalitis cases / 中华微生物学和免疫学杂志

Objective To analyze the genetic characteristics of echovirus 6 ( E-6) strains isolated from patients with acute meningitis/encephalitis syndrome ( AMES) in 2014 and sewage samples in 2013—2014 in Shandong province and to investigate their correlations.Methods Enterovirus strains were isolated from cerebrospinal fluid, stool and throat swab samples collected from 940 cases of AMES and 96 sewage samples used for environmental surveillance.The positive isolates were identified by molecular typing meth-od.Homologous and phylogenetic analyses based on the VP1 sequences of E-6 isolates were performed.Re-sults Altogether 47 E-6 strains were isolated from patients with AMES in 2014, accounting for 29.56%of all isolated enteroviruses ( EVs) strains.No E-6 strains were isolated from AMES cases in 2013.Data of the environmental surveillance showed that E-6 virus strains had been frequently detected in sewage samples since the summer of 2013 to the end of 2014.In total, 40 E-6 virus strains were isolated (7.87% of total isolated EVs strains) in 2013 and 139 E-6 virus strains (26.18%) in 2014.Phylogenetic analysis indicated that the E-6 isolates recruited in this study belonged to clusters A and C with high intracluster sequence iden-tities between AMES and environmental isolates.The nucleotide identities were 98.3%-100% among cluster A E-6 virus strains isolated from AMES cases in 2014 and 96.6%-100% among cluster A E-6 virus environ-mental isolates during the surveillance year 2013—2014.The cluster A E-6 virus strains shared 97.1%-100% nucleotide identities between the AMES and environmental isolates.For cluster C E-6 virus strains, the nucleotide identities were 100%, 98.7%-100% and 99.1%-100%, respectively.Conclusion The epidemic of viral encephalitis in Shandong province in 2014 was associated the transmission of two lineages of E-6 virus.Environmental surveillance revealed the potential epidemic of E-6 virus even before the epidemic of viral encephalitis in Shandong province, indicating the possibility of using environmental surveillance for early warning of related diseases.

Evolutionary characteristics of envelope glycoproteins in Ebora virus / 中华临床感染病杂志

Objective To study the evolutionary and mutant characteristics of Ebora virus envelope glycoprotein.Methods A total of 100 Ebora virus envelope glycoproteins amino acid sequences isolated during 1976 and 2014 were collected from National Center for Biotechnology Information (NCBI).Multiple sequence alignment and phylogenetic tree analysis were performed to investigate the evolutionary and mutant characteristics of Ebora virus envelope glycoprotein.Results Glycoprotein amino acid sequences of Ebora virus isolated during 1976 and 2014 showed only 54.00％-65.00％ homology among different subtypes,while 95.00％-100.00％ homology in same subtypes.Ebola virus isolated from different regions in 2014 showed a 99.70％-100.00％ homology of glycoprotein amino acid sequences in the same subtype.The homology of glycoprotein amino acid sequences of Ebola-Zaire virus isolated from Sierra Leone in 2014 was 100.00％,but three strains of Ebola-Zaire virus isolated from Guinea showed diversity in glycoprotein amino acid sequences.Glycoprotein amino acid sequences of Ebola virus with different subtypes were on different branches of phylogenetic tree.Glycoprotein amino acid sequences of Ebola-Zaire virus isolated from Sierra Leone in 2014 were on one branch,and those of Ebola-Zaire virus isolated from other countries during 1976 and 2014 were on the another branch.Conclusions Glycoprotein amino acid sequences of Ebora virus vary with time and region.Ebola-Zaire virus isolated from different regions in 2014 may be two variants with the same origin,and hybrid phenomenon is not observed among virus of different subtypes.

Detection, amplification & sequence homology of sodC in clinical isolates of Salmonella sp.

Background & objectives: Periplasmic copper and zinc superoxide dismutase (Cu,Zn-SOD or SodC) is an important component of the antioxidant shield which protects bacteria from the phagocytic oxidative burst. Cu,Zn-SODs protect Gram-negative bacteria against oxygen damage which have also been shown to contribute to the pathogenicity of these bacterial species. We report the presence of SodC in drug resistant Salmonella sp. isolated from patients suffering from enteric fever. Further sodC was amplified, cloned into Escherichia coli and the nucleotide sequence and amino acid sequence homology were compared with the standard strain sSalmonella Typhimurium 14028. Methods: Salmonella enterica serovar Typhi (S. Typhi) and Salmonella enterica serovar Paratyphi (S. Paratyphi) were isolated and identified from blood samples of the patients. The isolates were screened for the presence of Cu, Zn-SOD by PAGE using KCN as inhibitor of Cu,Zn-SOD. The gene (sodC) was amplified by PCR, cloned and sequenced. The nucleotide and amino acid sequences of sodC were compared using CLUSTAL X. Results: SodC was detected in 35 per cent of the Salmonella isolates. Amplification of the genomic DNA of S. Typhi and S. Paratyphi with sodC specific primers resulted in 519 and 515 bp amplicons respectively. Single mutational difference at position 489 was observed between the sodC of S. Typhi and S. Paratyphi while they differed at 6 positions with the sodC of S. Typhimurium 14028. The SodC amino acid sequences of the two isolates were homologous but 3 amino acid difference was observed with that of standard strain S. Typhimurium 14028. Interpretation & conclusions: The presence of SodC in pathogenic bacteria could be a novel candidate as phylogenetic marker.

