Microbiology
Saeed Mirsadraee; Mihan Pourabdollah Toutkaboni; Mehrdad Bakhshayeshkaram; Mitra sadat Rezaei; Elham Askari; Sara Haseli; Nazanin Sadraee
Abstract
Background & Objective: Diagnosis of coronavirus disease 2019 (COVID-19) can be challenging, especially when the realtime quantitative reverse transcription polymerase chain reaction (RT-PCR) is not available or it is negative. In this study, we evaluated imaging and laboratory findings in a ...
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Background & Objective: Diagnosis of coronavirus disease 2019 (COVID-19) can be challenging, especially when the realtime quantitative reverse transcription polymerase chain reaction (RT-PCR) is not available or it is negative. In this study, we evaluated imaging and laboratory findings in a group of patients with a multidisciplinary diagnosis of COVID-19 pneumonia. Methods: A total of 163 patients with a clinical diagnosis of COVID-19 pneumonia admitted to a specialised respiratory centre in Tehran, Iran were enrolled in this study. The distribution and characteristics of presenting radiological and laboratory findings were evaluated and the relationship to the outcome was investigated. Results: RTPCR was positive in 92 patients. The diagnosis of COVID-19 in RT-PCR negative patients was made on clinical and radiological grounds (n=71). Also, 24 (14.7%) patients died. The common computed tomography (CT) scan findings included ground-glass (94%) and consolidating opacification (12%), mainly in the lower lobes (90%). Peripheral and central lung changes were observed in 90% and 52% of patients, respectively. Lymphopenia, positive CRP, and raised LDH were present in 32%, 65%, and 96% of cases, respectively. A raised LDH of >500U/L was the best predictor of death in these patients (R2=0.6623; OR=24.4). Other markers of outcome were male gender, age (>50 years), lymphopenia, and severe CXR changes. Conclusion: Diagnosis of COVID-19 can be challenging, and a multidisciplinary approach is often needed. Whilst RT-PCR is the standard diagnostic test, a negative test should be interpreted with caution. Blood tests and imaging can be useful in the diagnosis, monitoring, and risk assessment in patients with COVID-19.
Microbiology
Mohammadreza Jalali Nadoushan; Soha Ahmadi; Paniz Jalali Nadoushan
Abstract
As COVID-19 was declared as a pandemic by the World Health Organization (WHO) in March 2020, it is an emerging need to discuss different aspects of this pandemic. In any pandemic, valid and rapid laboratory diagnostic tests are critically important for early diagnosis, which will increase the rate of ...
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As COVID-19 was declared as a pandemic by the World Health Organization (WHO) in March 2020, it is an emerging need to discuss different aspects of this pandemic. In any pandemic, valid and rapid laboratory diagnostic tests are critically important for early diagnosis, which will increase the rate of successful treatment and more importantly prevent the spread of the disease.
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.
Microbiology
Fatemeh Amraei; Negar Narimisa; Behroz Sadeghi; Vahid Lohrasbi; Faramarz Masjedian Jazi
Abstract
Background & Objective: Persister cells are defined as a subpopulation of bacteria that are capable of reducing their metabolism and switching to dormancy in stress conditions. Persister cells formation has been attributed to numerous mechanisms, including stringent response and Toxin-Antitoxin (TA) ...
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Background & Objective: Persister cells are defined as a subpopulation of bacteria that are capable of reducing their metabolism and switching to dormancy in stress conditions. Persister cells formation has been attributed to numerous mechanisms, including stringent response and Toxin-Antitoxin (TA) systems. This study aimed to investigate the hypothetical role of TA systems in persister cells formation of Brucella strains by evaluating toxins of type II TA systems (RelE, Fic, Brn T, cogT) expression. Methods: Brucella strains treated with a lethal dose of gentamicin and ampicillin and to determine the number of surviving cells, bacterial colonies were counted at different time intervals. The role of TA systems in persister cell formation was then determined by toxin expression levels using qRT- PCR method. Result: Our results showed the viability of persister cells after 7 h. The results of relative qRT- PCR showed higher levels of toxin gene expression due to stress conditions, suggesting the possible role of TA systems in persister cells formation and antibiotics tolerance. Conclusion: The results of this study showed that considering the importance of persistence and the tolerance to antibiotics, further studies on persister cells formation and related genes such as the TA system genes in Brucella strains might help us to identify the precise mechanisms leading to persister cells formation.
Microbiology
Sara Masoumi Zavaryani; Reza Mirnejad; Vahhab Piranfar; Mehrdad Moosazadeh Moghaddam; Nikta Sajjadi; Somayyeh Saeedi
Abstract
Background & Objective: Enterococcus Species are the common cause of nosocomial infections, which are highly resistant to different antibiotics. Therefore, determination of their antibiotic susceptibility patterns and simultaneous resistance to antibiotics is important for better treatment strategies. ...
