Etemadifar, Z.,
Harirchi, S.,
Rafieyan S.,
Nojoumi, S.A.,
Etemadifar z., Publication Date: 2022
2025 29th International Computer Conference, Computer Society of Iran, CSICC 2025pp. 487-514
Nowadays, pollution and the number of contaminated sites are increasing due to widespread industrialization around the world, which threatens the lives of humans and every living organism on Earth. Biological methods such as biodegradation, bioremediation, phytoremediation, and vermiremediation are effective ways to reduce pollution in contaminated sites. Microorganisms play an imperative role in the biodegradation and bioremediation of pollutants by catalyzing chemical and biochemical reactions via their enzymes. At present, exceptional novel enzymes with exceptional functions is in progress around the world. To date, many researchers have taken considerable efforts to improve the properties of the available enzymes by various methods such as protein engineering. However, there is still a great demand for enzymes with extraordinary properties that make them resistant yet still active under harsh conditions and extreme environments. The most important source of current enzymes is culturable microorganisms (nearly 0.1% of these microorganisms), whereas unculturable microorganisms have a great potential to be the source of novel enzymes. In this context, metagenomics, a culture-independent approach, enables us to excavate this diverse source. In this chapter, the metagenomic principle, along with recent advances, has been reviewed. Thereafter, contaminated sites and microbial biodegradation pathways are introduced. The main focus of this chapter is on exploring degrading enzymes by metagenomics and their applications in microbial biodegradation. © Springer Nature Singapore Pte Ltd. 2022.
Publication Date: 2020
Iranian Journal Of Basic Medical Sciences (20083874)23(7)pp. 886-893
Objective(s): Chemotherapies used to treat colon cancer might often fail due to the emergence of chemoresistance and side effects. Escherichia coli Nissle 1917 (EcN) is a beneficial probiotic, whose molecular mechanisms in the prevention of colon cancer are yet to be fully understood. The present study assessed the anti-cancer effects of EcN treatments in human colorectal cancer, HT-29 cell line, with the analysis of related mechanisms. Materials and Methods: The co-culture conditioned-media (CM) of EcN with adenocarcinoma HT-29 cells and heat-inactivated bacteria (HIB) were applied for the treatment of the HT-29 cells. To study the inhibition potential of CM and HIB on cancer cells, various cellular/molecular analyses were implemented, including DAPI-staining and DNA ladder assays, flow cytometry and Real-time quantitative PCR (qPCR), as well as Western blotting analyses. Results: Our results indicated that EcN could elicit apoptotic impacts on the colon cancer HT-29 cells by up-regulating PTEN and Bax and down-regulating AKT1 and Bcl-xL genes. Conclusion: Based on our findings, EcN is proposed as a useful supplemental probiotic treatment against colon cancer.
Talebi m., M.,
Sadeghi, J.,
Rahimi, F.,
Pourshafie, M.R. Publication Date: 2015
Jundishapur Journal Of Microbiology (20084161)8(4)
Background: Vancomycin-resistant enterococci (VRE) are important nosocomial pathogens and food chain has been considered as an assumed source for dissemination of VRE to human. Objectives: The presence of VRE isolates from food samples and typing of these isolates with Phene plate, a biochemical fingerprinting method, were investigated. Materials and Methods: Thirty samples of meat, chicken and cheese were analyzed for VRE during 2010. Antibiotic susceptibility tests and minimum inhibitory concentration (MIC) were also examined. VRE isolates were typed with the Phene plate system (PhPlate), a biochemical fingerprinting method. Results: A total of 70 VRE isolates were obtained and identified as Enterococcus faecium by species-specific PCR. All the isolates carried vanA, while none of them harbored vanB. The VRE isolates included 35, 27, and 8 isolates from meat, chicken and cheese, respectively. Typing with the PhPlate revealed a diversity index of 0.78 for E. faecium, containing 10 common and four single types. The results of antibiotic susceptibility and MIC tests showed an increased resistance to ciprofloxacin, erythromycin, ampicillin and gentamicin, to which, 100%, 100%, 100%, and 95% of VRE isolates were resistant, respectively. Only 5% of the isolates were resistant to chloramphenicol and the MIC of the isolates for vancomycin and teicoplanin was >= 256 mu g/mL and for gentamicin-resistant isolates it was 1024 mu g/mL. Conventional and molecular identification tests exhibited that all the isolates were E. faecium carrying vanA. None of the isolates harbored vanB. Conclusions: The results showed that enterococci are common contaminants in food. Indeed, this study indicates a high prevalence of multidrug-resistant enterococci in food of animal origin in Iran. Isolating some persisting enterococcal isolates revealed that continuous surveillance of antimicrobial resistance in enterococci from food is essential.
