Microbiology
Forough Goodarzi; Masoumeh Hallajzadeh; Mohammad Sholeh; Malihe Talebi; Vahid Pirhajati Mahabadi; Nour Amirmozafari
Abstract
Background & Objective: This study aims to isolate a lytic bacteriophage against planktonic Enterococcus faecalis V583 culture and evaluate its ability to disrupt and inhibit biofilm.Methods: An anti-E. faecalis phage was isolated from sewage and visualized by electron microscopy, the vB_EfsS_V583 ...
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Background & Objective: This study aims to isolate a lytic bacteriophage against planktonic Enterococcus faecalis V583 culture and evaluate its ability to disrupt and inhibit biofilm.Methods: An anti-E. faecalis phage was isolated from sewage and visualized by electron microscopy, the vB_EfsS_V583 (V583) host range was determined by spot test on 13 E. faecalis clinical strains. Inhibition and degradation experiments were designed to investigate the effect of phage on biofilm. In the inhibition and degradation assay, biofilms were formed in the presence and absence of phage, respectively. Finally, crystal violet method tested the effect of phage on biofilm.Results: Phage V583 belongs to the Siphoviridae family and can infect all E. faecalis strains. Antibacterial activity has been shown to degrade and inhibit biofilm produced by V583. The study results showed that phage v583 is more efficient in biofilm inhibition than biofilm degradation. In both assays, phage-treated wells' absorption is less than untreated wells. These results were confirmed by Colony-forming unit reduction in the treated biofilm.Conclusion: The anti-biofilm activity showed that phage therapy using phage V583 might be an alternative tool to remove E. faecalis biofilms.
Behnam Mohammadi-Ghalehbin; Shahram Habibzadeh; Mohsen Arzanlou; Roghayeh Teimourpour; Saeideh Amani Ghayum
Abstract
Background & objective: Pneumocystis pneumonia (PCP) is responsible for pulmonary infection in immunocompromised patients. This study aimed to investigating the frequency of Pneumocystis colonization in patients hospitalized in the intensive care unit (ICU) and evaluating the relationship between ...
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Background & objective: Pneumocystis pneumonia (PCP) is responsible for pulmonary infection in immunocompromised patients. This study aimed to investigating the frequency of Pneumocystis colonization in patients hospitalized in the intensive care unit (ICU) and evaluating the relationship between PCP and Pneumocystis colonization. Methods: In the current cross sectional study bronchoalveolar lavage (BAL)fluids of 100 patients were collected from surgery and neurosurgery ICUs with different underlying corticosteroid therapy conditions. Patients were divided into 2 groups (patients who received corticosteroids and not received corticosteroids). Direct examination on BAL fluids was performed by the Gomori methenamine silver andGiemsa staining techniques. Additionally, 2 filtered air samples of the 2 above mentioned units were collected. A nested-PCR targeted mtLSUrRNA gene and sequencing were used to identify Pneumocystis spp. Results: In direct microscopy, 31 out of 100 hospitalized patients (31%) showed positive results. Twenty-three (46%) of smear positive patients were from the group of patients who received corticosteroid, the other 8(16%) were from the group of patients who didn’t receive corticosteroids (P= 0.001). Pneumocystis jirovecii DNA was detected in 77 out of 100 BAL samples by nested-PCR (77%) in which 40(52%) and 37(48%) samples were obtained from the patients who received and not received corticosteroids, respectively. Pneumocystis genome was found in 1 of the 2 filtered air samples. Conclusion: A significant number of patients who received corticosteroids were also colonized by P. jirovecii that may predispose to PCP or be transmitted to susceptible patients. A significant relationship was observed between the mean hospital stay and detection rate.
Microbiology
Khashayar Mohseni; Reza Mirnejad; Vahab Piranfar; Shiva Mirkalantari
Abstract
Background & Objective: Since the symptoms of Brucellosis are often atypical and nonspecific, using clinical signs alone to diagnose brucellosis is not advised; therefore, the diagnosis relies predominantly on laboratory testing. Currently, molecular, serological, and microbiological methods are ...