Gene detection of vancomycin-resistant Enterococcus isolated from a teaching hospital in Shanghai / 中华检验医学杂志

Objective To investigate the prevalence of VRE in Huashan hospital of Shanghai from 2007 to 2009, and to examine the molecular characteristics of the VRE isolates.Methods A total of 890 non-repetive clinical isolates of Enterococcus were screened by the agar screening method ( ADSP method).Broth dilution susceptibility test was performed to determine the antimicrobial susceptibility of Enterococcus isolates to vancomycin and teicoplanin.The resistant genes and virulent genes of VRE isolates were investigated by PCR and sequencing methods.VRE isolates were classified by MLST and six isolates of VRE from 2007 to 2008 were analyzed by PFGE.Results Thirteen VRE isolates were identified by ADSP method and broth dilution susceptibility test. Six of them were resistant to vancomycin but sensitive to teicoplanin ( vancomycin MICs were from 64 to 256 μg/ml).The sequencing data of PCR products indicated these isolates might harbor a potential novel vancomycin resistant gene, which was different from the one reported in previous studies. The rest 7 isolates harbored vanA gene. The MICs of these isolates to vancomycin and teicoplanin were 32 - 64 μg/ml and 16 - 32 μg/ml, respectively.MLST results revealed 4 STs were identified in 13 VRE isolates.Eleven isolates belonged to clonal complexes(CC) 17.The positive rates of esp gene and hyl gene were 69.2% and 30.8%, respectively.Conclusions This study suggests that the most common VRE clone in Huashan Hospital was CC17.A potentially novel vancomycin resistance gene was identified, and further work needs to be done to investgate the function and the location of this novel gene.

Analysis on envelope gene of type Ⅰ dengue virus isolated from Guangzhou area in 2009 / 中华传染病杂志

Objective To sequence and analyze the envelope (E) gene of type Ⅰ dengue virus isolated from Guangzhou in 2009 for tracing the infection source. Methods The serum samples were collected from patients diagnosed with dengue fever in Guangzhou area during 2009. Dengue virus was isolated and cultured in C6/36 cells.The whole length of E gene was amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) and then sequenced. The phylogenetic tree was drawn by neighbor-joining method. The bioinformatics analysis was performed by combining the phylogenetic information and the epidemiology data. Results Four strains of type Ⅰ dengue virus were isolated from 19 samples. E gene of these strains was amplified and sequenced. The phylogenetic analysis showed that 09/GZ/9104 strain and 09/GZ/9236 strain had identical nucleotide sequence and fell within the American/African group, 09/GZ/11534 stain and 09/GZ/11562 strain had similar sequence homology and fell within the Asian group. Conclusion The typeⅠdengue viruses in Guangzhou area in 2009 are imported, which belong to two genotypes and may come from two independent origins respectively.

Nucleic acid sequence homologous analysis of the 6 kb plasmid of Yersinia pestis / 中国地方病学杂志

Objective To analyze nucleic acid sequence homology of the 6 kb(pYC) plasmid of Yersina. pestis (Y. pestis) isolated from Yurman by searching GenBank. Method The search of sequence similarity was accomplished with BLAST. Results The pYC plasmid sequence had high homology with some genes in nueleotide sequence, such as: 97.1% homology with Shigella sonnei pKYM, 92.1% homology with Haemophilus influenzae(H. influenzae) gene, Salmonella typhi (S. typhi) gene LT2 and plMVSI with 88.2% and 87.2% of homology respectively, Escherichia coli(E, coli) O157:H7 and K-12, ECOR31 with 81.4%, 81.4% and 84.7% of homology respectively. This plasmid ORFs could code for some proteins which were similar with others in GenBank, such as: ORFi and H. paragallinarum replication protein B(47.2%), ORF4 and E. coli hypothetical protein(52.7%), ORF5 and Y. pseudotuberculosis Tile (48.3%), ORF6 and E. coil Pilx5/VirB5-1ike protein (42.3%), Y. enterocolitica TriD protein(38.5%), ORFIO and S. typhimurium LT2, E. coli O157:H7 hypothetical protein(83.1% and 81.9%, respectively), ORF11 and E. coli, damage-inducible protein J(81.4%). Conclusions The pYC plasmid sequence has high homology with a few bacterial genes of Enterobacteriaceac. This plasmid may code for some proteins that are similar with hypothetical protein, damnge-indncible protein, TriD and TilE protein, Pilx5/VirB5-hke protein of Escherichia or Yersinia.