Aberuyi, N.,
Rahgozar, S.,
Dehaghi, Z.K.,
Moafi, A.,
Masotti, A.,
Paolini, A. Publication Date: 2017
ONCOTARGETS AND THERAPY (11786930)10pp. 3373-3380
Purpose: The aim of this work was to study the correlation between the expressions of the ABCA2 and ABCA3 genes at the mRNA and protein levels in children with acute lymphoblastic leukemia (ALL) and the effects of this association on multidrug resistance (MDR). Materials and methods: Sixty-nine children with de novo ALL and 25 controls were enrolled in the study. Mononuclear cells were isolated from the bone marrow. The mRNA levels of ABCA2 and ABCA3 were measured by real-time polymerase chain reaction (PCR). Samples with high mRNA levels were assessed for respective protein levels by Western blotting. Following the first year of treatment, persistent monoclonality of T-cell gamma receptors or immunoglobulin H (IgH) gene rearrangement was assessed and considered as the MDR. The tertiary structure of ABCA2 was predicted using Phyre2 and I-TASSER web systems and compared to that of ABCA3, which has been previously reported. Molecular docking was performed using DOCK 6.7. Results: Real-time quantitative PCR (qRT-PCR) showed high levels of ABCA2 and ABCA3 mRNAs in 13 and 17 samples, respectively. Among them, five and eight individuals demonstrated high levels of ABCA2 and ABCA3, respectively. Response to chemotherapy was significantly decreased (P=0.001) when the mRNA and protein of both genes were overexpressed compared to individuals with high transcriptional levels of either ABCA2 or ABCA3 alone. Close similarity between ABCA2 and ABCA3 structures was revealed by protein tertiary structure prediction, whereas molecular docking analysis suggested similar binding of chemotherapy drugs and therefore a potentially similar role in determining the MDR. Conclusion: Our findings suggested, for the first time, that quantification of the protein level of ABCA2 and ABCA3 transporters had a prognostic impact on pediatric ALL MDR. Furthermore, the tertiary structure of ABCA2 was predicted for the first time, and docking analysis revealed a possible compensatory effect between ABCA2 and ABCA3 transporters, which may contribute to the efflux of cytotoxic drugs and, ultimately, to chemoresistance.
Publication Date: 2021
Frontiers in Cellular Neuroscience (16625102)15
The development of dopaminergic (DA) neurons is a very complex process, and a combination of extrinsic and intrinsic factors involves their differentiation. Transcription factor, Nurr1 plays an essential role in the differentiation and maintenance of midbrain DA neurons. Nurr1-based therapies may restore DA function in Parkinson's disease (PD) by replacing damaged cells with differentiated cells derived from stem cells. Providing tissue-specific microenvironments such as brain extract can effectively induce dopaminergic gene expression in stem cells. The present study aimed to investigate the combined effects of Nurr1 gene overexpression and a neonatal rat brain extract (NRBE) induction on dopaminergic differentiation of P19 stem cells. In order to neural differentiation induction, stably Nurr1-transfected cells were treated with 100 μg/ml of NRBE. The differentiation potential of the cells was then evaluated during a period of 1–3 weeks via various methods. The initial evaluation of the cells by direct observation under a light microscope and cresyl violet specific staining, confirmed neuron-like morphology in the differentiated cells. In addition, different molecular and cellular techniques, including real-time PCR, immunofluorescence, and flow cytometry, demonstrated that the treated cells expressed pan-neuronal and dopaminergic markers. In all experimental groups, neuronal phenotype with dopaminergic neuron-like cells characteristics mainly appeared in the second week of the differentiation protocol. Overall, the results of the present study revealed for the first time the synergistic effects of Nurr1 gene overexpression and possible soluble factors that existed in NRBE on the differentiation of P19 stem cells into dopaminergic neuron-like cells. Copyright © 2022 Beiki, Khaghani, Esmaeili and Dehghanian.
Momendoust, N.,
Moshtaghian, J.,
Esmaeili, F.,
Dehghanian, F.,
Dumit, V. Publication Date: 2019
Developmental Neurobiology (19328451)79(6)pp. 559-577
A large number of studies have focused on the generation of dopaminergic neurons from pluripotent cells. Differentiation of stem cells into distinct cell types is influenced by tissue-specific microenvironment. Since, central nervous system undergoes further development during postnatal life, in the present study neonatal rat brain tissue extract (NRBE) was applied to direct the differentiation of embryonal carcinoma stem cell line, P19 into dopaminergic (DA) phenotypes. Additionally, a neuroprotective drug, deprenyl was used alone or in combination with the extract. Results from morphological, immunofluorescence, and qPCR analyses showed that during a period of one to three weeks, a large percentage of stem cells were differentiated into neural cells. The results also indicated the greater effect of NRBE on the differentiation of the cells into tyrosine hydroxylase-expressing cells. MS analysis of NRBE showed the enrichment of gene ontology terms related to cell differentiation and neurogenesis. Network analysis of the studied genes and some DA markers resulted in the suggestion of potential regulatory candidates such as AVP, ACHE, LHFPL5, and DLK1 genes. In conclusion, NRBE as a natural native inducer was apparently able to simulate the brain microenvironment and support neural differentiation of P19 cells. © 2019 Wiley Periodicals, Inc.
Khashei, S.,
Fazeli, H.,
Rahimi, F.,
Karbasizade, V. Publication Date: 2025
Frontiers in Pharmacology (16639812)16
Introduction: This research aimed to examine the action of commercial antibiotics against extensively drug-resistant (XDR) A. baumannii clinical strains when combined with Rosmarinus officinalis extracts. Methods: Agar well diffusion and broth microdilution were used to screen the antibacterial activity of crude ethanol extract and its fractions (hexane, intermediate, ethyl acetate, and water). The interactions between the extracts and antibiotics (gentamicin, tetracycline, cefepime, and ciprofloxacin) were evaluated by checkerboard assay. The anti-biofilm and efflux pump inhibition activities were determined by the microtiter plate method and dye accumulation assay using flow cytometry, respectively. The potential phytochemicals that contribute to the antibacterial effects of R. officinalis were identified using the liquid chromatography-mass spectrometry (LC–MS). Results: R. officinalis crude extract (CE) demonstrated the best antibacterial activity with MIC values ranging from 300 to 600 μg/mL. The combination of CE and tetracycline exhibited the highest overall synergistic effect. This combination hindered biofilm formation ranging from 21.4% to 57.31% and caused a significant increase (up to 14%) in the fluorescence intensity in 75% of the studied strains. The LC-MS analysis of CE exhibited eleven compounds in which rosmarinic acid (55.53%) was the most abundant phenolic compound followed by cirsimaritin (11.46%), and p-coumaroyl hexoside acid (10.5%). Discussion: Overall, this is the first direct report that demonstrated the efficacy of R. officinalis when applied with conventional antibiotics on biofilm formation and efflux pump activity in XDR A. baumannii clinical strains. Copyright © 2025 Khashei, Fazeli, Rahimi and Karbasizadeh.
