فهرست مطالب
Jundishapur Journal of Microbiology
Volume:9 Issue: 12, Dec 2016
- تاریخ انتشار: 1395/10/11
- تعداد عناوین: 12
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Page 1BackgroundOn March 31, 2013, human infections with a novel avian influenza A (H7N9) virus were firstly reported in China. By February 7, 2015, a total of 562 laboratory-confirmed human cases of H7N9 infection were reported in mainland China..ObjectivesThis study aimed to determine whether there is a novel H7N9 virus infection in human and animals in Taizhou city, China, in 2013..MethodsIn this study, we developed real-time reverse transcription-polymerase chain reaction (RT-PCR) assays to detect H7N9 virus infection in human and animals (chicken, pig, and pigeon) in Taizhou city in the beginning of H7N9 epidemics of 2013. Also, we studied the novel isolated H7N9 virus strain by using genome sequencing and phylogenetic analysis..ResultsOf 150 samples tested, 7 were detected to be H7N9 positive which all were collected from chickens. Also, a novel H7N9 virus strain (A/chicken/jiangsu/1021/2013) was isolated and studied. Phylogenetic analysis showed the novel isolated H7N9 virus had high identity to the four novel human H7N9 viruses (A/Shanghai/1/2013, A/Shanghai/2/2013, A/Anhui/1/2013, and A/Hangzhou/1/2013)..ConclusionsOur results demonstrated a novel H7N9 virus in chickens in Taizhou city in 2013 that may pose a potential risk to public health..Keywords: Influenza A Virus_H7N9 Subtype_Real_Time Polymerase Chain Reaction_Evolution_Molecular_China
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Page 2BackgroundThe hepatitis C virus (HCV) is an important human pathogen affecting an estimated 120 - 170 million individuals in the world. Polymorphisms of the IL28B gene are strongly associated with sustained virological response in patients with chronic hepatitis C treated with peginterferon and ribavirin..ObjectivesThe aims of this study were to compare the allelic and genotypic frequencies of the IL28B rs12979860 polymorphism in sustained virological response in patients who did not respond to the standard of care treatment and to verify whether there is a correlation between the viral load and the IL28B rs12979860 polymorphism..MethodsThis cross-sectional study was carried out on 75 HCV-infected patients, including 45 responders to treatment (group 1) and 30 nonresponders (group 2). We compared the allele and genotype frequencies of the IL28B rs12979860 between the two groups using the PCR-RFLP method..ResultsThe genotype frequencies of rs12979860 polymorphism in group 1 were CC (28.9%), CT (37.8%) and TT (33.3%) and in group 2 were CC (6.7%), CT (43.3%) and TT (50%). There was a significant difference in genotype frequencies of IL28B polymorphism between the two groups (P = 0.03). There was no significant association between the viral load and IL28B rs12979860 genotypes in either group 1 (P = 0.3) or group 2 (P = 0.2)..ConclusionsOur findings indicate that patients with the homozygous CC genotype in the IL28B gene had a significantly higher rate of response to treatment than those with the TT or CT genotypes. Nor does the IL28B rs12979860 polymorphism affect the viral load..Keywords: Hepatitis C Virus_Interleukin 28B_Genetic Polymorphism_Viral Genotypes_Viral Load_Sustained Virological Response
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Page 3BackgroundCo-infection with human immunodeficiency virus (HIV) and hepatitis B virus (HBV) is common due to shared routes of transmission, as reported approximately 10% of 33 million HIV-infected patients worldwide are chronically infected with HBV. Mutations of HBsAg especially within the a determinant could alter the antigenicity of the protein, causing failure of HBsAg neutralization and escaping from the hosts immune system. This results in active viral replication and liver disease..ObjectivesThe aim of the survey was to identify HBV genotype and subtype, and different mutations in HBV S gene in hepatitis B patients co-infected with HIV in Iran..MethodsPCR performance and HBV-DNA extraction from plasma of 124 samples obtained from treatment naive HIV/HBV co-infected participants were according to the protocol. Direct sequencing and alignment of surface gene were carried out using reference sequences from the Gene Bank database..ResultsFrom 124 HIV/HBV ELISA positive samples, 40 were HBV DNA-positive. The mean age of patients was 33.88 years. 20% of them were female and 80% were male. All isolates belonged to the sub genotype D1/ayw2 and genotype D. There were 50 point mutations including 23 (46%) missense and 27 (54%) silent mutations in amino acid level. Twenty three amino acid mutations occurred in different immune epitopes such as 11 (47.82%) in B cell, 6 (26.08%) in T helper and 2 (%8.6) in CTL. The prevalence of mutations in both a determinant region and Major Hydrophilic Region (MHR) was 5 (21.73%)..ConclusionsOur findings showed that P127T and A70P (Outside of MHR) were the most frequently occurring substitution mutations. P127T, P132T, G130R, and S136Y substitutions placed in the first loop of the a determinant and the other substitutions of P142T and D144N occurred in the second loop of a determinant. The results of our study showed that most of the mutations occurred in B cell epitopes. The mutation in a surface gene of HBV may be selected by immune pressure or anti-retroviral therapy..Keywords: HIV, HBV, Co, infection, S Gene, Mutation