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Background & Objective: Since the symptoms of Brucellosis are often atypical and nonspecific, using clinical signs alone to diagnose brucellosis is not advised; therefore, the diagnosis relies predominantly on laboratory testing. Currently, molecular, serological, and microbiological methods are used for diagnosis of this disease. In this study we examined ELISA, PCR and serum agglutination (SAT) methods on human patient serum samples. Methods:A total of 100 serum samples were collected from suspected patients. Fifty serum samples gave a positive result with the Wright test. The ELISA method was first employed on all samples for the detection of IgG and IgM antibodies against Brucella. Subsequently, the rapid PCR methodology was used to identify presence of Brucella genome in 500 µL of each serum sample. The B4/B5 primer pair was used for PCR amplification. Results:Out of the 100 serum samples obtained from patients with suspected brucellosis, 50 samples tested positive by SAT and displayed high titers of 1/160. Of these 50 positive samples, 49 samples were positive as per the ELISA test whereas one sample tested negative. The PCR test was conducted on all 100 serum samples and results showed that the 45 serum samples that gave a positive agglutination test were also positive by PCR. Conclusions: Various laboratory methods have beenused or introduced for the detection of Brucella. Molecular methods such as PCR, a rapid and sensitive method for detection of bacteria, have also been reported. Based on the results of this study, we propose that the simultaneous use of serology and molecular techniques has the potential to overcome limitations of detection thereby enabling the selection of appropriate treatment for the patient.
Microbiology
Sharareh Mohammad Hasani; Reza Mirnejad; Vahhab Piranfar; Jafar Amani; Mohamad javad Vafadar
Volume 11, Issue 2 , April 2016, , Pages 144-150
Abstract
Background: Rapid diagnosis and differentiation of Brucella is of high importance due to the side effects of antibiotics for the treatment of brucellosis. This study aimed to identify and compare PCR-ELISA as a more accurate diagnositc test with other common molecular and serological tests. Methods: ...
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Background: Rapid diagnosis and differentiation of Brucella is of high importance due to the side effects of antibiotics for the treatment of brucellosis. This study aimed to identify and compare PCR-ELISA as a more accurate diagnositc test with other common molecular and serological tests. Methods: In this experimental and sectional study, during March 2014 to Sep 2015, 52 blood samples of suspected patients with clinical symptoms of brucellosis were evaluated in medical centers all over Iran with serum titers higher than 1:80. Using two pairs of specific primers of Brucella abortus, B. melitensis and DIG-dUTP, Fragment IS711 (The common gene fragment in B. melitensis and B. abortus) was amplified. DIG-ELISA was performed using specific probes of these 2 species of Brucella and patterns were subsequently analyzed, then positive responses were compared by detecting gel electrophoresis. Results: PCR-ELISA method detected all 28 samples from 52 positive samples. Its sensitivity was 6.0 pg concentration of genomic DNA of Brucella. In gel electrophoresis method, 22 samples of all positive samples were detected. PCR-ELISA was more efficient than PCR and bacterial culture method at P-value Conclusion: PCR-ELISA molecular method is more sensitive than other molecular methods, lack of mutagenic color and also a semi-quantitative ability. This method is more effective and more accurate compared to PCR, serology and culture of bacteria. PCR-ELISA does not have false responses. The limitation of this method is detection of bacteria in the genus compared to Multiplex PCR and Gel Electrophoresis.
Microbiology
Massoud Hajia; Ali Akbar Amirzargar; Mina Nazari; Neda Razavi Davodi; Morteza Karami Zarandi
Abstract
Background: Tuberculous meningitis (TBM) is a severe form of extra pulmonary tuberculosis with high mortality and morbidity rate in all age group patients specific in adults and children. The incidence and prevalence are not exactly known in Iran. In this study, we tried to evaluate the role of rapid ...
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Background: Tuberculous meningitis (TBM) is a severe form of extra pulmonary tuberculosis with high mortality and morbidity rate in all age group patients specific in adults and children. The incidence and prevalence are not exactly known in Iran. In this study, we tried to evaluate the role of rapid diagnosis and to find out the highest risk group patients.
Methods:Totally, 1783-suspected patients with tuberculous meningitis whose CSF specimens were admitted at Noor Pathobiology Laboratory, Tehran, Iran were enrolled in this study from January 2009 until December 2013.All specimens were checked for MTB by direct examination, culture and PCR tests, andfor the adenosine deaminase (ADA).
Results:Confirmed positive cases were aged from 13 to 82 yr old with mean age 46.63 yr (SD±18.84). The number of diagnosed positive MTB was different by the 3 applied protocol, 64 by PCR, 28 by culture and 33 by direct examination. Considering the result of PCR protocol theTBM was approved in 64 patients with rate of 3.59%. Two patients had other infection as well, one 56 years old with VZV and the other patient who was HIV positive was 27 years old. Increased ADA titer higher than cutoff was relevant with other results of positive samples except in two cases.