Publication Date: 2024
Tehran University Medical Journal (16831764)82(7)pp. 528-537
Background: Biofilm producing uropathogenic Escherichia coli (UPEC) strains are of major concern in clinical settings which display increased resistance to conventional antimicrobial therapy. Nitric oxide (NO) has shown to exhibit anti-biofilm effects in a variety of bacterial species. In this study we aimed to evaluate the effectiveness of NO on the formation and eradication of biofilm of UPEC strains isolated from patients with urinary infection (UI) in Tehran. Methods: During May 2022 to April 2023, a total of 3814 suspected isolates of UPEC were collected from a pathobiology laboratory in Tehran and confirmed as E. coli strains using specific primers for elongation factor Tu (tufA) gene. All strains were screened for the ability to form biofilm by the microtiter plate (MTP) and Congo red agar (CRA) assays, and also the presence of biofilm genes were detected among biofilm producing strains. Moreover, the effect of NO on biofilm formation and its dispersal was evaluated by the high (30 mM) and low (125 nM) concentrations of sodium nitroprusside (SNP) as NO donor. Results: All collected isolates were confirmed by the polymerase chain reaction (PCR) using specific primers, in which 1309 strains (34%) were able to form colonies with red, dry and rough (rdar, curli and cellulose positive) (n=682, 52%), brown, dry and rough (bdar, curli positive and cellulose negative) (n=353, 27%) and pink, dry and rough (pdar, cellulose positive and curli negative) (n=274, 21%) morphotypes on CRA and selected as biofilm positive strains. Furthermore, 228 (17%), 402 (31%) and 679 (52%) strains were able to form a weak, moderate, and strong biofilm, respectively, and csgA, csgD, yedQ, and bcsA genes were found among 87, 98, 100 and 79% of biofilm-positive strains, respectively. The 30 mM concentration of SNP significantly decreased the biofilm formation (17-40%) and increased biofilm dispersal (20-45%) among UPEC strains. Conclusion: These findings confirmed the applicability of nitric oxide as an anti-biofilm agent for UPEC strains. These findings contribute to the development of novel strategies for fighting biofilm-associated infections. Copyright © 2024 Rahimi et al.
Publication Date: 2024
Archives Of Clinical Infectious Diseases (23452641)19(4)
Background: Over the past decades, the role of biofilm-forming Staphylococcus aureus strains in urinary tract infections (UTIs) has garnered significant attention. Objectives: This study aimed to determine the epidemiological characteristics and diversity of S. aureus strains isolated from patients with UTIs in Isfahan, Iran, in 2017, with regard to their antimicrobial resistance, biofilm formation, and phylogenetic profiles. Additionally, the study investigated potential relationships among these factors statistically to develop efficient control and treatment approaches. Methods: All patients with symptomatic UTIs who had positive urine cultures for S. aureus during the study period at the laboratory of a referral hospital in Isfahan were included. All isolates were identified using specific primers for the nucA gene. Their biofilm formation capacity was evaluated using a combination of the microtiter plate and Congo-red agar methods. Antibiotic susceptibility testing was performed using the disk diffusion method. The presence of genes involved in biofilm formation and resistance to cefoxitin, aminoglycosides, and fluoroquinolones was detected using polymerase chain reaction (PCR). Staphylococcal cassette chromosome mec (SCCmec) typing, agr typing, and phene plate (PhP) typing were employed to investigate the diversity of collected strains. Results: Results showed that 19%, 57%, and 24% of confirmed S. aureus strains were strong, intermediate, and non-biofilm formers, respectively. The highest rate of resistance was against nalidixic acid (77%), followed by streptomycin (73%). The icaD and icaA genes had the highest frequency among biofilm-producing strains. gyrA (44%) and grlA (35%) were the most frequent genes among fluoroquinolone-resistant strains, while aph(3′)-IIIa was the most prevalent aminoglycoside-modifying enzyme gene. The majority of bacterial strains harbored SCCmec type III and agr type I. PhP typing of strains revealed the presence of 8 common types (CTs) and 14 single types (STs), with CT2 being the dominant type. Conclusions: The present investigation revealed various biofilm production capacities, antimicrobial resistance profiles, and clonal lineages in S. aureus isolated from patients with UTIs. These findings provide further insights into the epidemiology and pathogenicity of S. aureus strains in Iran, thereby improving the quality of surveillance and therapeutic protocols. © 2024, Mostafavi et al.
