- Department of microbiology, Kerman University of Medical Sciences
- M.R. Shakibaie earned his PhD from University of Pune India from 1992 to 1997. His thesis was” Molecular Genetics of ... moreM.R. Shakibaie earned his PhD from University of Pune India from 1992 to 1997. His thesis was” Molecular Genetics of plasmid Mediated Silver and Antibiotic Resistances in Acinetobacter baumannii”. He completed one year Postdoctoral research training at Aquatic Microbial Lab in Mysore, India during 2006. His research title was Horizontal Gene Transfer in Gram Negative Bacteria. Dr. Shakibaie Joined the Department of Microbiology, Kerman University of Medical Sciences in 1998. He guided more than 34 master (M.Sc.) and 4 PhD thesis and projected. He received university award for best researcher in 20013 and 2017 MEMBERSHIP IN SCIENTIFIC SOCIETIES Member, New York Academy of Science, Science Advisory Board (USA) Member, Asian -Pacific Research Foundation for Infectious Diseases (ARFFID) Affiliated member of European Society for Microbiologists (FEMS) Member of Iranian Society of Microbiology Editorial Board Member – JMC (Journal of Microscopic Creatures) Editorial board World Academy of Sciences (Waset) Editor of International Journal Biological and Life Sciences Editorial team J Biotechnology and Molecular Biology Review Editor of Current Research Journal of Biological Sciences Editor team of African Journal of Bacteriology Research - Academic Journals Editorial board of Current Research Journal of Biological Sciences, Maxwell Scientific organization Editorial team Journal of Environmental Health Science and Engineering Editor Journal of report of biochemistry and molecular biology Member Iranian biotechnology society.edit
"This book briefly describes the basic molecular bacteriology including bacterial chromosome, molecular techniques used in bacteriology, quorum sensing, Bacterial signal transduction, gene transfer among bacteria in the... more
"This book briefly describes the basic molecular bacteriology including bacterial chromosome, molecular techniques used in bacteriology, quorum sensing, Bacterial signal transduction, gene transfer among bacteria in the natural environment, mitochondrial DNA, Index and References……... ISBN1449542832 EAN‐139781449542832 Primary Category Science / General Publication Date October 4 2009 Language English Authored by Dr Mohammad Rza ‐ Shakibaie Ph.D."
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Background and objectives: The objectives of this study were to evaluate the antibiotic resistance profiles, biofilm formation, presence of antigen 43 (Ag43) gene, and transfer of antibiotic resistance phenotype among non-O157 Shiga toxin... more
Background and objectives: The objectives of this study were to evaluate the antibiotic resistance profiles, biofilm formation, presence of antigen 43 (Ag43) gene, and transfer of antibiotic resistance phenotype among non-O157 Shiga toxin producing Escherichia coli (STEC). Materials and methods: From October 2014 to November 2015 a total of 276 stool samples were collected from healthy calves, goats and 395 patients with the sign of nonbloody diarrhea and screened for presence of stx and serotype O157 genes by polymerase chain reaction (PCR) technique. Susceptibility to 14 antibiotics was determined as per CLSI guideline. Presence of Ag43 and intimin (eaeA) genes were detected by PCR. Biofilm formation was measured by microtiter plate method. Conjugation was carried out by membrane filter technique. Results: We isolated 74 (93.6%) non-O157 STEC strains from 41 calves, 33 goats and 5 (6.3%) patients' stools, however, no O157 serotype was detected in our study. Resistance was observed most commonly to tobramycin (66.2%), kanamycin (48.6%), and amikacin (29.7%) and less frequently to ciprofloxacin (4.1%), amoxicillin-clavulanic acid (5.4%), and ceftriaxone (9.5%) in isolates recovered from calves and goats fecal samples, whereas, all human isolates were sensitive to ceftazidime, ciprofloxacin, tobramycin and imipenem, respectively. Furthermore, Ag43 was detected in 60 STEC isolated from animals and 5 human origins (no eaeA gene was found in this study). Biofilm formation from Ag43+ and Ag43- colonies showed 20 isolates with strong biofilm activities. Cefotaxime resistance phenotype was transferred to E. coli ATCC 25922.1 (Nalr) by conjugation at a frequency of 1.6×10-4. Conclusion: From the above results we concluded that, human infections with non-O157 STEC were significantly low in Kerman. Ag43 was insignificant with biofilm quantity in most cases.