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Page 4BackgroundLeishmaniasis has been known as an endemic disease since ancient times in Iran. Cell-mediated immunity plays a decisive role in Leishmaniasis. A promising vaccine against Leishmania could stimulate the Th1 immune response..ObjectivesIn the present study, the cellular immunogenicity of the pEGFP-N1, pEGFP-KMP and KMP11-NTGP96-GFP fusion in induction of Th1 platform immune response was evaluated in susceptible BALB/c mice..MethodsRecombinant plasmid construction of pEGFP-N1, pEGFP-KMP and KMP11-NTGP96-GFP fusion was prepared. The mice were assigned to four groups (each 15) and immunization was performed with three times (0, 21 and 42 days) with PBS, pEGFP-N1, pEGFP-KMP and pEGFP-KMP-GP96 (FUSION), subcutaneously via footpad. Cytokines assay was performed a day before and seven weeks following immunization..ResultsAccording to the results, the level of cytokines interferon-gamma (IFN-γ) and interleukin (IL)-4, and ratio of IFN-γ /IL4 was changed among different groups of mice before and seven weeks after immunization. The cytokines were increased significantly in the groups that received pEGFP-KMP and pEGFP-KMP-GP96 (FUSION) compared to PBS and pEGFP-N1 groups (PConclusionsIn conclusion, pEGFP-KMP-GP96 (FUSION) induced Th1 platform immune response against Leishmania major (MRHO/IR/75/ER) infection..Keywords: pEGFP, KMP, GP96, Cytokines, Immunization, Balb, c Mice, Leishmania major
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Page 5BackgroundStreptococcus agalactiae colonization in pregnant women leads to prenatal and neonatal infections worldwide; thus, early detection is very crucial..ObjectivesDevelopment of a rapid detection method for S. agalactiae..MethodsGenomic DNA of cultured S. agalactiae was prepared and loop-mediated isothermal amplification (LAMP) primers were designed based on the cAMP gene in bacteria. The optimum primer set was selected based on the reaction speed and specificity. The reaction result was monitored visually. The sensitivity and specificity of the LAMP method were evaluated and compared with polymerase chain reaction (PCR) method..ResultsUsing the optimum primer set the reaction can be completed in 40 minutes at 63°C in a water bath. The LAMP assay was 10 - 100 times more sensitive than PCR, with a detection limit of 10 CFU/mL of S. agalactiae. Forty vaginal swab were examined by LAMP, and the specificity was 100%..ConclusionsThus, for S. agalactiae detection, the LAMP method is a valuable diagnostic tool, with easy, rapid, visual, accurate, and sensitive advantages..Keywords: Streptococcus agalactiae, DNA Amplification Technics, Laboratory Diagnosis, Prenatal Screening
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Page 6BackgroundEnterococcus faecium is an important nosocomial pathogen and has developed resistance to multiple antibiotics, such as vancomycin. Nitrofurantoin is active against E. faecium and E. faecalis, including vanA- and vanB-positive isolates..ObjectivesTo investigate the role of rpoB mutation in E. faecium..MethodsThe growth rate and reactive oxygen species (ROS) levels were determined. The proteomic profiles of E. faecium B42 and its Rifr mutant B42-R7 were also compared. Complement experiments were performed to elucidate the role of nitroreductase in nitrofurantoin resistance..ResultsThe Rifr mutant (B42-R7, rpoB H489D) of E. faecium had a lower growth rate and higher ROS levels. Overexpression of nitroreductase in E. faecium B42-R7 was observed in proteomic analyses. Enhanced expression of nitroreductase in Escherichia coli increased the sensitivity to nitrofurantoin..ConclusionsThe rpoB mutation in E. faecium not only altered the susceptibility to rifampin, but also affected global protein expression, including nitroreductase. Nitroreductase expression in E. faecium B42-R7 might play a role in nitrofurantoin resistance..Keywords: Enterococcus faecium, rpoB, nitrofurantoin, nitroreductase