Publication Date: 2024
Archives Of Clinical Infectious Diseases (23452641)19(3)
Background: The increasing incidence of methicillin-resistant Staphylococcus aureus (MRSA) poses a significant challenge in the treatment of diabetic foot infections (DFIs). Objectives: This study aimed to investigate the prevalence and diversity of clonal groups of MRSA strains isolated from patients with DFIs in a major referral hospital in Tehran. Methods: We determined the prevalence, diversity, and antibiotic susceptibility profiles of MRSA isolated from patients with DFIs attending a referral hospital in Tehran, Iran, during 2019-2020. Staphylococcal cassette chromosome mec (SCCmec) typing, ccr typing, PhP typing, and detection of the Panton-Valentine Leukocidin (pvl) gene were performed to explore the diversity of the strains. Antibiotic susceptibility profiles of the strains were determined using the disk diffusion method and broth microdilution assay. Results: Of the 238 S. aureus strains isolated, 73 were identified as MRSA. The highest antibiotic resistance was observed against ciprofloxacin (86%), followed by kanamycin and tobramycin (84%). Additionally, 49% of the strains exhibited high-level oxacillin resistance (MIC ≥ 256 µg/mL). SCCmec type III and type 3 ccr were detected in 86% of the strains, classifying them as hospital-acquired (HA)-MRSA. PhP typing revealed the presence of 8 common types (CTs) and 11 single types (STs), with CT2 comprising 41% of the strains. Conclusions: Our data suggest that MRSA strains isolated from DFIs in this region are diverse and resistant to clinically important antibiotics. Diabetic patients can serve as a reservoir for the dissemination of these bacteria between community and clinical environments. © 2024, Rahimi et al.
Publication Date: 2023
Infection, Epidemiology And Microbiology (25884107)9(1)pp. 15-23
Backgrounds: Diabetic patients are at risk of developing serious foot infections with methicillin-resistant Staphylococcus aureus (MRSA) strains, which are associated with high morbidity and mortality. This study aimed to investigate the frequency of different prophage types and virulence factors among MRSA strains isolated from patients with diabetic foot infections (DFIs) in a referral hospital in Tehran, Iran during 2019 and 2020. Materials & Methods: A total of 238 S. aureus isolates were collected and confirmed using specific primers. The presence of staphylococcal enterotoxins (sea-seq) and hlb, sak, eta, etb, and tsst-1 genes among MRSA isolates was tested using separate polymerase chain reaction (PCR) assays. Also, multiplex PCR was employed for prophage typing of MRSA isolates. Findings: A total of 73 (31%) isolates were confirmed as MRSA, among which four prophage types and 13 different prophage patterns were identified, and prophage type SGF and prophage pattern 7 consisting of SGB, SGF, SGFa, and SGFb types were the dominant ones. Also, 11 enterotoxin-encoding genes and four virulence factor genes were detected among the isolates. All MRSA isolates were positive for sea, sek, seq, and hlb genes. Moreover, out of 12 different enterotoxin patterns, most MRSA isolates were classified into enterotoxin pattern 1, harboring three enterotoxin genes (sea, sek, and seq). Conclusion: This study results indicated the presence of different prophage types and virulence factor genes among MRSA strains isolated from DFI patients, which enable them to produce a variety of diseases. © 2023, TMU Press.
Publication Date: 2022
International Microbiology (11396709)25(2)pp. 297-307
Uropathogenic E. coli (UPEC) strains exhibit different levels of biofilm formation that help adhesion of the bacteria to uroepithelial cells. We investigated the genetic diversity and virulence-associated genes (VAGs) of biofilm-producing UPEC. A collection of 107 biofilm-producing (BFP) UPEC strains isolated from patients with UTI in Iran were divided into three groups of strong, moderate, and weak BFPs after a quantitative microtiter plate assay, and the involvement of curli and cellulose in adhesion of the strains to T24 cell line was confirmed by the construction of csgD and yedQ mutants of two representative UPEC strains. BFP strains were tested for their genetic diversity, phylogenetic groups, and the presence of 15 VAGs. A significant decrease in adhesion of csgD and yedQ mutant strains confirmed the role of biofilm production in adhesion to uroepithelial cells. A high diversity was found among all three groups of strong (Di = 0.998), moderate (Di = 0.998), and weak (Di = 0.988) BFPs with majority of the strains belonging to phylogroups B2 (44.9%) and A (24.3%). Strong BFP strains carried significantly higher level papEF, hlyA, and iutA than other BFP groups. In contrast, the presence of fimH, focG, sfaS, set-1, and cvaC was more pronounced among weak BFP strains. There exists a high genetic diversity among the BFP strains with different VGA profiles. However, the high prevalence of phylogroup A among BFP strains suggests the fitness of commensal E. coli strains to cause UTI in this country. © 2021, The Author(s), under exclusive licence to Springer Nature Switzerland AG.
Publication Date: 2022
Pathogens and Global Health (20477724)116(8)pp. 485-497
Pathogenicity of a bacterium is affected by the social characteristics of the population and environmental factors. The ability of biofilm formation among β-lactamase-producing uropathogenic Escherichia coli (UPEC) could facilitate the exchange of antibiotic-resistance genes, which resulted in widespread dissemination of antibacterial drug resistance. We investigated the prevalence of biofilm and β-lactamase producing UPECs among patients with urinary tract infection (UTI) in two cities with different demographics and climates in Iran. A total of 265 E. coli was isolated from patients with UTIs from two referral hospitals (n = 191) and two outpatient clinics (n = 74) in Isfahan and Zahedan, Iran. Production of curli and cellulose, and, biofilm formation was investigated using Congo red agar and microtiter plate methods, respectively. Biofilm producing (BFP) isolates (n = 107) were further characterized using rep-PCR, antimicrobial susceptibility testing and extended-spectrum β-lactamase (ESBL)/AmpC phenotypic production. Isolates were also screened for the presence of carbapenemase, ESBL and AmpC genes using multiplex PCR. High diversity was found among BFP strains in both cities, with 58% strains producing ESBL and 21% producing AmpC. ESBL (98%), AmpC (50%) and carbapenemase genes (40%) were identified in BFP strains with ESBL-positive phenotype, respectively. The prevalence of BFP strains, antibiotic resistance and β-lactamase genes in Zahedan, a low socioeconomic city with a warm climate, was significantly higher than that of Isfahan. High prevalence of biofilm and β-lactamase producing UPEC strains among strains from Zahedan suggests that socioeconomic status and environmental factors might have a role in pathogenicity of the strains. © 2021 Informa UK Limited, trading as Taylor & Francis Group.