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Background & Objective: Enterococcus Species are the common cause of nosocomial infections, which are highly resistant to different antibiotics. Therefore, determination of their antibiotic susceptibility patterns and simultaneous resistance to antibiotics is important for better treatment strategies. Methods: 400 clinical Enterococcus isolates were collected from different hospitals in Tehran, Iran. Standard phenotypic-biochemical tests and PCR were used to identify the Enterococcus species. The antimicrobial susceptibility patterns and simultaneous resistance to selected antibiotics were determined by disk diffusion method according to the CLSI guidelines. All data analysis was performed using Python packages Scipy and Stats models. Result: According to the biochemical and PCR analyses, among 400 Enterococcus species, 72% of samples were Enterococcus faecalis, 10.75% Enterococcus faecium, and 17.25% other Enterococcus species. The results determined antimicrobial resistances of these strains against gentamicin, vancomycin, fosfomycin trometamol, teicoplanin, and quinupristin/dalfopristin. Results confirmed a significant correlation between resistance to vancomycin and resistance to teicoplanin. This correlation remains significant when including only E. faecium or E. faecalis species. We also found a negative correlation between resistance to teicoplanin and quinupristin/dalfopristin. Additionally, Quinupristin/dalfopristin was the least effective antibiotic while vancomycin and teicoplanin were the most effective ones. Conclusion: Based on the results and association between simultaneous resistance to some antibiotics such as vancomycin and teicoplanin, in the case of antibiotic resistance, the choice of a second antibiotic can be very important which can lead to good or bad effects.
Microbiology
Zeynab Mohseni Moghadam; Raheleh Halabian; Hamid Sedighian; Elham Behzadi; Jafar Amani; Abbas ali Imani fooladi
Abstract
Background & Objective: A main contest in chemotherapy is to obtain regulator above the biodistribution of cytotoxic drugs. The utmost promising strategy comprises of drugs coupled with a tumor-targeting bearer that results in wide cytotoxic activity and particular delivery. The B-subunit of Shiga ...
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Background & Objective: A main contest in chemotherapy is to obtain regulator above the biodistribution of cytotoxic drugs. The utmost promising strategy comprises of drugs coupled with a tumor-targeting bearer that results in wide cytotoxic activity and particular delivery. The B-subunit of Shiga toxin (STxB) is nontoxic and possesses low immunogenicity that exactly binds to the globotriaosylceramide (Gb3/CD77). Gb3/CD77 extremely expresses on a number of human tumors such as pancreatic, colon, and breast cancer and acts as a functional receptor for Shiga toxin (STx). Then, this toxin can be applied to target Gb3-positive human tumors. In this study, we evaluated DT390-STXB chimeric protein as a new anti-tumor candidate via genetically fusing the DT390 fragment of DT538 (Native diphtheria toxin) to STxB. Methods: This study intended to investigate the DT390- STxB fusion protein structure in silico. Considering the Escherichia coli codon usage, the genomic construct was designed. The properties and the structure of the protein were determined by an in silico technique. The mRNA structure and the physicochemical characteristics, construction, and the stability of the designed chimeric protein were analyzed using computational and bioinformatics tools and servers. Hence, the GOR4 and I-TASSER online web servers were used to predict the secondary and tertiary structures of the designed protein. Result: The results demonstrated that codon adaptation index (CAI) of dt390-stxB chimeric gene raised from 0.6 in the wild type to 0.9 in the chimeric optimized gene. The mfold data revealed that the dt390-stxB mRNA was completely stable to be translated effectively in the novel host. The normal activity of the fusion protein determined by considering the secondary and tertiary structure of each construct. Energy calculation data indicated that the thermodynamic ensemble for mRNA structure was -427.40 kJ/mol. The stability index (SI) of DT390-STxB was 36.95, which is quite appropriate to preserve the stability of the construct. Ultimately, the DT390-STxB was classified as a steady fusion protein according to the Ramachandran plot. Conclusion: Our results showed that DT390-STXB was a stable chimeric protein and it can be recruited as a candidate of novel anti-tumor agents for the development of breast cancer treatment.
Microbiology
Pegah Kananizadeh; Solmaz Ohadian Moghadam; Yasaman Sadeghi; Abbas Rahimi Foroushani; Hossein Adibi; Mohammad Reza Pourmand
Abstract
Background & Objective: Diabetic foot ulcer (DFU), is one of the most frequent causes for hospitalizations in patients with diabetes. A major problem in the treatment of DFU is the increased-incidence of methicillin-resistant Staphylococcus aureus (MRSA). The aim of this study was to determine the ...
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Background & Objective: Diabetic foot ulcer (DFU), is one of the most frequent causes for hospitalizations in patients with diabetes. A major problem in the treatment of DFU is the increased-incidence of methicillin-resistant Staphylococcus aureus (MRSA). The aim of this study was to determine the SCCmec types of MRSA isolates and their epidemiology among patients with diabetes. Methods: This study was carried out on 145 diabetic patients with DFUs. The antibiotic susceptibility tests (ASTs) were performed using the disk diffusion method and E-test technique. SCCmec typing was done by multiplex PCR. Moreover, the presence of virulence toxin genes, including pvl and lukED was detected by PCR assay. Result: In 145 samples from which S. aureus was predominantly isolated, 19.48% were MRSA. Analysis of MRSA isolates revealed that the most prevalent SCCmec type was type IV (46.7%) followed by type III (30.0%) and type V (20.0%). One strain (3.3%) was untypeable. The prevalence of pvl and lukED was 56.7% and 100%, respectively. Conclusion: The high prevalence of MRSA in DFUs represents the high levels of antibiotic usage among patients with diabetes. In this study, resistance to other important clinical antibiotics was detected among MRSA isolates. The high proportion of SCCmec type IV and V strains, even in former hospitalized patients, indicates the entrance of these clones to the clinical setting.