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Page 7BackgroundAmpC β-lactamase confers resistance to a variety of β-lactam agents, and all plasmid-mediated AmpC genes are considered clinically significant. The transfer of the AmpC gene to plasmid has resulted in dissemination among the Enterobacteriaceae family, including Escherichia coli, Klebsiella spp., and Proteus mirabilis..ObjectivesThe prevalence of plasmid-mediated AmpC genes was determined in isolates of E. coli, Klebsiella spp., and P. mirabilis with reduced susceptibility to cefoxitin or extended-spectrum cephalosporins by the multiplex PCR method..MethodsA total of 310 consecutive non-duplicate isolates of E. coli, Klebsiella spp., and P. mirabilis were obtained from various clinical specimens. Isolates with positive screening test results were subjected to further molecular evaluation..ResultsFifty isolates were positive on the screening test. Among them, positive PCR reactions were identified in 35/221 and 12/77 isolates of E. coli and Klebsiella spp., respectively, including 16 (34.0%) for CIT only, 7 (14.8%) for DHA only, and 24 (51.0%) for both DHA and CIT. No isolate was positive for FOX or MOX. No Proteus organism was positive for AmpC genes..ConclusionsCurrently, phenotypic tests are unable to accurately and reliably recognize plasmid-mediated AmpC β-lactamase-producing organisms. Although not possible for routine testing, clinical laboratories, especially in referral centers, should employ molecular testing for surveillance studies..Keywords: PCR, AmpC β, lactamase, Escherichia coli, Proteus mirabilis, Klebsiella
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Page 8BackgroundPseudomonas aeruginosa is main bacterial pathogen accountable for nosocomial infections. Furthermore, it could potentially become resistant to β-lactams, aminoglycosides and fluoroquinolones antibiotics..ObjectivesThe purpose of this study was to determine the antibiotic susceptibility pattern and genotyping of P. aeruginosa in hospitals of Tabriz (Iran) and investigate the prevalence of OXA producer isolates..MethodsOverall, 151 non-replicated isolates of P. aeruginosa were collected from October 2013 until September 2014. Antibiotic susceptibility pattern was determined by disk diffusion (Kirby Bauer) method, according to the clinical laboratory standards institute (CLSI) guideline. Genes encoding OXA (Ambler class D) β-lactamase were detected by PCR for all isolates. Polymerase chain reaction with Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) primers was used to establish the clonal relationship between the different isolates..ResultsThe frequencies of resistance to antibiotics were as follows: gentamicin: 68%, ceftazidime: 67%, piperacillin: 66%, cefepime: 64%, ciprofloxacin: 62%, tobramycin: 61%, amikacin: 60%, imipenem: 52%, gatifloxacin: 28%, polymyxin B: 2 % and colistin: 2%. The OXA group I genes was identified in 82 (56%), the OXA group II gene in 26 (18%), OXA group III in 14 (9%), OXA-1 in 22 (15%) and OXA-4 in 3 (2%) isolates. The ERIC-PCR indicated high genetic diversity among P. aeruginosa isolates..ConclusionsThe high prevalence of OXA β-lactamase and high genetic diversity of P. aeruginosa indicated that the resistance of P. aeruginosa might be expanding in our studied hospitals..Keywords: Antibiotic, Pseudomonas aeruginosa, Genotyping, Beta, Lactamase OXA, Polymerase Chain Reaction
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Page 9BackgroundEthambutol (EMB) is the first-line drug used for the treatment of tuberculosis. Recent reports on the EMB-resistant isolates of Mycobacterium tuberculosis in different geographical regions of the world have revealed the EMB resistance patterns of M. tuberculosis and mutations in the embB gene..ObjectivesIn this study, we determined the emb locus in sensitive and resistant Iranian M. tuberculosis isolates using two effective methods for the detection of point mutation, i.e., single-strand conformational polymorphism (SSCP) and direct sequencing..MethodsThirty-two M. tuberculosis isolates from the Isfahan tuberculosis center were characterized by conventional methods and specific amplification of the regions of difference (rd) gene and internal transcribed spacer (its) gene. Observing standard operational procedures, EMB susceptibility tests were performed on the LJ medium using the proportion method with 2, 5, and 10 μg/mL concentrations. PCR-SSCP and direct sequencing were used to detect different kinds of mutation in the embB gene with precision..ResultsIn a total of 32 isolates, two isolates (6.25%) were found to be resistant to EMB in 2, 5, and 10 μg/mL concentrations. Single-strand conformational polymorphism showed altered mobility with triple bands in the resistant isolates and double bands in the sensitive isolates. In the two EMB-resistant cases, mutation was found to occur codons 309and 299..ConclusionsWe concluded from the results that the frequency of EMB-resistant M. tuberculosis cases in Iran is lower than that of many other regions. The PCR-SSCP technique can separate resistant isolates from sensitive isolates. The sequencing results of this study showed mutation in codons 309 and 299 of the embB gene. In none of the resistant isolates, mutation was observed in codon 306. Further studies are required to determine other point mutations and analyze other genetic loci associated with EMB resistance in M. tuberculosis isolates in Iran.Keywords: Mycobacterium tuberculosis, Ethambutol, embB, PCR, SSCP, Sequencing