Publication Date: 2021
Journal of Water and Health (14778920)19(2)pp. 216-228
Multidrug-resistant Staphylococcus aureus strains have been commonly found in hospitals and communities causing wide ranges of infections among humans and animals. Typing of these strains is a key factor to reveal their clonal dissemination in different regions. We investigated the prevalence and dissemination of different clonal groups of S. aureus with resistance phenotype to multiple antibiotics in two sewage treatment plants (STPs) in Tehran, Iran over four sampling occasions. A total of 576 S. aureus were isolated from the inlet, sludge and outlet. Of these, 80 were identified as methicillin-resistant S. aureus (MRSA) and were further characterized using a combination of Phene Plate (PhP) typing, staphylococcal cassette chromosome mec (SCCmec), ccr types, prophage and antibiotic-resistant profiling. In all, eight common type (CT) and 13 single PhP type were identified in both STPs, with one major CT accounting for 38.8% of the MRSA strains. These strains belonged to three prophage patterns and five prophage types with SCCmec type III being the predominant type. Resistance to 11 out of the 17 antibiotics tested was significantly (P < 0.0059) higher among the MRSA isolates than methicillin-sensitive S. aureus (MSSA) strains. The persistence of the strains in samples collected from the outlet of both STPs was 31.9% for MRSA and 23.1% for MSSA. These data indicated that while the sewage treatment process, in general, is still useful for removing most MRSA populations, some strains with SCCmec type III may have a better ability to survive the STP process. © 2021 IWA Publishing. All rights reserved.
Publication Date: 2021
Infection, Epidemiology And Microbiology (25884107)7(3)pp. 215-227
Backgrounds: Hospital sewage is known as an important source of human pathogenic bacteria such as methicillin resistant Staphylococcus aureus (MRSA) strains disseminated from hospital to the environment. This study aimed to investigate the presence of MRSA in the treated outgoing wastewater collected from a referral hospital in Tehran, Iran. Materials & Methods: During 2015, sampling was carried out at two stages from a hospital wastewater. All black colonies with halos on HiCrome aureus agar medium supplemented with oxacillin were collected and identified as MRSA using specific primers for nucA and mecA genes. Isolates susceptibility to 18 antibiotics was determined according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI). Bacterial typing was performed for the isolates using a combination of Phene plate (PhP) typing, prophage typing, staphylococcal cassette chromosome mec (SCCmec) and ccr typing methods. Findings: A total of 79 MRSA isolates were confirmed using specific primers and showed susceptibility to quinupristin-dalfopristin, vancomycin, chloramphenicol, and linezolid. High resistance to penicillin, ciprofloxacin, kanamycin, tobramycin, and erythromycin was reported. Sixteen PhP types consisting of eight common types (CTs) and eight single types (STs) were identified among the strains, among which CT1 was the dominant type. Also, two prophage patterns and four prophage types were identified, and all the strains were positive for SCCmec type III and ccr type 3. Conclusion: The results of this study revealed that sewage-treatment process was able to remove community-acquired MRSA (CA-MRSA) strains; however, hospital-acquired MRSA (HA-MRSA) strains were able to survive during the treatment process in this hospital. © 2021, TMU Press.
Publication Date: 2021
Infection, Epidemiology And Microbiology (25884107)7(1)pp. 1-15
Background: Staphylococcus epidermidis isolates are among the most important causes of nosocomial infections and could be classified as health threatening agents. This study aimed to determine the biofilm formation ability and clonal dissemination of S. epidermidis strains isolated from patients and healthy people in Isfahan during 2016 and 2017. Materials & Methods: A total of 139 and 123 suspected colonies of S. epidermidis were collected from different clinical specimens and the arm of healthy people, respectively. The ability to form biofilm was determined using a combination of Congo-red agar (CRA) and microtiter plate (MTP) assays. The presence of genes involved in biofilm formation was also tested by the polymerase chain reaction (PCR) test. The susceptibility of all strains to 12 antibiotics was evaluated using the disk diffusion method according to the Clinical & Laboratory Standards Institute (CLSI) guidelines. Moreover, all biofilm-producing strains were typed using PhenePlate system as well as cassette chromosome mec (SCCmec) and accessory gene regulator (agr) locus typing method. Findings: A total of 43 biofilm-producing S. epidermidis strains were identified among 107 and 123 confirmed strains isolated from hospitalized patients and healthy people, respectively; all of which were positive for aap gene, and the presence of ica operon was limited to 86 and 27% of the strains isolated from patients and healthy people, respectively. All the strains showed susceptibility to vancomycin, quinupristin-dalfopristin, and linezolid. Moreover, SCCmec Types III, IV, and V were detected among all methicillin-resistant S. epidermidis (MRSE) strains, and agr Type I was the most frequent one. Among all biofilm-positive strains, 3 common types (CTs) and 7 single types (STs) were determined; CT1 and CT2 were the most common types among the strains isolated from hospitalized patients and healthy people. Conclusion: These findings indicated the presence and persistence of diverse clone types of biofilm-producing S. epidermidis strains with common types of PhP, agr, and SCCmec in the hospital and the community of Isfahan. © 2021, TMU Press.
