فهرست مطالب

Jundishapur Journal of Microbiology - Volume:9 Issue: 12, Dec 2016

Jundishapur Journal of Microbiology
Volume:9 Issue: 12, Dec 2016

  • تاریخ انتشار: 1395/10/11
  • تعداد عناوین: 12
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  • Zhu Yang*, Zenglin Pei, Kejia Jiang, Wenqing Yu, Yu Wang Page 1
    Background
    On 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..
    Objectives
    This study aimed to determine whether there is a novel H7N9 virus infection in human and animals in Taizhou city, China, in 2013..
    Methods
    In 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..
    Results
    Of 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)..
    Conclusions
    Our 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
  • Fateme Zare, Hossein Hadinedoushan*, Mohsen Akhondi Meybodi, Mahdi Dehghanmanshadi, Seyyed Ali Mirghanizade Bafghi, Mahmood Vakili Page 2
    Background
    The 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..
    Objectives
    The 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..
    Methods
    This 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..
    Results
    The 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)..
    Conclusions
    Our 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
  • Chiman Karami, Ahmad H. Adli, Sareh Zhand, Alijan Tabarraei, Reza Talei, Mohsen Saeidi, Abdolvahab Moradi * Page 3
    Background
    Co-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 host’s immune system. This results in active viral replication and liver disease..
    Objectives
    The 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..
    Methods
    PCR 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..
    Results
    From 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%)..
    Conclusions
    Our 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
  • Abdolhossein Dalimi *, Vahid Nasiri Page 4
    Background
    Leishmaniasis 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..
    Objectives
    In 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..
    Methods
    Recombinant 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..
    Results
    According 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 (P
    Conclusions
    In 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
  • Weihua Yang, Cuiming Cao, Weichen Wang, Yunshan Wang* Page 5
    Background
    Streptococcus agalactiae colonization in pregnant women leads to prenatal and neonatal infections worldwide; thus, early detection is very crucial..
    Objectives
    Development of a rapid detection method for S. agalactiae..
    Methods
    Genomic 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..
    Results
    Using 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%..
    Conclusions
    Thus, 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
  • Xiaoting Hua, Tingting Qu, Xi Li, Qiong Chen, Zhi Ruan, Yunsong Yu* Page 6
    Background
    Enterococcus 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..
    Objectives
    To investigate the role of rpoB mutation in E. faecium..
    Methods
    The 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..
    Results
    The 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..
    Conclusions
    The 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
  • Hiva Saffar*, Neda Asgari Niaraki, Arash Ghahroudi Tali, Zohre Baseri, Alireza Abdollahi, Rouzbeh Yalfani Page 7
    Background
    AmpC 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..
    Objectives
    The 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..
    Methods
    A 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..
    Results
    Fifty 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..
    Conclusions
    Currently, 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
  • Mohammad Aghazadeh, Hossein Samadi Kafil, Reza Ghotaslou, Mohammad Asgharzadeh, Maryam Moghadami, Mohammad Taghi Akhi, Zoya Hojabri, Behrouz Naghili, Khadijeh Najafi, Somayeh Azimi, Saeed Shokrian* Page 8
    Background
    Pseudomonas aeruginosa is main bacterial pathogen accountable for nosocomial infections. Furthermore, it could potentially become resistant to β-lactams, aminoglycosides and fluoroquinolones antibiotics..
    Objectives
    The 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..
    Methods
    Overall, 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..
    Results
    The 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..
    Conclusions
    The 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
  • Bahram Nasr Esfahani, Fatemeh Sadat Zarkesh, Hadi Rezaei Yazdi, Tooba Radaee* Page 9
    Background
    Ethambutol (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..
    Objectives
    In 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..
    Methods
    Thirty-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..
    Results
    In 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..
    Conclusions
    We 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
  • Sadaf Sadat Rafati, Bahar Shahnavaz *, Ali Makhdoumi Page 10
    Background
    The ever-increasing resistance of microorganisms to pathogens and our inability to control infectious diseases indicate the importance of conducting research to find new antibiotics..
    Objectives
    The aim of the present research was to isolate, identify, and optimize a cold and pH resistant strain of Streptomyces with high antibiotic production capability..
    Methods
    Soil 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..
    Results
    Streptomyces 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..
    Conclusions
    The 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
  • Nadia Mukhtar*, Tahir Yaqub, Ambreen Masood, Hasnain Javed, Jawad Nazir, Asim Aslam, Akhtar Ali, Maryam Javed, Asif Nadeem, Tanveer Hussain, Zarfashan Tahir, Hassaan Bin Aslam Page 11
    Background
    Group 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..
    Methods
    A 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..
    Results
    In 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)..
    Conclusions
    Bovine 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
  • Mehrdad Zalipour, Hadi Sedigh Ebrahim, Saraie, Jamal Sarvari, Reza Khashei * Page 12
    Background
    Biofilm formation capacity is recognized as an important virulence factor in staphylococci that makes the organisms more resistant to antibiotics and host defenses..
    Objectives
    This study aimed to determine the biofilm producing ability and presence of icaA/D genes in staphylococcal isolates obtained from different clinical specimens..
    Methods
    This 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..
    Results
    Overall, 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..
    Conclusions
    The 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