Research Interests: Microbiology, Biology, Medicine, Pubmed, Cefotaxime, and 3 moreCiprofloxacin, Imipenem, and Ceftazidime
Aim: The present study was conducted to detect the occurrence, serogroups, virulence genes and phylogenetic relationship of shiga toxin-producing Escherichia coli (STEC) in human, clave and goat in Kerman (southeast of Iran). Background:... more
Aim: The present study was conducted to detect the occurrence, serogroups, virulence genes and phylogenetic relationship of shiga toxin-producing Escherichia coli (STEC) in human, clave and goat in Kerman (southeast of Iran). Background: STEC have emerged as the important foodborne zoonotic pathogens causing human gastrointestinal disease and confirming the risk to public health. Methods: A total of 671 fecal samples were collected from diarrheic patients (n=395) and healthy calves (n=156) and goats (n=120) and screened for the presence of stx gene. Furthermore, the prevalence of stx1 and stx2 variants, serotypes (O157, O145, O103, O26, O111, O91, O128, and O45), phylogenetic groups and the presence of ehxA, eae, hylA, iha and saa virulence genes were studied. Results: Prevalence of STEC in human diarrheic isolates was 1.3% (5 isolates), in claves was 26.3% (41 isolates) and in goats was 27.5% (33 isolates). stx1 gene was the most prevalent variant and detected in 75 isolates. Furthermore, stx1c was the most predominant stx subtype, found in 56 isolates. The ehxA identified in 36 (45.6%) isolates, followed by iha 5 (6.3%), eaeA 4 (5.1%), hlyA 2 (2.5%) and saa 2 (2.5%). Most of the isolates belonged to phylogroup B1. Only two O26 and one O91 isolates were detected in our study. Conclusion: Our results show that STEC strains were widespread among healthy domestic animals in the southeast of Iran.
Research Interests: Microbiology, Biology, Medicine, Virulence, Escherichia coli, and 6 morePubmed, Feces, Shiga Toxin, Phylogenetic Tree, STX, and Serotype
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Research Interests: Medical Microbiology, Biology, Horizontal Gene Transfer, Medicine, Hospitals, and 15 moreIran, Biological Sciences, Humans, Female, Male, DNA fingerprinting, Integron, Integrons, Genotype, Adult, Acinetobacter baumannii, Acinetobacter Infections, Beta Lactamases, alleles, and Medical and Health Sciences
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Background: Chronic supportive otitis media (CSOM) is one of the commonest illnesses in ENT practice. This study was conducted to find out the various aerobic microorganisms associated with CSOM and their current antimicrobial... more
Background: Chronic supportive otitis media (CSOM) is one of the commonest illnesses in ENT practice. This study was conducted to find out the various aerobic microorganisms associated with CSOM and their current antimicrobial susceptibility patterns to commonly used antimicrobials. Methods: samples were collected from 117 clinically diagnosed cases of CSOM and processed according to standard protocols. Results: Out of 117 CSOM cases, 105 (86%) showed positive bacterial culture. The Staphylococcus aureus was the ...
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Background and Objectives: Due to the unique physicochemical properties of selenium nanoparticles (Se NPs), identification of microbial strains capable to biosynthesize Se NPs has recently attracted attention. The current study aimed at... more
Background and Objectives: Due to the unique physicochemical properties of selenium nanoparticles (Se NPs), identification of microbial strains capable to biosynthesize Se NPs has recently attracted attention. The current study aimed at introducing Se NPs producing actinomycete strain, characterizing Se NPs as well as evaluating its cytotoxic effect against breast cancer cell line (MCF-7). Materials and Methods: In the present laboratory investigation, first, the Se NPs producing strain was isolated from soil samples. The selected isolate was then identified using morphological and biochemical examinations as well as 16S rDNA sequencing protocol. The UV-visible spectrum, particle-size distribution (PSD) pattern, Fourier-transform infrared (FTIR), and energy-dispersive X-ray (EDX) profiles of the nanostructures as well as transmission electron microscope (TEM) image of Se NPs were determined. In order to evaluate the cytotoxicity of the Se NPs, the MTT (Methylthiazolyldiphenyl-tetrazolium bromide) based colorimetric protocol was applied where the viability percent was firstly determined and then the related IC50 (Half inhibitory concentration) was calculated. Results: The selected bacterial isolate was identified as Streptomyces lavendulae FSHJ9. TEM micrographs of the biogenic Se NPs exhibited spherical nanostructures with the size range of 28–123 nm. The FTIR pattern showed no functional group present on the surface of Se NPs. The obtained results of cytotoxicity revealed that IC50 of Se NPs (77.1±42.23 µg/mL) was more than IC50 of sodium selenite (3.0±41.53 µg/mL). Conclusion: The results of the present study showed that Streptomyces lavendulae FSHJ9 was able to produce Se NPs. The produced biogenic Se NPs, after performing complementary studies, might be applied as supplement in human food and animal feeding. Key words: Selenium nanoparticles, Biosynthesis, Streptomyces, Cytotoxicity, MCF-7 cell line Funding: This study was funded by Kerman University of Medical Sciences. Conflict of interest: None declared. Ethical approval: The Ethics Committee of Kerman University of Medical Sciences approved the study (930160). How to cite this article: Shakibaie M, Jafari M, Ameri A, Rahimi H.R, Forootanfar H. Biosynthesis and Physicochemical Characterization, and Cytotoxic Evaluation of Selenium Nanoparticles Produced by Streptomyces Lavendulae FSHJ9 Against MCF-7 Cell Line. J Rafsanjan Univ Med Sci 2018; 17 (7): 625-38. [Farsi]