Publication Date: 2019
Infectious Diseases in Clinical Practice (10569103)27(3)pp. 163-169
Background: Methicillin-resistant Staphylococcus aureus (MRSA) strains are known as one of the most important multidrug-resistant organisms causing infections in humans and animals. The objectives of this experimental study were to characterize the clonality and antibiotic resistance of MRSA strains isolated from patients in 2 different cities in Iran. Methods: During 2 years, a total of 536 S. aureus isolates were collected from 2 reference hospitals in Tehran and Isfahan and were identified as MRSA using specific primers. The antibiotic susceptibility and their clonality were determined using the PhenePlate typing system. Furthermore, the presence of different classes of prophages and the structure of staphylococcal cassette chromosome mec elements and cassette chromosome recombinases types were characterized. Results: Of the 536 strains, 129 MRSA were identified using species-specific primers and discriminated into 26 PhenePlate types consisted of 12 common types (CTs) and 14 single types, in which CT2 was the predominant type and 6 CTs were common among MRSA isolated in both cities. Staphylococcal cassette chromosome mec types III and IV were also detected in 89% and 11% of the strains, and SGF prophage type was the dominant one. Thirty-four antibiotic patterns were detected among the MRSA strains, and none of the isolates showed resistance to linezolid, quinupristin-dalfopristin, and vancomycin. Conclusions: High prevalence of antibiotic-resistant common clonal groups of MRSA strains in 2 different cities in this study indicated the spread of these clonal types in north and center of Iran and highlighted the common origin of such strains, which are believed to be endemic in various sources. © 2019 Wolters Kluwer Health, Inc. All rights reserved.
Publication Date: 2018
Archives Of Clinical Infectious Diseases (23452641)13(6)
Background: Coagulase-negative Staphylococcus epidermidis is the most prevalent member of the human skin normal biota that plays an important role as a common cause of catheter and prosthetic device-related infections from, for example, indwelling catheters. Objectives: This study aimed to characterize the clonality of biofilm-producing methicillin-resistant S. epidermidis (MRSE) strains isolated from catheterized patients with urinary tract infection at a referral hospital in Tehran, Iran. Methods: Between 2014 and 2016, a total of 56 methicillin-resistant S. epidermidis (MRSE) strains were recovered from catheterized patients. The MRSE isolates were tested for biofilm formation and different genes involved in this process were detected. Clonal dissemination of MRSE isolates was determined using the combination of pulsed-field gel electrophoresis (PFGE) and SCCmec typing. Results: Out of the 56 MRSE strains, 50 (89%) formed biofilm and were positive for icaA and icaD genes, and 73% (n = 41) harbored IS256. The PFGE patterns revealed a total of 32 different pulsotypes consisting of 16 single types (STs), 16 common types (CTs), and 2 SCCmec types (III and IV) were detected. Moreover, all STs carried SCCmec type IV and classified as community-acquired strains. Four CTs were common among biofilm and non-biofilm producing strains. Conclusions: The presence of icaA and icaD genes with a high prevalence of IS256 element in clonal groups of MRSE strains suggests that ica, IS256, and biofilm forming ability occur simultaneously in specific S. epidermidis clones and spread preferentially in hospitals and community. © 2018, Archives of Clinical Infectious Diseases.
Publication Date: 2018
Archives Of Clinical Infectious Diseases (23452641)13(5)
Background: Methicillin-resistant Staphylococcus aureus (MRSA) has been considered as an important pathogen with a variety of virulence factors in communities and hospitals worldwide. Objectives: In this study, we focused on the detection of different virulence factors and enterotoxin genes of MRSA strains isolated from a referral hospital in Tehran, Iran. Moreover, the presence of different prophage types was studied. Methods: A total of 491 MRSA strains were isolated during three years from a referral hospital in Tehran. The staphylococcal enterotoxin (sea-seq) and pvl, hlb, sak, eta and tst genes were detected. A multiplex-polymerase chain reaction (PCR) assay was used for prophage typing of MRSA isolates. Results: Totally, 11 enterotoxin and 5 virulence factor genes were detected in MRSA strains. The sea, sek, seq, and hlb genes were present in all the MRSA and other enterotoxin genes. sel, seg, sem, sei, sen, seo, sec and sep were detected in 32.8%, 20.3%, 12.6%, 8.3%, 4.1%, 2.6%, 1.6% and 0.4% of the strains, respectively. A total of 93%, 81%, 15.9% and 5.7% of the strains harbored the sak, eta, tst and pvl genes, respectively. SGF, SGFa and SGFb proghage type genes were detected in 100% of the MRSA strains, and four different prophage patterns were identified among the strains. Conclusions: The presence of different prophage-encoded virulence factors among MRSA strains enable MRSA to produce a broad range of diseases, indicating MRSA strains as a potential threat to patients’ health. © 2018, Archives of Clinical Infectious Diseases.