Analysis of an outbreak of nosocomial infection caused by Burkholderia cepacla using Sau-PCR method / 中华检验医学杂志

Objective San-PCR was used to analyze an outbreak of nosocomial infection caused by Brukholderia cepacia.Meanwhile a new DNA amplification technique for genetic fingerprinting-San-PCR was introduced,which owns high sensitivity and facility for homology analysis.Methods The proposed technique was based on the digestion of genomic DNA with the restriction endonuclease Sau3AI and subsequent amplification with primers which carried San3AI recognition site.Finally the homology among the DNA samples was analyzed on the basis of the profiles of agarose gel electrophoresis.Results All of the 11 strains isolated from the patients shclwed the homology except one.The results were confirmed by using PFGE and the results showed consistence with PFGE results.Condusion Sau-PCR is simple,robust,rapid method for DNA fingerprinting with broad perspective.

Analysis of HEV genetic structure and nucleotide homology isolated from sporadic acute hepatitis E in Changchun / 吉林大学学报(医学版)

Objective To analyze the HEV genetic structure and nucleotide homology isolated from sporadic acute hepatitis E in Changchun.Methods HEV RNA was detected with reverse transcription nested polymerase(RT-nPCR) and sequenced by automatic sequenator.Results The length of acquisitive HEV-CCC220 was 7193 bp coding 2397 amino acid.The gene of HEV-CCC220 was composed of 5'-UTR(nt 1-9),3'UTR(nt 7152-7193) and three open reading frames(ORFs).Its homology with HEV IV was obviously higher than that with HEV(I-III.) The whole genome sequence nucleotide homology was 83.2%-85.0%,85.0%-93.9% and 80.6%-86.7% as compared with 300nt and 98nt partial nucleotide sequence of ORF2.The homology comparison of various areas and various lengths of nucleotide was different.Conclusion The HEV-ccc220,which sporadically happened in Changchun,is the subtype IV of HEV.The 300nt of ORF2 can replace the whole gene order to perform genotype analysis of HEV.

VIM-2 Metallo-?-lactamase Producing Pseudomonas aeruginosa in Burn Wards / 中华医院感染学杂志

OBJECTIVE To analyze homology,antimicrobial susceptibility and metallo-?-lactamase gene type of metallo-?lactamase producing Pseudomonas aeruginosa in burn wards.METHODS Antimicrobial susceptibility tests were performed with E-tests.Using 2-mercaptoethanol disc synergy test to screen metallo-?-lactamase(positive) strains from imipenem-resistant P.aeruginosa in burn wards.Metallo-?-lactamase gene and integrase gene were amplified and sequenced.Resistance plasmid transfer and curing experiments were implemented to study the transfer of imipenem resistance and plasmid DNA was extracted and purified with Qiagen Plasmid Mini Kit.Random amplified polymorphic DNA(RAPD) typing was carried out to analyze the homology of the isolates.(RESULTS) Six strains of P.aeruginosa were suggested to produce metallo-?-(lactamase) by 2(-mercaptoethanol) disc synergy test.Using primers described for bla(VIM),the amplifications were observed among all 6 isolates and a VIM-2 metallo-?-(lactamase) gene was identified by sequencing.All isolates which producing VIM-2 metallo-?-(lactamase) had class 1 integrase gene and derived from a same clonal origin.CONCLUSIONS(VIM-2) metallo-?-(lactamase) producing P.aeruginosa is prevalent in burn wards,all isolates which producing VIM-2 metallo-?-(lactamase) have class 1 integrase gene.

In silico data mining of the human programmed cell death 5 (PDCD5) sequences / 北京大学学报(医学版)

Objective:To lay foundation for the functional studies of programmed cell death 5 ( PDCD5 ) and develop new technical pathway for bioinformatics analysis of human functional genes. Methods:Using PDCD5 as the target molecule, intensive bioinformatics analysis of the nucleic acid and protein sequences were conducted. Data mining and comprehensive analysis by sequence against database similarity searching, ortholog structure comparison, expression profile analysis and gene “neighbor” listing were performed. Results: Two human putative pseudogenes on chromosomes 12 and 5, and one mouse putative pseudogene on chromosome 1 were identified. The methanobacterium thermoautotrophicum ortholog was classified as the same fold as ubiquitin and ribosomal protein S13. The C. elegans ortholog, ubiquitin and IAP (inhibitor of apoptosis proteins) belonged to the same expression profile cluster. This cluster was related to biosynthesis and protein synthesis. PDCD5 orthologs in various genomes were adjacent to various ribosomal proteins on the chromosome. Conclusion: The human genome contains at least two processed pseudogenes of PDCD5 . Besides the relationship with cell apoptosis, PDCD5 is predicted to have functional relationship with ubiquitin and participate in the translation regulation.