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Abstract Colistin is drug of choice for treatment of carbapenem-resistant Acinetobacter baumannii infections. Unfortunately, global increase in clinical outbreaks of colistin and carbapenem resistant A. baumannii infections is on the rise... more
Abstract Colistin is drug of choice for treatment of carbapenem-resistant Acinetobacter baumannii infections. Unfortunately, global increase in clinical outbreaks of colistin and carbapenem resistant A. baumannii infections is on the rise and cause public health concern. In the present study, a total of 187 A. baumannii recovered from specimens of 240 patients admitted to intensive care units (ICUs) of two hospitals in Kerman, Iran during 2017–2018. Among the isolates, we found four extensive drug-resistant (XDR) with Minimum Inhibitory Concentration (MIC) ≥4 μg/mL against colistin. The Col-R isolates harbored blaOXA–51 and blaOXA-23 carbapenemase genes, exhibited resistance to all antibiotic classes except tigecycline and ampicillin-sulbactam. They belonged to clonal complex 2, a new MLST type 1752 and displayed identical RAPD-PCR fingerprints. Phylogenetic tree analysis suggested that, the Col-R A. baumannii emerged by endogenous mutations rather than acquisition of preexisting clones. Expressions of pmrCAB by quantitative real-time PCR (qRT-PCR) revealed 8 and 7 folds increased in the transcription level of pmrB/C genes in strain 1 grown in presence of 16 μg/mL colistin (p ≤ 0.01). However, no change in the expression of the pmrA was observed. Furthermore, DNA sequencing of Col-R genes illustrated three nonsynonymous substitutions in the LpxA (N136 → K), LpxC (P293 → Q), and PmrB (V21 → F, S28 → R, I149 → F) in the strains 1 and 3, respectively showing MIC 32 μg/mL against colistin. Multiple amino acids alignments displayed several substitutions in N-terminal region of PmrB. In conclusion, the above results provide valuable insights into the mechanism of Col-R in A. baumannii and the expressions of relative genes.
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Transfer of antibiotic resistance genes among gram negative bacteria in sewage and lake water and easy access of these bacteria to the community are major environmental and public health concern. The aim of this study was to determine... more
Transfer of antibiotic resistance genes among gram negative bacteria in sewage and lake water and easy access of these bacteria to the community are major environmental and public health concern. The aim of this study was to determine transfer of the antimicrobial resistance genes from resistant to susceptible gram negative bacteria in the sewage and lake water by conjugation process and to determine the influence of some physico-chemical parameters of sewage and lake water on the transfer of these resistance genes. For this reason, we isolated 20 liter of each sewage and lake water from coconut area within university campus and Lingambudi lake respectively in Mysore city, India, during monsoon season and studied different physical parameters of the water samples like pH, temperature, conductivity turbidity and color as well as chemical parameters like BOD, COD, field DO and total chloride ion. The gram negative bacteria were isolated and identified from the above water samples using microbiological and biochemical methods and their sensitivity to different antibiotics was determined by disc diffusion break point assay. Conjugation between two multiple antibiotic resistant isolates Pseudomonas aeuginosa and E. coli as donor and E. coli Rif(r) (sensitive to antibiotics) as recipient were carried out in 5ml sterile sewage and lake water. All isolates were resistant to Am, moderately resistant to Te and E, while majority were sensitive to Cip, Gm and CAZ antibiotics. Horizontal transfer of antibiotic resistance genes by conjugation process revealed transfer of Gm, Te and E resistant genes from Ps. aeruginosa to E. coli Rif(r) recipient with mean frequency of +/- 2.3 x 10(-4) in sewage and +/- 2.6 x 10(-6) in lake water respectively Frequency of conjugation in sewage was two fold more as compared to lake water (p< or =0.05). Co- transfer study revealed simultaneous transfer of above resistant markers together to the recipient cells. As the above results indicate, due to selective pressure in sewage (presence of antibiotics), the isolates from sewage were more resistant to different antibiotics as compared to those from lake water. Furthermore, these resistance genes can transfer to sensitive bacteria by conjugation. Physico-chemical parameters of water may play role in this process.