Publication Date: 2017
Iranian Red Crescent Medical Journal (20741804)19(2)
Background: Approximately 80% of nosocomial infections are caused by strains of Klebsiella pneumoniae. Resistance to β-lactam antibiotics is a result of expression of extended-spectrum β-lactamase (ESBL) genes. Recently, phage therapy has gained increasing attention due to its many advantages over chemotherapy. Objectives: The aim of this study was to isolate ESBL-positive Klebsiella pneumoniae strains from different types of wounds, and a lytic bacteriophage against them. Methods: During a two-year period from January 2013 to February 2015, in a cross-sectional study, 41 K. pneumoniae strains were isolated from 193 categories of infected wounds at three hospitals in Isfahan, Iran. Phenotypic and genotypic methods were used to detect the ESBL-positive strains. A lytic phage against K. pneumoniae was isolated, and its host range, morphology, thermal and pH stability, saline stress, and estimated genome size were determined. Results: Of the 41 K. pneumoniae isolates, 18 were ESBL-producing and 36 carried antibiotic-resistance genes. A total of 36 out of 41 isolated samples carried one or more resistance genes. The results showed that the differences between phenotypic and genotypic identification methods were significant (P = 0.0001). The SHV, CTX-M, and TEM genes were detected in 29, 10, and 9 isolates of the tested bacteria, respectively. No bacteria contained both the SHV and the CTX-M genes. The frequency of the SHV gene was significantly higher than that of the other genes (P = 0.0001). The phage’s morphology features placed it in the Myoviridae family. Only 38 out of 41 clinical isolates were susceptible to the phage. Phage titers were completely preserved after one hour of incubation at 30°C and 40°C, and they were stable at different pH values. The phage’s survival decreased when the salt concentration was increased. Conclusions: The high rate of isolation of antibiotic-resistant strains of K. pneumoniae was consistent with other studies. As the phage was virulent and specific for K. pneumoniae, and was stable and active at different pH values, salt concentrations, and temperatures, its application in phage therapy of infected wounds is suggested. © 2016, Iranian Red Crescent Medical Journal.
Publication Date: 2016
Archives Of Clinical Infectious Diseases (23452641)11(4)
Background: Methicillin-resistant Staphylococcus aureus (MRSA) strains are known as one of the most common causes of infection in humans and animals can produce a variety of virulence factors such as enterotoxins. Staphylococcal food poisoning is one of the most common food-borne diseases in the world. Objectives: The current experimental study aimed to isolate and determine the clonality of MRSA strains isolated from chicken meat samples, and describe the presence of different prophage types, enterotoxin genes and also the expression of Staphylococcus cassette chromosome mec (SCCmec) gene types. Methods: During six months in 2014, a total of 36 chicken meat samples were collected from Isfahan local markets and analyzed to screen MRSA strains. All isolates were typed using high resolution automated Phene plate (PhP) system and tested for the presence of different enterotoxin genes. Different staphylococcal cassette chromosome mec (SCCmec) and prophage types were determined. Results: All 116 isolated MRSA strains were discriminated into seven PhP types consisting of seven common types (CTs) and were positive for mecA gene. All isolates harbored SCCmec type III and SGF, SGFa and SGFb prophage types. Genes encoding enterotoxins SEA, SEK and SEQ were detected in all MRSA isolates. Conclusions: These findings illustrated the presence and persistence of clonal groups of MRSA strains, in chicken meat in Isfahan, Iran, that serve as reservoirs to disseminate bacteriophage encoded enterotoxin and virulence agents. © 2016, Infectious Diseases and Tropical Medicine Research Center.
Publication Date: 2016
Microbial Pathogenesis (08824010)98pp. 69-76
Between June 2011 and May 2014, we isolated a total of 419 Staphylococcus aureus strains from catheterized patients with UTI in a referral hospital in Tehran. Of these, 108 were identified as methicillin resistant (MRSA) based on their phenotypic resistance to oxacillin and the presence of mecA gene. The MRSA isolates were tested for their clonality using a combination of PFGE, prophage typing, SCCmec and ccr typing and examined for their biofilm formation as well as their resistance against 17 antibiotics. In all, 15 common pulsotypes consisted of 105 isolates and 3 single types were identified among the MRSA strains of which, 97% carried SCCmec type III and type 3 ccr. Eighty three (77%) strains were positive for biofilm formation and also carried icaA and icaD genes. Moreover, agr group III and its related tst gene were detected in 81% and 77% of biofilm producing strains, respectively 105 of the 108 MRSA were multidrug resistant with 82.4% being resistant to more than 10 antibiotics. Strains with SCCmec type IV and type 2 ccr, contained SGA and SGL prophage types, were positive for pvl gene and belonged to single PFGE types. This study highlights the important role of biofilm formation and virulence factors of MRSA strains in catheterized patients. © 2016 Elsevier Ltd
Publication Date: 2016
Microbial Pathogenesis (08824010)97pp. 89-93
Methicillin resistant Staphylococcus aureus is one of the most common causes of a variety of infections ranging from wound infections to urinary tract infections (UTI) in hospital and community. In this study during 3 years we characterized the antibiotic resistance patterns of 491 hospital acquired MRSA and community associated MRSA strains by the guidelines of clinical and laboratory standard institute. A combination of high resolution PhP typing method and SCCmec typing were used for clonal dissemination of isolates. Among all 491 MRSA strains, diverse PhP types consisting of 29 common types (CTs) and 4 single types (STs) and also 2 different SCCmec types (III and IVa) were detected. In addition, 18 CTs were common among CA- and HA-MRSA strains and the presence of all 4 STs was limited to HA-MRSA strains. All isolates were resistant to penicillin and high level resistance was observed against ciprofloxacin, erythromycin, tobramycin and kanamycin and the rate of resistance to most of the antibiotic tested among HA-MRSA was significantly higher than CA-MRSA isolates. Moreover, all isolates showed susceptibility to linezolid, vancomycin and quinupristin-dalfopristin and very low resistance to fusidic acid, nitrofurantoin and chloramphenicol were detected. Our findings illustrated the increasing rate of clonal dissemination and persistence of highly antibiotic resistant CA-MRSA strains in Tehran hospitals, and also indicated the important role of the hospitals as the reservoir of MRSA strains. © 2016 Elsevier Ltd.
