Microbiology
Kosar Jalalvand; Nasrin Shayanfar; Freshteh Shahcheraghi; Elahe Amini; Masha Mohammadpour; Pegah Babaheidarian
Abstract
Background & Objective: Carbapenem-resistant Enterobacteriaceae is a growing concern worldwide including Iran. The emergence of this pathogen is worrying as carbapenem is one of the 'last-line' antibiotics for treatment of infections caused by multi drug resistant gram- negative bacteria. The main ...
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Background & Objective: Carbapenem-resistant Enterobacteriaceae is a growing concern worldwide including Iran. The emergence of this pathogen is worrying as carbapenem is one of the 'last-line' antibiotics for treatment of infections caused by multi drug resistant gram- negative bacteria. The main objective of this study was to determine the prevalence of carbapenem-resistant Enterobacteriaceae in a referral hospital in Tehran, Iran. Methods: In this study, all positive isolates of Enterobacteriaceae recorded in blood, urine, and other body fluids were studied during April 2017 to April 2018 in a referral hospital in Tehran. All cases of resistance to carbapenems were first tested by modified Hodge test. All cases with positive or negative test, after gene extraction, were examined genotypically based on the primers designed for the three Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), and OXA-48 genes by conventional PCR method. Result: 108 isolates (13.6%) were resistant to all cephalosporins as well as to imipenem and meropenem. In a genotypic study, including 45 isolates, 13 isolates were positive for OXA-48 gene, 11 isolates for OXA-48 and NDM genes, 11 isolates for OXA-48, NDM and KPC genes, 4 isolates for OXA-48 genes and KPC, 3 isolates for NDM, one isolate for KPC. On the other hand, two isolates were negative for all three genes examined. Conclusion: OXA-48 gene was one of the most common genes resistant to carbapenems in Iran. According to studies, the prevalence of antibiotic resistance in Iran is rising dramatically, which reduces the choice of antibiotics to treat severe infections in the future.
Molecular Pathology
Amir Hossein Jafarian; Nema Mohammadian Roshan; Hossein Ayatollahi; Abbas Ali Omidi; Masoumeh Ghaznavi; Masoumeh Gharib
Abstract
Background & Objective:Idiopathic pulmonary fibrosis (IPF) is a chronic and uniformly fatal interstitial lung disease with incompletely understood pathogenesis. Several studies have given the evidence for and against viral cofactors in the pathogenesis of Idiopathic pulmonary fibrosis. In this study ...
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Background & Objective:Idiopathic pulmonary fibrosis (IPF) is a chronic and uniformly fatal interstitial lung disease with incompletely understood pathogenesis. Several studies have given the evidence for and against viral cofactors in the pathogenesis of Idiopathic pulmonary fibrosis. In this study Epstein-Bar Virus (EBV) and Human Herpesvirus 8 (HHV-8) have been studied for a possible role in the pathogenesis of IPF.Methods:Polymerase chain reaction (PCR) was employed for the detection of EBV and HHV-8 in 58 formalin-fixed paraffin-embedded lung tissue specimens (29 controls and 29 IPF specimens).Results:EBV DNA was present in the lung tissue of 6 out of 29 (20.7%) IPF specimens compared with 1 out of 29 (3.4%) controls (P=0.102). The HHV-8 gene was identified in 3 out of 29 (10.3%) cases of IPF specimens. The control group showed no evidence of HHV-8 gene (P=0.227).Conclusion:Although multiple studies are strongly suggestive of a role for EBV and HHV-8 in the development of IPF, there was no statistically significant difference in the prevalence of EBV and HHV-8 DNA in the IPF specimens and controls in this study.
Gynecologic Pathology
Maryam Kazemi Aghdam; Seyed Alireza Nadji; Azadeh Alvandimanesh; Maliheh Khoddami; Yassaman Khademi
Abstract
Background & Objective: Malignant breast tumors, which are one of the most important deadly cancers in women, like many other cancers, are proposed to be related to viruses etiologically. Proper management of breast carcinoma necessitates an identification of the etiological factors. Human Papilomavirus is ...