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Mastoparan B (MP‐B) is an amphiphilic peptide with a potent antimicrobial activity against most Gram‐negative bacteria. However, there is little information available on the inhibition of the Acinetobacter baumannii... more
Mastoparan B (MP‐B) is an amphiphilic peptide with a potent antimicrobial activity against most Gram‐negative bacteria. However, there is little information available on the inhibition of the Acinetobacter baumannii resistance‐nodulation‐cell‐division (RND) efflux pump using this antimicrobial peptide. Here, we carried out a series of in‐silico experiments to find the mechanisms underlying the anti‐efflux activity of MP‐B using a multi‐drug resistant (MDR) strain of A. baumannii (AB). According to our findings, MP‐B demonstrated a potent antibacterial activity against an MDR‐AB (minimum inhibitory concentration [MIC] = 1 μg/mL) followed by a 20‐fold reduction in the adeB gene expression in the presence of sub‐MIC of this peptide. Using Groningen Machine for Chemicals Simulation (GROMACS) via PyMOL Graphical User Interface (GUI), (we observed that, the AdeB transporter had conserved helix‐turn‐helix regions and a tight pore rich in Phe and Ala residues. To understand how inhibition o...
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No report exists on the role of Mastoparan B (MP-B) as an RND efflux pump inhibitor in multi-drug resistant (MDR) Acinetobacter baumannii. Here, we performed a series of in-silico experiments to predict the inhibition of the AdeB efflux... more
No report exists on the role of Mastoparan B (MP-B) as an RND efflux pump inhibitor in multi-drug resistant (MDR) Acinetobacter baumannii. Here, we performed a series of in-silico experiments to predict the inhibition of the AdeB efflux pump by MP-B as a drug target agent. For this reason, an MDR strain of A. baumannii was subjected to minimum inhibitory concentration (MIC) against 12 antibiotics as well as MP-B. Expression of the a deB gene in the absence and presence of sub-MIC of MP-B was studied by qRT-PCR. It was found that MP-B had potent antimicrobial activity (MIC=1 µg/ml) associated with a 20-fold decrease in its expression at sub-MIC of MP-B. The stereochemical analysis using several automated servers confirmed that the AdeB is an inner membrane of the RND tripartite complex system with helix-turn-helix conformation and a pore rich in Phe, Ala, and Lys residue. The best model that showed high accuracy (Z=1.2, C=1.41, TM=0.99, and RMSD=4.4) was selected for docking purposes...
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Antibiotic-resistant Pseudomonas aeruginosa infections are usually difficult to treat, and there are limited antibiotics for treating them. Increased antibiotic resistance of this bacterium, especially in a multidrug form, has caused many... more
Antibiotic-resistant Pseudomonas aeruginosa infections are usually difficult to treat, and there are limited antibiotics for treating them. Increased antibiotic resistance of this bacterium, especially in a multidrug form, has caused many problems for treatment. Nowadays, metal nanoparticles are considered as appropriate alternatives to antibiotics. The objective of the present study was to investigate the effect of gold nanoparticles on the expression of MexB and MexA genes in Pseudomonas aeruginosa isolates.Pseudomonas aeruginosa isolate was identified using biochemical tests and an API kit. The antibiotic sensitivitytest for different antibiotics was performed withthe Kirby-Bauer test according to the CLSI standard. The presence of MexB and MexA genes was assessed by PCR. The effect of gold nanoparticles was investigated by microdilution to evaluate the minimum inhibitory concentration, and the expression of MexB and MexA treated genes was done with silver nanoparticles by the Re...
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Background and Aims: screening of soil samples to isolate microorganisms able to produce antibiotic is the first step in novel antibiotic production. In the present study isolation of a bacterial strain capable to show antimicrobial... more
Background and Aims: screening of soil samples to isolate microorganisms able to produce antibiotic is the first step in novel antibiotic production. In the present study isolation of a bacterial strain capable to show antimicrobial activity on 6 bacterial and 3 fungal standard strains was aimed. Methods: soil samples were collected from different green places and parks in Kerman, Iran. After spreading of each soil extract on agar plate containing standard bacterial and fungal strains incubation was done to observe inhibition zone. The antibiotic ...