Microbiology
Hassan Ehteram; Mohaddeseh Sadat Mousavian; Tahereh Mazoochi; Tahereh Khamehchian; Mohammad Karimian
Abstract
Background & Objective: Squamous cell carcinoma (SCC) is the second most common non-melanoma skin cancer that may be caused by Human papillomavirus (HPV), especially in immunosuppressed patients. However, the role of the mucosal types of HPV in SCC patients with normal immunity has not been extensively ...
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Background & Objective: Squamous cell carcinoma (SCC) is the second most common non-melanoma skin cancer that may be caused by Human papillomavirus (HPV), especially in immunosuppressed patients. However, the role of the mucosal types of HPV in SCC patients with normal immunity has not been extensively confirmed. The aim of this study was to investigate the association of some high-risk mucosal types of HPV with cutaneous SCC in an Iranian population. Methods: Sixty-five formalin-fixed, paraffin-embedded tissue specimens with a diagnosis of cutaneous SCC as the case group and sixty-five healthy skin specimens as the control group were included in our case-control study. Genomic DNA was extracted from tissue samples and then PCR was used for the detection of HPV genotypes by a commercial kit. Result: Our data revealed that 6 out of 65 SCC samples (9.2%) were infected by high-risk mucosal types of HPV whereas none of the 65 control samples were infected by the mentioned HPVs. Statistical analysis showed a significant association between these types of HPV infection and SCC risk in our studied population (P=0.028). Conclusion: These findings suggested that some high-risk mucosal types of HPV are significant risk factors for cutaneous SCC.
Microbiology
Samira Tajik; Shahin Najar Peerayeh; Bita Bakhshi; Reza Golmohammadi
Abstract
Background & Objective: Methicillin-resistant Staphylococcus aureus (MRSA) is reported as one of the important bacterial causes of burn wound infections. This study was carried out to investigate molecular characterization of community-associated MRSA (CA-MRSA) isolated from Iranian burn ...
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Background & Objective: Methicillin-resistant Staphylococcus aureus (MRSA) is reported as one of the important bacterial causes of burn wound infections. This study was carried out to investigate molecular characterization of community-associated MRSA (CA-MRSA) isolated from Iranian burn patients. Methods: A total of 31 isolates of S. aureus were collected from the Motahari Burns Hospital (Tehran, Iran) in 2016. All isolates were collected from outpatients and inpatients within 48 hours of admission. The mecA, pvl, tsst-1, hla-α, and psmα genes detecting, SCCmec, agr and PFGE typing were done. Result: A total of 13 (41.9%) isolates were cefoxitin-resistant and mecA-positive, which were considered as MRSA. The SCCmec typing MRSA strains revealed type II in 1 (7.7%), type III in 9 (69.2%), and other types in 3 isolates (23.7%) cases. The agr typing of all 31 isolates showed that 14 (45.2%), 1 (3.2%), 6 (19.4%), and 10 (32.3%) strains belonged to agr groups 1, 3, 4, and unknown type, respectively. The pvl, tsst-1, hla-α, and psmα genes were positive in 3 (9.7%), 4 (12.9%), 21 (67.7%), and 31 (100%) isolates, respectively. Considering the cut-off values of ≥50%, 3 groups of related isolates (cluster A1, B1, and C1) in PFGE study were observed. Conclusion: The MRSA strains of this study were initially isolated as Community-associated S. aureus (CA-MRSA); however molecular characterization showed that a significant proportion of them had hospital-associated MRSA (HA-MRSA) features. Therefore, it is likely that the HA-MRSA strains are spread among the community.
Microbiology
Zahra Naseri; Nasrin Bahmani; Mohammad Yosef Alikhani; Seyed Hamid Hashemi; Ghodratollah Roshanaei
Abstract
Background & Objective: Brucellosis is one of the most prevalent bacterial zoonotic diseases which afflicts both humans and animals. Genetic factors play an important role in susceptibility to brucellosis. One of these factors is interferon-gamma (IFN-g), which is vital in the defense mechanism against ...
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Background & Objective: Brucellosis is one of the most prevalent bacterial zoonotic diseases which afflicts both humans and animals. Genetic factors play an important role in susceptibility to brucellosis. One of these factors is interferon-gamma (IFN-g), which is vital in the defense mechanism against infectious diseases such as brucellosis. The purpose of this study was to evaluate the relationship between two single nucleotide polymorphisms (SNPs) at positions -611 and -56 within the promoter region of interferon-gamma receptor-1 gene (IFN-g R1) and brucellosis. Methods: In this research,thegenomic DNA was collected from 60 peripheral blood samples infected with brucellosis and 68 healthy volunteers. DNA was extracted by salting out method. Then, DNA genotypes were analyzed using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Results: The results showed that there is a significant difference in -611 SNP frequencies between control and patient groups. At position -611, CC genotype was related to patient group (P=0.024) and TT genotype was related to the control group. According to the results, males had a higher frequency of Brucella infection. Conclusion: The presence of C allele in position -611 in IFNγ R1 gene promoter was related to a higher risk of disease and susceptibility to brucellosis. Moreover, the presence of T allele in position -611 in IFN-g R1 gene promoter was related to a lower risk of disease.