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Page 10BackgroundThe ever-increasing resistance of microorganisms to pathogens and our inability to control infectious diseases indicate the importance of conducting research to find new antibiotics..ObjectivesThe aim of the present research was to isolate, identify, and optimize a cold and pH resistant strain of Streptomyces with high antibiotic production capability..MethodsSoil samples were taken from the Telar forests of northern Iran, and the ACS52 strain was identified as a Streptomyces strain based on the morphological, biochemical, and 16S rRNA gene analysis. Antibacterial features of the obtained strain were studied against a wide range of Gram-positive and Gram-negative bacteria using the cross-culture method. In order to evaluate the antibacterial activity of culture product, two seed cultures and three fermentation media were examined. Finally, the effects of various factors such as the type of carbon and nitrogen sources, temperature, pH, and inoculation rate were investigated..ResultsStreptomyces sp. ACS52 is a cold-resistant alkalophilic bacterium strain with antibacterial activity against a broad spectrum of pathogenic bacteria. The fermentation medium containing glycerol and ethyl acetate was suitable for the production and extraction of antibacterial compound, respectively. Glycerol and starch as the carbon source, soybean extract as the nitrogen source, temperature of 25°C, pH of 7, and inoculation rate of 10% were found to provide the optimal conditions for the antibacterial activity..ConclusionsThe crude extract of Streptomyces sp. ACS52 had high antibacterial activity against a wide spectrum of bacteria and could be of interest due to its features such as ability to grow at low temperatures and alkaline pH levels..Keywords: Streptomyces sp., Telar Forests, Optimization
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Page 11BackgroundGroup A bovine Rotaviruses (BRV) are one of the main factors of neonatal calf diarrhea and mortality around the world. The current study was carried out to assess the genetics of BRV circulating in the Pakistani livestock and characterize the antigenic genes of Rotavirus contributing towards calf diarrhea..MethodsA total of 200 fecal samples were collected from diarrheic buffalo and cattle calves from ten districts of Punjab, Pakistan. Samples were selected on the basis of agro-ecological zones of the province. Fecal samples were analyzed for the presence of BRV using Ag-capture ELISA. Positive samples were subjected to PCR for the amplification of VP4 and VP6 genes and subsequent sequencing. Phylodynamics was performed to infer genetic clustering and evolutionary distances of characterized strains of BRV in accordance to the BRV available publically..ResultsIn ELISA, a total of 12 calf samples (5 cattle and 7 buffalo), 6%, were found positive. The sequencing and phylogenetic analysis of both genes showed that Pakistani BRV (BRV/QOL/13) depicted maximum identity (98%) of the VP4 gene with Indian BRV VP4 gene. Pakistani BRV VP6 gene (Pakistan/MM85/QOL) showed maximum identity of 98% with Indian BRV A VP6 gene (accession No. JF720873, EF200565)..ConclusionsBovine rotavirus presents 6% of calf diarrhea in Pakistani cattle and buffalo samples. The VP4 and VP6 genes show closed relationships with bovine rotavirus reported from Indian isolates..Keywords: Animals, Antigens, Viral, Cattle, Pakistan, Rotavirus, Rotavirus Infections
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Page 12BackgroundBiofilm formation capacity is recognized as an important virulence factor in staphylococci that makes the organisms more resistant to antibiotics and host defenses..ObjectivesThis study aimed to determine the biofilm producing ability and presence of icaA/D genes in staphylococcal isolates obtained from different clinical specimens..MethodsThis cross-sectional study was performed on a total of 151 staphylococcal isolates (79 Staphylococcus aureus and 72 S. epidermidis) obtained from different clinical specimens from February to August 2013 in Shiraz, Southwest of Iran. Slime production ability was evaluated using the both phenotypic (by cultivation of staphylococcal isolates on Congo red agar (CRA)) and genotypic (detection of the presence of icaA/D genes by PCR) methods..ResultsOverall, of the 79 S. aureus isolates tested with CRA method, 64.7% of methicillin-resistant S. aureus (MRSA) isolates, and 46.7% of methicillin-sensitive S. aureus (MSSA) isolates were able to produce biofilm. The relative frequency of biofilm producing S. epidermidis isolates was 70.8% that was significantly higher than that of S. aureus isolates. The most common source of biofilm producing isolates in both S. aureus and S. epidermidis isolates was endotracheal tube (ETT) with 100% biofilm formation. Moreover, the presence of icaA/D genes was detected in 63.3% and 81.9% of S. aureus and S. epidermidis isolates, respectively..ConclusionsThe remarkable rates of biofilm production ability among clinically isolated staphylococci emphasize the necessity of more effective infections control policies to prevent biofilm formation on medical devices and hospital environmental surfaces..Keywords: MRSA, Biofilm, Antibiotic Resistance, Staphylococcus