Conclusion:Analysis of the results proved adults are more at risk for tuberculous meningitis than children in Iran are. It is also confirmed PCR method provide the most efficient, rapid and reliable results for these patients who are at the critical situations.
Sedigheh Khazaei; Babak Izadi; Zhaleh Zandieh; Azadeh Alvandimanesh; Siavash Vaziri
Volume 9, Issue 3 , July 2014, , Pages 206-212
Abstract
Background and Objective: Tuberculosis is still a major health problem, involving about 1/3 of the world´s population. Diagnosis is difficult when we only use Ziehl-Neelson staining. Many cases may be missed. A more rapid and sensitive diagnostic method is necessary. PCR may be helpful. The aim ...
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Background and Objective: Tuberculosis is still a major health problem, involving about 1/3 of the world´s population. Diagnosis is difficult when we only use Ziehl-Neelson staining. Many cases may be missed. A more rapid and sensitive diagnostic method is necessary. PCR may be helpful. The aim of this study was to compare PCR, Zieh-Neelsen staining and histopathologic findings in diagnosis of tuberculosis on formalin-fixed paraffin-embedded tissues. Methods: Paraffin blocks of the submitted specimens of the patients clinically suspicious for tuberculosis or containing granuloma were selected. Ziehl-Neelsen Staining & TB-PCR (IS6110 element) was carried out. The results of the tests were compared by using the McNemar test. Statistical significance was accepted when the P value was less than 0.05. Results: Forty five specimens were included in the study, 35 had granulomas (19 with caseous necrosis). Acid-fast bacilli were identified in 17 specimens (37.8%). TB-PCR was positive in 16specimens (84%) with caseating granulomatous, 11 specimens (68.8%) with non-caseating granulomas & 6 specimens (60%) without granulomas. (P value = 0.59). Conclusions: TB-PCR on paraffin–embedded tissue is a potentially useful approach for early, rapid and sensitive diagnosis of tuberculosis. It is especially useful when granuloma is seen in tissue section, while acid-fast stain is negative. If there was no facilities for PCR, histopathological diagnosis with clinical correlation are more reliable in comparison to AFB results.
Majid Sharbatdaran; Sepideh Siadati; Mahtab Zeinalzadeh; Shahriar Shafaei; Zahra Basirat; Amir Esmi
Volume 8, Issue 1 , January 2013, , Pages 17-20
Abstract
Background: Cervical cancer is the second most common cancer in the world among women and human papilloma virus (HPV) plays a major role in its development. The aim of this study was to determine the frequency of HPV type 16 and 18 in cervical discharge by polymerase chain reaction (PCR) method ...
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Background: Cervical cancer is the second most common cancer in the world among women and human papilloma virus (HPV) plays a major role in its development. The aim of this study was to determine the frequency of HPV type 16 and 18 in cervical discharge by polymerase chain reaction (PCR) method in women with atypical biopsy or papsmear.
Method: This case- control study was performed on women in Yahyanejad Hospital, Babol University of Medical Sciences, Babol, Iran during 2008-2009. Sixty women with normal papsmear (group1) and 30 women with atypical papsmear or biopsy (group 2) were enrolled in the study and their cervical discharge was assessed for HPV type 16 and 18. Data was analyzed with SPSS, Chi-Square, Fisher,s Exact test and t-test and P<0.05 was considered significant.
Results: HPV type 16 was founded in 10% women of group 2 but not seen in group1. HPV 18 was not detected. All women had one partner and none of them had alcohol consumption.
Conclusion: In comparison with other studies, the frequency of HPV infection is lower in our study. We considered this is strongly related to our culture and religious beliefs.
Fatemeh Fattahi; Alireza Mirvaghefi; Hamid Farahmand; Gholamreza Rafiee; Alireza Abdollahi
Volume 8, Issue 1 , January 2013, , Pages 36-44
Abstract
Objectives: The presence of E.coli in fish intended for human consumption may constitute a potential danger, not only in causing disease, but also because of the possible transfer of antibiotic resistance from aquatic bacteria to those infecting humans. The objective of this study was to develop ...