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Background & Objective: Malignant breast tumors, which are one of the most important deadly cancers in women, like many other cancers, are proposed to be related to viruses etiologically. Proper management of breast carcinoma necessitates an identification of the etiological factors. Human Papilomavirus is considered to have an etiological role in breast carcinoma. We carried out this study to find out if Human Papilomavirus-DNA is present in the malignant and benign breast tissue in our patients. Methods: Seventy five paraffin-embedded breast cancer tissues and 75 normal breast tissues and benign breast lesions were examined in this study (case-control) to look for Human Papilomavirus-DNA employing Nested Polymerase Chain reaction. The tissues were examined over a period of ten years in the pathology department of the Pathobiology Laboratory Center of Tehran. Result: No Human Papilomavirus-DNA was found in any of the malignant or control group specimens. Conclusion: Our results showed no evidence of Human Papilomavirus in cancerous and benign tissues, which is consistent with some other studies in English medical literature. More investigations using more specimens from different parts of the country are required to confirm the presence or absence of any connection between Human Papilomavirus and development of breast carcinoma in Iran.
Molecular Pathology
Geita Saadatnia; Aboutaleb Saremi; Behrouz Salehian; Pirooz Salehian
Abstract
Background and Objective: For nearly a century, it has been suspected that reproductive tract infections play an etiologic role in uterine leiomyoma. However, no epidemiologic study of leiomyoma has used the polymerase chain reaction (PCR) to compare uterine tissues from cases and non-cases, and to investigate ...
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Background and Objective: For nearly a century, it has been suspected that reproductive tract infections play an etiologic role in uterine leiomyoma. However, no epidemiologic study of leiomyoma has used the polymerase chain reaction (PCR) to compare uterine tissues from cases and non-cases, and to investigate associations between uterine leiomyoma and infections detected by PCR.Methods: In this case-control study, 92 leiomyoma tissues from cases, and 94 myometrial tissue from controls were screened by PCR for cytomegalovirus, Chlamydia trachomatis, herpes simplex virus-1, 2, and human papillomavirus typed as 16/18 or another strain. Multivariable analysis used age-adjusted logistic regression, and generalized linear regression as appropriate.Results: In the uterine tissues of cases and unmatched controls, the prevalence of infection was: cytomegalovirus (32.6%, 7.4%), C. trachomatis (23.9%, 37.2%), herpes simplex virus-1,2 (25.0%, 13.8%), human papillomavirus 16/18 (13.0%, 10.5%). Leiomyoma was associated with cytomegalovirus (Odds Ratio (O.R.) 6.10; 95% confidence interval (C.I.), 2.40, 15.55) and Chlamydia (O.R. 0.47; 95% C.I. 0.23, 0.97). Likewise, the log count of leiomyoma was higher with cytomegalovirus (+0.65, 95% C.I. +0.34, +0.95) and lower with Chlamydia (-0.71, 95% C.I. -1.12, -0.29).Conclusion: This first application of PCR to leiomyomata and control uterine tissues from non-cases reveals that cytomegalovirus is associated with the presence, number, and volume of uterine leiomyoma, while C. trachomatis is inversely associated with leiomyoma, but only in the absence of cytomegalovirus. Current findings provide preliminary evidence that common reproductive tract infections contribute to the growth and control of at least some cases of uterine leiomyoma.
Microbiology
Reza Ranjbar; Afsar Tabatabaee; Payam Behzadi; Rohollah Kheiri
Abstract
Background: Escherichia coli is a commensal-pathogenic organism, which includes a wide range of strains. Despite several advanced molecular-genomic technologies for detecting and identifying different strains of E. coli, Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction ...
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Background: Escherichia coli is a commensal-pathogenic organism, which includes a wide range of strains. Despite several advanced molecular-genomic technologies for detecting and identifying different strains of E. coli, Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) technique is a quick, sharp and cost effective fingerprint method. The major purpose of the present study was to determine the distribution of ERICs within E. coli strains isolated from different healthy animal stool specimens including hens, sheep, and cows, as an appropriate and quick molecular-genomic tool. Methods: The animal stool samples were obtained during 1 year (October 2012 to October 2013), from animal husbandries around Tehran and Alborz provinces, Iran. After screening processes, the E. coli bacteria were isolated and cultured via standard microbiological methods. The DNA molecules of E. coli bacteria were harvested and Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) was applied for bacterial molecular genotyping. The ERIC-PCR products were run on 1% gel electrophoresis. The final images regarding gel electrophoresis banding patterns were used for dendrogram generation via the GelClust software. Results: Of 120 isolated samples, 115 different strains were recognized as E. coli. The fingerprint patterns involved 380 to 3280 bp bands. The predominant bands included 2900 bp, 1200 bp, and 1200 bp in stool samples of hens, sheep, and cows, respectively. The highest frequencies and diversities were seen among E. coli strains isolated from hens and sheep stool samples. Conclusion: The DNA profiles were clearly detectable via specific fingerprint patterns. The ERIC-PCR seemed to be a good approach for molecular typing of E. coli strains isolated from different animal sources.