Microbiology
Mina Mobini Kesheh; Hossein Keyvani
Abstract
Background & Objective: Human papillomavirus (HPV) is the main cause of genital warts and some anogenital cancers in male and female subjects which is commonly transmitted by sexual contacts. The objective of this cross-sectional study was to examine the prevalence of HPV genotypes in 10,266 Iranian ...
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Background & Objective: Human papillomavirus (HPV) is the main cause of genital warts and some anogenital cancers in male and female subjects which is commonly transmitted by sexual contacts. The objective of this cross-sectional study was to examine the prevalence of HPV genotypes in 10,266 Iranian male and female population, according to their age. Methods: Samples were collected from the penile and anal sites of male subjects and the vagina and cervix of female subjects in a time period between 2011 and 2016. HPV DNA was detected in PCR using the MY09 and MY11 primers, and the INNO-LiPA assay was applied for HPV genotyping. To investigate the relevance of HPV infection and age, the samples were classified into 4 age groups (13-29, 30-44, 45-59, and 60-74). Results: Totally, the most common low risk HPV genotypes detected in the studied male and female subjects were HPV-6 (77.7% and 43.3%) and HPV-11 (13.7% and 11.4%), and more frequent high risk HPV genotypes were HPV-16 (5.5% and 16.6%) and HPV-52 (3.2% and 9.6%), respectively. High burden of the HPV infection was observed at ranges of 30 and 44 years (51.8%) with a peak at ranges between 30 and 32 years. No considerable statistically significant correlation was found between HPV infection and age (P=1). Conclusion: This study gave an epidemiological overview of circulating HPV genotypes in Iranian population to develop future vaccination policies, though the findings of prevalent HPV genotypes in female subjects were inconsistent with the previous studies reported in Iran.
Microbiology
Mehdi Yousefipour; Mehrnaz Rasoulinejad; Azar Hadadi; Negin Esmaeilpour; Alireza Abdollahi; Siroos Jafari; Atieh khorsand
Abstract
Background and Objective: There is a growing concern regarding the lack of new antibiotics, especially for multidrug-resistant bacteria that produce Extended Spectrum β-Lactamases (ESBLs). The present study aims to assess the prevalence of bacteria producing ESBLs, their antimicrobial resistance ...
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Background and Objective: There is a growing concern regarding the lack of new antibiotics, especially for multidrug-resistant bacteria that produce Extended Spectrum β-Lactamases (ESBLs). The present study aims to assess the prevalence of bacteria producing ESBLs, their antimicrobial resistance pattern, and its main determinants among hospitalized patients.Methods: The study population included 383 consecutive patients with a definitive diagnosis of urinary tract infection (UTI). All eligible subjects for the study had a positive culture for gram-negative microorganisms in urine specimens. ESBL producing isolates were characterized phenotypically for ESBL production using the double disc synergy test.Results: In total, 383 specimens were assessed, among which 212 (55.4%) were related to bacteria producing ESBLs (ESBL+). Of those with ESBL + infections, 65.5% were sourced from catheters (as hospital-associated UTIs), and 35.5% were categorized as community-associated UTIs. In the group consisting of bacteria producing ESBLs, the highest sensitivity was observed with Imipenem (72.2%), while the highest resistance was revealed with ceftriaxone (100%). Conclusion: We have shown that our community faces a high prevalence of bacteria producing ESBLs, mostly sourced from the catheterization of hospitalized patients. The highest bacterial sensitivity was observed with Imipenem, nitrofurantoin, and amikacin, while the highest resistance was found with ceftriaxone and cotrimoxazole, suggesting the ineffectiveness of using the two latter antibiotics for eradicating these bacterial infections. On the other hand, a history of urinary catheterization and previous hospitalization were two main determinants of their presence, a finding which emphasizes the importance of avoiding catheterization and hospitalization of patients with UTIs without proper indications.
Microbiology
Faria Hasanzadeh Haghighi; Ehsan Aryan; Mohammad Derakhshan; Aida Gholoobi; Zahra Meshkat
Volume 13, Issue 4 , Autumn 2018, , Pages 403-407
Abstract
Background & objective: Tuberculosis (TB) remains a major cause of death around the world. Bacillus Calmette Guérin (BCG) is the only vaccine used in TB prevention that has a protective effect in children, but its effectiveness declines in adults. Design and development of new vaccines ...