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Objectives: The presence of E.coli in fish intended for human consumption may constitute a potential danger, not only in causing disease, but also because of the possible transfer of antibiotic resistance from aquatic bacteria to those infecting humans. The objective of this study was to develop an improved PCR method based on species – specific 16 S rRNA gene primers (FES, RES) for detection of E. coli from agar plates and fish tissues.
Materials and Methods: In this study, For the rapid detection of E .coli from fish a set of primers (FES, RES), targeting 16S rRNA gene sequences of the specific microorganism was designed, and fifty two rainbow trout were obtained from Karaj fish farm. Then 1mL of bacterial concentration of 106CFU/ml was injected into intraperitoneal cavity. Samples were collected from liver and kidney after 48h injection. The PCR reaction conditions were optimized to permit detection of organism from agar plates and fish tissue in a day.
Results: All tissue samples were positive for microbiological and PCR identification. DNA was successfully extracted by a boiled – extraction method or by phenol – chloroform – isoamyl alcohol. The BLAST analysis from sequencing of 4 amplicons randomly selected showed similar results, with the match being E .coli with a 100% similarity (not shown here).
Conclusion: It is concluded that this method is fast, specific and sensitive to detect E.coli in infected and asymptomatic animals, fish product, and may have a positive impact on public and environmental health.
Farideh Ebrahimi Taj; Samileh Noorbakhsh; Hamid Reza Monavari; Azardokht Tabatabaei; Masomeh Bakhshyeh
Volume 7, Issue 2 , April 2012, , Pages 107-111
Abstract
Background and Objectives: Meningoencephalitis in Iranian children is frequent, but encephalitis is rare .The frequency of HHV-6 and HHV-7 in central nervous system diseases of our children is unclear. The aim of this study was searching the DNA-s of HHV-6 & HHV-7 in CSF samples of children with ...
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Background and Objectives: Meningoencephalitis in Iranian children is frequent, but encephalitis is rare .The frequency of HHV-6 and HHV-7 in central nervous system diseases of our children is unclear. The aim of this study was searching the DNA-s of HHV-6 & HHV-7 in CSF samples of children with meningoencephalitis
Materials and Methods: A cross sectional study (2007-2009) was done in Pediatric Ward in Rasoul Hospital, Tehran Iran. Totally, 150 CSF samples obtained from children (1-180 months) with meningoencephalitis. Conventional and BACTEC Ped Plus medium, latex agglutination tests were used for ruling out the bacterial causes. We searched the DNA-s of HHV-6 & HHV-6 quantitatively by Real time - PCR in 150 CSF samples obtained from children with meningoencephalitis.
Results: 60.7 % of cases were male. Fever was reported (>38.5) in 74%; irritability in 70%; Convulsion was seen in 53% of cases. Herpes virus was detected in 12% (18/150) of cases. Both HHV-6 & HHV-7 were found in 6% of all cases. HHV-6 DNA was detected in 4.7% (6) and HHV-7 DNA was detected in 2 cases (1.4%) without any correlation to age, sex and clinical signs. HHV-6 was slightly more frequent than HHV-7.
Conclusion: Our data indicate that herpes viruses are not uncommon causes in children with meningoencephalitis. The incidence was lower than other references.
Horieh Saderi; Mehri Habibi; Parviz Owlia; Mohammadreza Asadi Karam
Volume 3, Issue 1 , January 2008, , Pages 11-14
Abstract
Background and Objective: Methicillin resistance in Staphylococcus aureus is an increasingly important clinical problem. A chromosomal gene, mecA, mediates resistance to penicillinase-resistant penicillins such as methicillin and oxacillin in Staphylococcus aureus. We evaluated the validity of ...
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Background and Objective: Methicillin resistance in Staphylococcus aureus is an increasingly important clinical problem. A chromosomal gene, mecA, mediates resistance to penicillinase-resistant penicillins such as methicillin and oxacillin in Staphylococcus aureus. We evaluated the validity of disk diffusion test by using oxacillin, methicillin and cefoxitin disks with consideration of the presence of mecA gene as the reference method for detection of methicillin resistant Staphylococcus aureus (MRSA). Materials and Methods: The susceptibility testing of 222 S. aureus clinical isolates to oxacillin (1 µg), cefoxitin (30 µg) and methicillin (5 µg) was carried out by the disk diffusion method according to the Clinical Laboratory Standards Institute guidelines. Detection of mecA gene was performed using PCR method. Results: An amplified mecA gene of 310 bp was detected in 55% of examined strains by PCR, thus 55% strains were considered MRSA. Sensitivity of oxacillin, methicillin and cefoxitin disks were determined 100%, 99.1% and 98.3% respectively. All MRSA strains in PCR had shown resistance to penicillinase-resistant penicillins by oxacillin disk, but two and one strains were sensitive by cefoxitin and methicillin disk respectively. Thus, oxacillin was the most appropriate disk for detecting MRSA. Conclusion: The prevalence of MRSA in this study is comparable to that found in United States, Canada, Europe and Iran, but the percentage of MRSA isolates is almost twice of percentage reported from Japan.