Phiza Aggarwal; Deepak Aggarwal
Abstract
Dear Editor-in-Chief We read with interest the study by Khazaei et al. (1) in which the authors have nicely concluded that PCR is more sensitive test than Ziehl-Neelsen staining and histo-pathological examination for the diagnosis of tuberculosis (TB). They have rightly pointed to use PCR, selectively, ...
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Dear Editor-in-Chief We read with interest the study by Khazaei et al. (1) in which the authors have nicely concluded that PCR is more sensitive test than Ziehl-Neelsen staining and histo-pathological examination for the diagnosis of tuberculosis (TB). They have rightly pointed to use PCR, selectively, in acidfast bacilli negative paucibacillary forms of TB. However, we intend to highlight few points regarding PCR which may add to practical applicability of the study. PCR detects mycobacterial DNA in specimens and does not represent disease activity which is important for diagnosis of tuberculosis. Due to inadvertent exposure to the environment, relevance of PCR in pulmonary specimens is debatable. In the study, 12 patients (41%), positive for acid fast bacilli (AFB) by ZiehlNeelsen stain, were negative by PCR (1). This raises serious concern regarding the credibility of the test and needs to be discussed. Culture for tubercle bacillus is the only gold standard investigation for diagnosis of TB. The presence of granuloma on histopathology is quite suggestive for TB. However, it should always be differentiated from other granulomatous pathologies like sarcoidosis which can also present with positive PCR for Mycobacterium tuberculosis(MTB) (2). In the study, 16 subjects had non-caseating granulomas out of which 11 were positive PCR for MTB (1). Now, whether they were really having tuberculosis, is questionable. In the absence of culture, response to anti-tubercular treatment is a good surrogate marker for tuberculosis confirmation. It would be useful if authors mention the treatment response in their subjects and correlate it with PCR to reestablish its diagnostic value. As concluded by authors, PCR is a sensitive test for diagnosis of paucibacillary tuberculosis, but pending limitations, it should always be interpreted in light of relevant and comprehensive picture. Acknowledgements The authors declare that there is no conflict of interests.
Amitis Ramezani; Ali Eslamifar; Arezoo Aghakhani; Ebrahim Kalantar; Mohammad Banifazl; Akbar Velayati
Volume 4, Issue 2 , Spring 2009, , Pages 71-74
Abstract
Background and Objective: The outcome of hepatitis B virus (HBV) infection may be influenced by host factors like Human Leukocyte Antigen (HLA). We have investigated HLA-A and DRB1 alleles in patients with persistent hepatitis B infection compared to subjects who had spontaneously recovered from ...
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Background and Objective: The outcome of hepatitis B virus (HBV) infection may be influenced by host factors like Human Leukocyte Antigen (HLA). We have investigated HLA-A and DRB1 alleles in patients with persistent hepatitis B infection compared to subjects who had spontaneously recovered from HBV infection. To complete the findings of this study we performed another survey in certain HLA alleles that were significantly related to the outcome of HBV infection. The current study aimed to determine association between HBV infection outcome and HLA-A and DRB1 genotyping in North part of Iran. Patients and Methods: Ninety-four HBV infected patients were enrolled in this cross sectional study. First HLA-A and DRB1 alleles were analyzed by using low resolution PCR sequence-specific-primer (PCR-SSP) and then we used high resolution PCR-SSP method for subtyping HLA-A*33 and DRB1*13 alleles which were significantly related to the outcome of HBV infection. Results: HLA-A*33 allele was significantly higher in persistent group than recovered group and sub typing showed HLA-A*3303 in 75% and HLA-A*3301 in 25% of cases. HLA-DRB1*13 allele was significantly lower in persistent group than in recovered group and its subtypes were DRB1*1301 in 66.7% and DRB1*1303 in 33.3% of subjects. Conclusion: Host HLA polymorphism is an important factor to determining the outcome of HBV infection. HLA-A*3303 and DRB1*1301 were the predominant subtypes of HLA-A*33 and DRB1*13 alleles in Iranian HBV infected patients.