Publication Date: 2016
Archives Of Clinical Infectious Diseases (23452641)11(3)
Background: Staphylococcus epidermidis is well documented as an opportunistic pathogen causing biofilm in patients and healthy individuals. Objectives: The aim of this experimental study was to describe the antibiotic resistance patterns of biofilm producing S. epidermidis strains isolated from clinical samples in Tehran, Iran. Moreover, the role of different genes in biofilm formation was also described. Patients and Methods: A total of 250 S. epidermidis strains were isolated from patients in a private hospital of Tehran, Iran from February to December 2014. The biofilm formation of each strain was determined using combination of qualitative Congo-Red agar and quantitative microtiter plate assay, and presence of different genes involved in control and formation of biofilm was detected by the polymerase chain reaction (PCR). Susceptibility of S. epidermidis strains to 19 antibiotics was examined. Results: The results of the biofilm assay revealed that 82% of strains produced black colonies on Congo red agar plates and 68% were able to attach strongly to polystyrene microplates. One hundred percent, 88%, 84%, 64% and 60% of biofilm-producing strains were resistant to penicillin, cefoxitin, erythromycin, trimethoprim-sulfamethoxazole and kanamycin, respectively. On the other hand, none of the strains showed resistance to vancomycin, linezolid, quinupristin/dalfopristin. The icaA, icaD, aap and atlE genes were detected in all biofilm-producing strains and presence of IS256 transposon was limited to 84% of biofilm positive strains. Conclusions: The results of this study illustrated the high prevalence of antibiotic resistant biofilm-producing S. epidermidis strains in this hospital, which could be a reservoir for antibiotic resistance genes. © 2016, Infectious Diseases and Tropical Medicine Research Center.
Mohkam, M.,
Rasoul-amini, S.,
Shokri, D.,
Berenjian, A.,
Rahimi, F.,
Sadraeian, M.,
Khalvati, B.,
Gholami, A.,
Ghasemi, Y. Publication Date: 2016
Minerva Biotecnologica (11204826)28(1)pp. 19-28
BACKGROUND: Probiotics mainly Bacillus species can be advantageous to the host by promoting its intestinal balance. Attempts were made to isolate and identify Bacillus strains from rhizosphere environment. METHODS: The in vitro probiotic criteria were used for screening and characterizing potential Bacillus probiotics. Morphological, physiological and biochemical characteristics as well as 16S rRNA gene sequence analysis were utilized for identification of the isolates. Seven isolates were chosen based on withstanding to acidic condition (pH 2.5) and various bile salt concentrations (1-4%(w/v)). RESULTS: Isolates found to have the least antimicrobial activity against Listeria monocytogenes PTCC 1163, Staphylococcus aureus ATCC 1912 and Bacillus cereus PTCC 1015; however, no activity against Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 25922 was observed. The Bacillus Isolates showed different variation in auto-aggregation features and adhesion to hydrocarbons ranging from 60% to 90% and 10% to 60%, respectively. Excluding isolate 14 that exhibited resistance to penicillin and ampicillin, all the other Bacillus strains were sensitive to the tested antibiotics. All isolates showed relatively low cytotoxic effect on HepG2 cell line except strains 12 and 14. CONCLUSION: Taking together, among the investigated Bacillus isolates, strains 17 and S10 found to be the most promising candidates to fulfill in vitro probiotic specifications. © 2016 EDIZIONI MINERVA MEDICA.
Publication Date: 2016
Archives Of Clinical Infectious Diseases (23452641)11(1)
Background: Methicillin-resistant Staphylococcus aureus (MRSA) has been known as one of the most important nosocomial pathogens that able to produce a variety of virulence factors. Objectives: In this study, we aimed to describe the prevalence, presence of different virulence factors, staphylococcal cassette chromosome mec (SCCmec) and prophage typing of MRSA strains isolated from a referral hospital in Tehran, Iran. Materials and Methods: A total of 279 S. aureus strains were collected from a referral hospital in Tehran during August to December of 2013. All isolates were confirmed using species specific primers and were tested for susceptibility to oxacillin and cefoxitin disks by the recommendations of clinical and laboratory standards institute (CLSI). The staphylococcal enterotoxin (sea-seq) and pvl, hlb and sak genes were detected and typed using prophage typing and SCCmec typing methods. Results: Out of the 279 S. aureus isolates, 91 (32.6%) strains were confirmed as MRSA. Totally, 6 enterotoxin and 2 virulence factor genes were detected in MRSA strains. The sea, sek, seq and hlb genes were present in all MRSA and sak, seg, sei and sel were detected in 85%, 35%, 23% and 44% of the strains. Only SCCmec type III and type 3 ccr and 2 different prophage patterns were identified among the strains. Conclusions: Our results show the presence of clonal groups of enterotoxin-producing MRSA strains in this hospital in Tehran. The presence of bacteriophage encoded virulence factors and resistance to oxacillin enable bacteria to produce a broad spectrum range of diseases. © 2016 Infectious Desieases and Tropical Medicine Research Center.