Farzaneh Jadali; Abdollah Karimi; Shahnaz Armin; Atoussa Gharib; Fatemeh Fallah; Mohammad Sharifian; Elham Mazaheri-tehrani
Volume 2, Issue 3 , June 2007, , Pages 89-93
Abstract
Background and Objective: BCG vaccination is used in many countries with a high prevalence of TB to prevent childhood tuberculosis meningitis and miliary disease. Local and systemic sideeffects are associated with BCG vaccine. The most critical reaction is disseminated BCG infection which occurs in mostly ...
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Background and Objective: BCG vaccination is used in many countries with a high prevalence of TB to prevent childhood tuberculosis meningitis and miliary disease. Local and systemic sideeffects are associated with BCG vaccine. The most critical reaction is disseminated BCG infection which occurs in mostly immunodeficient patients. Materials and Methods: We performed 4 autopsies during 2001-2003 which were suspected for BCGosis clinically and histologically by presence of granulomatous foci in several organs with acid fast bacilli. The mycobacteria were identified by PCR. Their DNA was extracted from the tissue blocks, identified with primers which were designed to detect the RD1 deletion. Results: We found BCG genome by PCR in 3 out of 4 patients. These patients had acid fast bacilli in special staining. Conclusion: Since BCGosis is a fatal and uncommon disease, occurring after vaccination with numerous complications, its diagnosis is of paramount importance and should be considered in the appropriate clinical setting.
Mehdi Nassiri; Mehrdad Nadji
Volume 1, Issue 1 , January 2006, , Pages 1-6
Abstract
The rapidly expanding fields of pharmacogenomics and pharmacodiagnostics have presented the pathology laboratories with many challenges and opportunities. As custodians of patient tissues, these laboratories are in the logical position to perform biomolecular testing for proper management of patients. ...
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The rapidly expanding fields of pharmacogenomics and pharmacodiagnostics have presented the pathology laboratories with many challenges and opportunities. As custodians of patient tissues, these laboratories are in the logical position to perform biomolecular testing for proper management of patients. In order to meet these challenges, the pathology laboratories of the twenty-first century should design and execute a biomarker-friendly, standardized tissue handling, including fixation and processing, to ensure uniform protection of macromolecules for clinically useful molecular assays. This important pre-analytic phase cannot be successful if tissues are handled in the traditional manner that includes the use of conventional fixation and processing. The recent progress in fixation and processing methods are rapidly replacing the time-honored routine formalin fixation and overnight processing. In this article we describe our experience with such system that not only produces good histomorphology but also preserves high quality RNA, DNA, and proteins in paraffin embedded material.
Mohammad Ebrahim Yarmohammadi; Horieh Saderi; S.Hadi Saghelaini; Jamshid Narenjkar J
Volume 1, Issue 1 , January 2006, , Pages 31-34
Abstract
Objective: To investigate the presence of Helicobacter pylori in sinonasal mucosa of patients with chronic sinusitis Design: A prospective case-control study Materials and methods: Mucosal specimens were collected from the mid-third middle meatus and lateral side of mid-cornea. H. pylori has been investigated ...
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Objective: To investigate the presence of Helicobacter pylori in sinonasal mucosa of patients with chronic sinusitis Design: A prospective case-control study Materials and methods: Mucosal specimens were collected from the mid-third middle meatus and lateral side of mid-cornea. H. pylori has been investigated using PCR after DNA extraction and urease test. Results: H. pylori was not found in any of the sample taken from both groups (case and control patients). Conclusion: This is the first reported study to investigate the presence of H. pylori in sinonasal mucosa in Iran. In this study, H. pylori was not determined in these sites, although its possible presence could not be excluded. Thus, further investigation on more patients and application of sensitive diagnostic techniques are recommended.