R, Salehi; B. Tabanifar; E. Asgarani; M. Faghihi; T. Allame
Volume 3, Issue 4 , Summer 2008, , Pages 173-178
Abstract
Background and Objective: Formalin-fixed paraffin-embedded tissues are a valuable source of DNA for molecular studies. We designed and optimized an efficient procedure for DNA extraction from formalin-fixed paraffin embedded tissues. Materials and Methods: Seventy three blocks of cervical paraffin-embedded ...
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Background and Objective: Formalin-fixed paraffin-embedded tissues are a valuable source of DNA for molecular studies. We designed and optimized an efficient procedure for DNA extraction from formalin-fixed paraffin embedded tissues. Materials and Methods: Seventy three blocks of cervical paraffin-embedded tissues were investigated. DNA was extracted using 45 minutes boiling in alkaline solution together with 10 beads of Chelex-20, followed by phenol-chloroform extraction and alcohol precipitation. Results: This method produced DNA suitable for amplification using primers specific for human SMN and β globin genes in 98.63% and 82.2% of samples respectively. We also detected human papillomavirus DNA in 58.33% of appropriate samples. Conclusion: This procedure provides simple and efficient method for recovery of amplifiable genomic and viral DNA from paraffin wax embedded tissues.
Ali Sadeghi; Alireza Sobhani; Zahra Etaati; Ali Jahanlu; Mahnaz Shiroodi
Volume 3, Issue 4 , Summer 2008, , Pages 183-185
Abstract
Background and Objective: To estimate the risk of human papilloma virus (HPV) infection for cervical malignancies, we conducted a case-control study in southern Iran (Hormozgan province). Materials and Methods: For this purpose,52 paraffin embedded blocks with exact diagnosis of cervical carcinoma(50 ...
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Background and Objective: To estimate the risk of human papilloma virus (HPV) infection for cervical malignancies, we conducted a case-control study in southern Iran (Hormozgan province). Materials and Methods: For this purpose,52 paraffin embedded blocks with exact diagnosis of cervical carcinoma(50 carcinomas and 2 carcinomas in situ) from 2001 to 2006 and 52 praffin embedded blocks of cervical tissue specimens with normal histopathology as the control group were tested for the presence of HPV DNA using PCR based assay. Results: HPV DNA was found out in 16 out of 52 patients (30.7%), while it was not detected in any of the control group samples. Conclusion: Considering the fact that unrestrained sexual behavior increases risk of becoming infected with HPV, our finding is in favor of the concept of low frequency of HPV infection and thus its less important role in women with cervical cancer in islamic countries.
Ali Eslamifar; Farrokh Tirgari; Rasool Hamkar; Amitis Ramezani; Hossein Frootan pishbigar; Shahrum Mirmomen; Azin Nahvigoo; Vahideh Shahnazi; Zahra Deljoodokht; Shifteh Vahidi; Arezoo Aghakhani
Volume 2, Issue 1 , Winter 2007, , Pages 11-16
Abstract
Background and Objective: Human papillomavirus (HPV) is one of the possible etiologic factors in development of esophageal squamous cell carcinoma (ESCC). In this study we aimed to study the role of HPV in ESCC.
Patients and Methods:In this study, 140 cases of ESCC were analyzed for the ...
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Background and Objective: Human papillomavirus (HPV) is one of the possible etiologic factors in development of esophageal squamous cell carcinoma (ESCC). In this study we aimed to study the role of HPV in ESCC.
Patients and Methods:In this study, 140 cases of ESCC were analyzed for the HPV DNA by polymerase chain reaction (PCR) using GP5+/GP6+ primers for L1 open reading frame (ORF) to amplify a 150-bp segment of HPV L1 ORF. This region was subsequently sequenced to identify the type of HPV.
Results:A total of 140 patients enrolled in our study. In this respect, 50.7% of them were females and 49.3% were males, aged between 20 and 81 years old. In addition, 33 tumor specimens (23.6%) and 12 (8.6%) non-involved tumor margins were HPV positive. In HPV positive tumor cases, 36% were also positive in tumor margins. The HPV positive cases were 21.7% males and 25.3% females. There was no correlation between the presence and types of HPV with patients’ sex and age. The frequency of HPV subtypes in tumoral regions were as follow: HPV-16: 60.6%, HPV-18: 30.3%, HPV-33: 6.1%, and HPV-31: 3 %. We found only HPV-16 in tumor margins.
Conclusion:Our results support a causal association between HPV infection and ESCC which is consistent with HPV studies conducted in other high-risk areas.