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Background & objective: Tuberculosis (TB) remains a major cause of death around the world. Bacillus Calmette Guérin (BCG) is the only vaccine used in TB prevention that has a protective effect in children, but its effectiveness declines in adults. Design and development of new vaccines is the most effective way against TB. The aim of this study was to design and construct a DNA vaccine encoding mtb32C and mpt51 fusion genes of Mycobacterium tuberculosis. Methods: First, mpt51 fragment was amplified by PCR method. The pcDNA3.1+/mtb32C plasmid was transformed into E. coli JM109 and then extracted. The mpt51 gene and pcDNA3.1+/mtb32C plasmid were both digested with EcoRI and BamHI restriction enzymes followed by ligation of mpt51 fragment into the digested vector. The recombinant plasmid containing mtb32C and mpt51 was subsequently transformed into competent E. coli TOP10 strain. The clones were confirmed by colony-PCR, restriction enzyme digestion and sequencing. Results: Using agarose gel electrophoresis, a 926 bp fragment corresponded to mpt51 was observed. Digestion of the vector pcDNa3.1+/mtb32C and mpt51 gene was confirmed by electrophoresis. Then, the pcDNA3.1+/mtb32C plasmid was extracted. Sequencing results confirmed the accuracy of the desired plasmid. Conclusion: In this study, we constructed a cloning vector encoding Mtb32C/Mpt51 gene of Mycobacterium tuberculosis. The eukaryotic expression of this vector can be confirmed in future studies. It can be considered as a DNA vaccine in animal models later. Successful cloning provides a basis for the development of new DNA vaccines against tuberculosis.
Microbiology
Mahsa Asadi; Mohamad Fazeli; Azar Sabokbar
Volume 13, Issue 3 , Summer 2018, , Pages 301-307
Abstract
Background and Objective: Acute microbial diarrheal diseases are the major public health problems in the developing countries. People affected by diarrheal diseases have the lowest financial resources and poorest hygienic facilities. Children under five, primarily in Asian and African countries, are ...
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Background and Objective: Acute microbial diarrheal diseases are the major public health problems in the developing countries. People affected by diarrheal diseases have the lowest financial resources and poorest hygienic facilities. Children under five, primarily in Asian and African countries, are mostly the subjects affected by microbial diseases transmitted through water.The current study aimed at investigating the comparative inhibitory effect of Lactocare (commercial probiotic) on clinical samples and standard strains of Vibrio cholerae.Methods: A total of 20 clinical samples and a standard strain (ATCC 14035) were provided by Health Reference Laboratory and Biotechnology Institute, respectively. In order to confirm the samples, biochemical analysis and the polymerase chain reaction (PCR) were performed on intergenic space. Afterward, agar well diffusion method was performed in order to measure the minimum inhibitory concentration to monitor the antimicrobial activity of Lactocare.Results: Colony count of V. cholerae for the standard strain in 30% and mean for clinical samples in 50% concentration of Lactocare treatment revealed that it would propel to death phase. Since the number of colonies decreased to 100, it was considered that higher concentrations of Lactocare would completely inhibit the growth of V. cholera.Conclusion: Probiotics are employed to develop new pharmaceutical preparations and functional foods in order to promote the public health.
Microbiology
Samaneh Rouhi; Rashid Ramazanzadeh
Volume 13, Issue 3 , Summer 2018, , Pages 348-356
Abstract
Background and Objective: Pseudomonas aeruginosa (P. aeruginosa) causes serious nosocomial and non-nosocomial infections. blaOxacillinases (OXA)-23 and blaOXA24/40 provide resistance to carbapenem antibiotics. The aim of this study was assessment of blaOXA-23 and blaOXA-24/40 in P. aeruginosa isolated ...
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Background and Objective: Pseudomonas aeruginosa (P. aeruginosa) causes serious nosocomial and non-nosocomial infections. blaOxacillinases (OXA)-23 and blaOXA24/40 provide resistance to carbapenem antibiotics. The aim of this study was assessment of blaOXA-23 and blaOXA-24/40 in P. aeruginosa isolated from patients with nosocomial and non-nosocomial infections. Methods: In this descriptive cross-sectional study performed in Sanandaj, Iran (Kurdistan province) in a period from December 2015 to August 2017, 146 isolates of Pseudomonas spp. were collected from patients’ specimens. Microbiological methods and polymerase chain reaction (PCR) with gyrB were applied for P. aeruginosa detection. Disk diffusion method with imipenem (IMP) (10µg) was performed for detection of resistant bacteria, and multiplex PCR of OXA-23 and OXA-24/40 were performed as well. Stata 12 with Fisher’s exact test and logistic regression were used for data analysis (P≤0.05).Results: PCR gyrB gene proved the existence of 91.78% P. aeruginosa isolates. Nosocomial infection with P. aeruginosa was observed in 41.79%. 27.61% of P. aeruginosa strains were resistant to IMP. blaOXA-23 and blaOXA24/40 were detected in 11.19% and 2.24% of the strains, respectively. 2.23% strains of P. aeruginosa showed a co-existence of blaOXA-23 and blaOXA24/40. There were no significant relationships between antibiotic resistance and presence of genes, and between IMP resistance and age, sex, city of residence, inpatient/outpatient, and specimen’s type (P≥0.05).Conclusion: Resistance to IMP and the presence of resistant genes in this study were observed in patients. More precautions should be taken in prescribing antibiotics and applying molecular techniques to detect genes, since they can cause antibiotic resistant.
Microbiology
Faezeh Ghasemi; Majid Ghayour Mobarhan; Hamed Gouklani; Zahra Meshkat
Abstract
Hepatitis C virus (HCV) is responsible for a vast majority of liver failure cases. HCV is a kind of blood disease appraised to chronically infect 3% of the worlds’ population causing significant morbidity and mortality. Therefore, a complete knowledge of humoral responses against HCV, resulting ...
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Hepatitis C virus (HCV) is responsible for a vast majority of liver failure cases. HCV is a kind of blood disease appraised to chronically infect 3% of the worlds’ population causing significant morbidity and mortality. Therefore, a complete knowledge of humoral responses against HCV, resulting antibodies, and virus-receptor and virus-antibody interactions, are essential to design a vaccine. HCV epitopes or full sequence of HCV proteins can induce HCV specific immune responses. In fact, structural proteins are usually the main target of humoral responses and non-structural proteins are usually the main target of cellular responses. Hence, various vaccines based on distinct antigenic combinations are developed to prevent HCV infection and the current study tried to summarize them.
Microbiology
Mohsen Nakhaie; Hoorieh Soleimanjahi; Hamid Reza Mollaie; Seyed Mohamad Ali Arabzadeh
Abstract
Background and objective:Millions of people in developing countries lose their lives due to acute respiratory infections, such as Influenza A & B and Adeno viruses. Given the importance of rapid identification of the virus, in this study the researchers attempted to design a method that enables detection ...
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Background and objective:Millions of people in developing countries lose their lives due to acute respiratory infections, such as Influenza A & B and Adeno viruses. Given the importance of rapid identification of the virus, in this study the researchers attempted to design a method that enables detection of influenza A, B, and adenoviruses, quickly and simultaneously. The Multiplex RT PCR method was the preferred method for the detection of influenza A, B, and adenoviruses in clinical specimens because it is rapid, sensitive, specific, and more cost-effective than alternative methods Methods:After collecting samples from patients with respiratory disease, virus genome was extracted, then Monoplex PCR was used on positive samples and Multiplex RT-PCR on clinical specimens. Finally, by comparing the bands of these samples, the type of virus in the clinical samples was determined. Results:Performing Multiplex RT-PCR on 50 samples of respiratory tract led to following results; flu A: 12.5%, fluB: 50%, adeno: 27.5%, negative: 7.5%, and 2.5% contamination. Conclusion: Reverse transcription-multiplex Polymerase Chain Reaction (PCR) technique, a rapid diagnostic tool, has potential for high-throughput testing. This method has a significant advantage, which provides simultaneous amplification of numerous viruses in a single reaction. This study concentrates on multiplex molecular technologies and their clinical application for the detection and quantification of respiratory pathogens. The improvement in diagnostic testing for viral respiratory pathogens effects patient management, and leads to more cost-effective delivery of care. It limits unnecessary antibiotic use and improves clinical management by use of suitable treatment.
Microbiology
Fahimeh Safarnezhad Tameshkel; Mohammad Hadi Karbalaie Niya; Zahedin Kheyri; Davood Azizi; Farzin Roozafzai; Samaneh Khorrami
Abstract
Background and Objectives: Iran, as a developing country, is experiencing high burdens of Helicobacter pylori (Hp)-associated non-communicable diseases. Hp stool antigen test (HpSA) is widely used as an inexpensive and feasible noninvasive method to diagnose Hp infection, instead of invasive approaches. ...
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Background and Objectives: Iran, as a developing country, is experiencing high burdens of Helicobacter pylori (Hp)-associated non-communicable diseases. Hp stool antigen test (HpSA) is widely used as an inexpensive and feasible noninvasive method to diagnose Hp infection, instead of invasive approaches. The current study aimed at evaluating the diagnostic and predictive values of HpSA test for Hp infection in Iranian patients with dyspepsia. Materials and methods: The current cross sectional study was performed on 100 patients with dyspepsia. Gastric mucosal specimens were taken, processed, and examined according to the standard protocols. Simultaneously, stool samples were obtained and sent to laboratory for further analyses. Hp stool antigen titers were assessed using enzyme-linked immunosorbent assay (ELISA) technique. Results:Stool antigen titers were not associated with gender (P-value=0.284), but correlated to age (r=0.213, P-value=0.034).Considering0.385 as a cutoff point, the HpSA test had 80.4% sensitivity and 85.7% specificity. Conclusion: Based on cost-effectiveness of HpSA test, the current study findings corroborated the use of HpSA test to detect and follow-up patients with Hp infection, as an alternative method to detect Hp rather than invasive procedures.
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
Mehrdad Gholami; Mohammadreza Haghshenas; Mona Moshiri; Shbnam Razavi; Abazar Pournajaf; Gholamreza Irajian; Mohsen Heidary
Abstract
Background & objective: Multidrug-resistant Acinetobacter baumannii (MDR-AB) is an important nosocomial pathogen which is associated with significant morbidity and mortality, particularly in high-risk populations. Aminoglycoside-modifying enzymes (AMEs) and 16S ribosomal RNA (16S rRNA) ...
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Background & objective: Multidrug-resistant Acinetobacter baumannii (MDR-AB) is an important nosocomial pathogen which is associated with significant morbidity and mortality, particularly in high-risk populations. Aminoglycoside-modifying enzymes (AMEs) and 16S ribosomal RNA (16S rRNA) methylation are two important mechanisms of resistance to aminoglycosides. The aim of this study was to determine the prevalence of 16S rRNA methylase (armA, rmtA, rmtB, rmtC, and rmtD), and the AME genes [aac(6′)-Ib, aac(3)-I, ant(3′′)-I, aph(3′)-I and aac(6')-Id], among clinical isolates of A. baumannii in Tehran, Iran. Methods: Between November 2015 to July 2016, a total of 110 clinical strains of A. baumannii were isolated from patients in two teaching hospitals in Tehran, Iran. Antimicrobial susceptibility testing was performed according to Clinical and Laboratory Standards Institute guidelines. The presence of genes encoding the AMEs and16S rRNA methylases responsible for resistance was investigated by multiplex polymerase chain reaction. Results: The results showed that colistin was an effective antibiotic and could be used as a last-resort treatment of infections caused by MDR-AB. The resistance rate to aminoglycosides were 100%, 96.36% and 90.9% for tobramycin, gentamicin and amikacin, respectively. In this study, AME genes of aac(6′)-Ib, aac(3)-I and ant(3′′)-I were most prevalent among the isolated strains. Conclusion Markedly high resistance to tobramycin, gentamicin and amikacin was noted in current study. Our results suggested that modifying enzyme genes in conjunction with methylation of 16S rRNA might contribute to aminoglycoside resistance induced in vivo in A. baumannii.Further studies are required to determine the prevalence of the aminoglycoside resistance genes in other hospitals of Iran.
Microbiology
Fatemeh Haj Ebrahim Tehrani; Mohammad Moradi; Narjes Ghorbani
Abstract
Background & Objective: Neonatal sepsis is one of the leading causes of mortality in neonatology wards. The aim of this study was to assess sepsis pathogens and antibacterial resistance patterns in a teaching hospital during seven years in Tehran, Iran. Methods: In this retrospective study, all neonates ...
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Background & Objective: Neonatal sepsis is one of the leading causes of mortality in neonatology wards. The aim of this study was to assess sepsis pathogens and antibacterial resistance patterns in a teaching hospital during seven years in Tehran, Iran. Methods: In this retrospective study, all neonates suspected to sepsis and fulfilling the sepsis criteria admitted to NICU ward of Mustafa Khomeini Hospital, Tehran, Iran during 2007 to 2014 were included. Demographic information, blood test results, blood culture results of neonates and antibiogram findings were extracted from their documents. Data was analyzed using SPSS 15. Results:Ninety neonates with positive culture test were included. Fifty-three were male (58.9%). Thirty neonates were delivered vaginally (33.3%) and 60 caesarean section (66.7%). Most bacterial growths in culture were Staphylococcus aureus and E. coli. The rates of resistance for antibiotics like ceftriaxone, cefotaxim and gentamycin were 5%, 30% and 15%, correspondingly. There were 15 cases (16.7%) with resistance to imipenem. Conclusion: Antibacterial resistance patterns vary in different parts of the world and even within a country, therefore assessing resistance patterns in a region is of great importance for proper management and treatment. Our findings might help physicians for proper selection of antibiotics for treatment of neonatal sepsis.
Microbiology
Nafiseh Izadi; Mahboubeh Naderi Nasab; Elnaz Harifi Mood; Zahra Meshkat
Abstract
Background and Objectives: Since the fluoroquinolones are the broad-spectrum antibiotics, they affect both Gram-negative and Gram-positive bacteria. These antibiotics are widely prescribed by physicians. As a result, some bacteria, especially Enterobacteriaceae, have shown a resistance to this family ...
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Background and Objectives: Since the fluoroquinolones are the broad-spectrum antibiotics, they affect both Gram-negative and Gram-positive bacteria. These antibiotics are widely prescribed by physicians. As a result, some bacteria, especially Enterobacteriaceae, have shown a resistance to this family of antibiotics. The current study aimed at detecting the frequency of qnrA, qnrB, and qnrS genes, novel plasmid-mediated quinolone-resistance genes, among extended-spectrum β-lactamases (ESBL)-positive and ESBL-negative Klebsiella pneumoniae isolates. Materials and Methods: One hundred and thirty isolates of K. pneumoniae were collected from Imam Reza Hospital and its associated clinics from May 2011 to July 2012. The isolates were tested for ESBLs by the conventional methods. Polymerase chain reaction (PCR) was performed to amplify qnr A, B, and S. Results: Thirty-eight (29.3%) isolates were ciprofloxacin-resistant. Among 130 K. pneumoniae infectious isolates, 56 (43%) were capable of producing ESBL; 10.8% (n=14), 15.4% (n=20), and 20.8% (n=27) of ESBL-producing K. pneumonia were positive for qnrA, qnrS, and qnrB, respectively, and 13.8% (n=18) of the isolates harbored 2 or 3 qnr genes. Conclusion: The results of the current study showed that quinolone-resistance genes were more frequent in ESBL-producing K. pneumoniae (37.5%) isolates, compared with the ESBL-negative isolates (20.89%). The prevalence of qnr genes was high in K. pneumoniae isolates, with higher frequency in ESBL-positive strains. Most of the isolates were positive for all 3 groups of qnr genes and the qnrB was the most common one.
Microbiology
Behrang Kazeminezhad; Arezoo Bostanmanesh Rad; Atoosa Gharib; Sara Zahedifard
Abstract
Background & objective: Beta-lactam antibiotics resistance specifically Imipenem and Meropenem, the last choices of treatment, causes fatal events in patients with P.aeruginosa infection. The aim of this study was to detect the VIM and IMP of metallo-beta-lactamase genes in 103 isolates of P. aeruginosa ...
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Background & objective: Beta-lactam antibiotics resistance specifically Imipenem and Meropenem, the last choices of treatment, causes fatal events in patients with P.aeruginosa infection. The aim of this study was to detect the VIM and IMP of metallo-beta-lactamase genes in 103 isolates of P. aeruginosa in two Iranian hospitals. Methods: In this study, we evaluated the susceptibility of P. aeruginosa to a range of β-lactam antibiotics using disk diffusion method as a standard biochemical test. Combined disk test of Imipenem (IMP) and Imipenem plus Ethylenediaminetetraacetic acid (EDTA) was performed as a phenotypic method to find metallo-beta-lactamase producing isolates.Using conventional PCR method; we evaluated VIM and IMP of metallo-beta-lactamase (MBL) genes in 103 isolates of P.aeruginosa. Results: Twenty six (25.2%) out of 103 isolates were resistant to Imipenem and 26 (25.2%) to Meropenem. Among 26 Imipenem and Meropenem-resistant strains (25.2%), 19 cases (73.0%) were MBL producing. Using PCR method, we detected the blaVIM and blaIMP genes in 6 (5.8%) and 2(1.9%) of 19 MBL producing isolates, respectively. Conclusions: Evaluation of these carbepenemases genes improve epidemiologic researches and also, can be used as a diagnostic tool for discriminating between antibiotics resistant and sensitive strains of P.aeruginosa as well as follow-up the patients after treatment.
Microbiology
Sina Rostami; Alireza Pasdar; Sina Gerayli; Hamed Hatami; Samaneh Sepahi; Fatemeh Nategh; Mojtaba Meshkat; Seyed Mousalreza Hoseini; Mitra Ahadi; Hamid Reza Sima; Hasan Vosughinia; Mohammad Reza Sarvghad; Abbas Esmaeelzade; Hosein Nomani; Homan Mosanan Mozafari; Fariba Rezai Talab; Mohammad Taghi Shakeri; Zahra Meshkat
Abstract
Background and Objectives: Interferon-gamma is an important cytokine, which facilitates immunity against intracellular pathogens. Several factors, including genetic variations of cytokine-producing genes have been shown to influence the progression and severity of Hepatitis C virus (HCV) infection. Methods: ...
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Background and Objectives: Interferon-gamma is an important cytokine, which facilitates immunity against intracellular pathogens. Several factors, including genetic variations of cytokine-producing genes have been shown to influence the progression and severity of Hepatitis C virus (HCV) infection. Methods: Between January and December 2012, 87 HCV-infected individuals and 89 individuals without HCV infection were recruited for the study of Single Nucleotide Polymorphism (SNP) at Interferon Gamma (IFNG) +874 T/A. After extraction of genomic DNA from Peripheral Blood Mononuclear Cells (PBMCs) in blood sample of the individuals, Amplification Refractory Mutation System (ARMS) polymerase chain reaction was performed to evaluate the SNP at this position. Results: The frequency of genotype TA was 62.1% in the HCV-infected group, while it was 47.2% for the control group (p=0.033). However, after adjusting for confounders (including alcohol consumption, drug addiction, transfusion, and tattoos), the genotypes at this position did not show any statistically significant association with HCV infection (adjusted P values were above 0.05). The frequency of allele A was slightly higher in patients than the controls (55.2% versus 48.3%).Carriers of A allele were more frequent in patients with HCV infection compared to the control group (55.17% in patients versus 48.31% in the control group; P=0.02). However, after adjustment for confounders, the results were no longer statistically significant (P=0.2). Conclusion: A carrier status for certain alleles and genotypes at Interferon Gamma (IFNG) +874 T/A may lead to higher susceptibility to HCV infection in a certain population.
Microbiology
Ehsan Kazemi Moghaddam; Parviz Owlia; Abolfazl Jahangiri; Iraj Rasooli; Mohammad Reza Rahbar; Marjan Aghajani
Abstract
Background & Objectives: Due to the importance of Pseudomonas aeruginosa in severe inpatient infections and high mortality, the need for an efficient vaccine against these bacteria is increasing. In this regard, the general outer membrane porin of the most problematic microorganism P. aeruginosa, ...
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Background & Objectives: Due to the importance of Pseudomonas aeruginosa in severe inpatient infections and high mortality, the need for an efficient vaccine against these bacteria is increasing. In this regard, the general outer membrane porin of the most problematic microorganism P. aeruginosa, outer membrane protein F (OprF), is a good vaccine candidate. Methods:The databank of NCBI was used to retrieve protein sequences recorded for OprF in P. aeruginosa.The current study aimed at investigating the conservation of the OprF in 150 reference sequences, clinical, and environmental strains of P. aeruginosa from different countries via bioinformatic tools.T-COFFEE and PRALINE software were used for alignment. Results: Of these, 134 strains were isolated from clinical specimens and other strains from environmental samples. Evaluation of alignment by the mentioned software clearly showed that this protein was conserved. Antigenicity and grand average of hydropathicity were favorable. Conclusion: Conservation of OprF in all pathogenic and environmental strains of P. aeruginosa indicated that it can be considered as a good immunogen; however, the protectivity of OprF should be validated experimentally.