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Conclusions: Five actinomycetes with inhibitory effect on bacterial and fungal pathogens were introduced in the present study among which isolate D5 showed highest activity on both Gram positive and Gram negative bacterial strains as well... more
Conclusions: Five actinomycetes with inhibitory effect on bacterial and fungal pathogens were introduced in the present study among which isolate D5 showed highest activity on both Gram positive and Gram negative bacterial strains as well as fungal pathogens. Keywords: Actinomycetes; 16S rDNA; Antibacterial activity; Antifungal activity
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Background and objectives: In present study we aimed to clone the luxI gene encoding N-acyl-homoserine synthase detected in clinical isolates of Acinetobacter baumannii and study its expression in Escherichia coli transformants. Materials... more
Background and objectives: In present study we aimed to clone the luxI gene encoding N-acyl-homoserine synthase detected in clinical isolates of Acinetobacter baumannii and study its expression in Escherichia coli transformants. Materials and methods: Four A. baumannii hospital strains which demonstrated strong biofilm activity were selected in this investigation. The presence of luxI gene was detected using PCR technique. Purified PCR product DNA was initially cloned into pTG19 and transformed to E. coli DH5α. The gene was then recovered from agarose gel and ligated by T4 DNA ligase into pET28a expression vector using NdeI and XhoI enzymes. pET28a + luxI was transformed into E. coli BL21 (DE3). The luxI putative gene was further detected in the transformants by colony PCR. Expression of the luxI gene in the recombinant E. coli BL21 cells was studied by quantitative real time PCR (qRT-PCR) and the presence of N-acylhomoserine lactone (AHL) was checked by colorimetric assay and Fourier Transform Infra-Red (FT-IR) spectroscopy. Results: We successfully cloned AHL gene from A. baumannii strain 23 to pET28a expression vector. There was four fold increases in expression of luxI in the transformants (P ≤ 0.05). It was found that, strain 23 and the transformants showed highest amount of AHL activity (OD = 1.524). The FT-IR analysis indicated stretching C=O bond of the lactone ring and primary amides (N=H) at 1764.69 cm(-1) and 1659.23 cm(-1) respectively. Conclusion: From above results we concluded that, luxI in A. baumannii is indeed responsible for AHL production and not regulation and pET28a vector allows efficient AHL expression in E. coli BL21 transformants.
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In present study we aimed to clone the luxI gene encoding N-acyl-homoserine synthase detected in clinical isolates of Acinetobacter baumannii and study its expression in Escherichia coli transformants. Four A. baumannii hospital strains... more
In present study we aimed to clone the luxI gene encoding N-acyl-homoserine synthase detected in clinical isolates of Acinetobacter baumannii and study its expression in Escherichia coli transformants. Four A. baumannii hospital strains which demonstrated strong biofilm activity were selected in this investigation. The presence of luxI gene was detected using PCR technique. Purified PCR product DNA was initially cloned into pTG19 and transformed to E. coli DH5α. The gene was then recovered from agarose gel and ligated by T4 DNA ligase into pET28a expression vector using NdeI and XhoI enzymes. pET28a + luxI was transformed into E. coli BL21 (DE3). The luxI putative gene was further detected in the transformants by colony PCR. Expression of the luxI gene in the recombinant E. coli BL21 cells was studied by quantitative real time PCR (qRT-PCR) and the presence of N-acylhomoserine lactone (AHL) was checked by colorimetric assay and Fourier Transform Infra-Red (FT-IR) spectroscopy. We su...
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www.RBMB.net Biochemical detection of N-Acyl homoserine lactone from biofilm-forming uropathogenic Escherichia coli isolated from urinary tract infection samples
The objectives of this study were to evaluate the antibiotic resistance profiles, biofilm formation, presence of antigen 43 (43) gene, and transfer of antibiotic resistance phenotype among non-O157 Shiga toxin producing (STEC). From... more
The objectives of this study were to evaluate the antibiotic resistance profiles, biofilm formation, presence of antigen 43 (43) gene, and transfer of antibiotic resistance phenotype among non-O157 Shiga toxin producing (STEC). From October 2014 to November 2015 a total of 276 stool samples were collected from healthy calves, goats and 395 patients with the sign of nonbloody diarrhea and screened for presence of and serotype O157 genes by polymerase chain reaction (PCR) technique. Susceptibility to 14 antibiotics was determined as per CLSI guideline. Presence of 43 and intimin () genes were detected by PCR. Biofilm formation was measured by microtiter plate method. Conjugation was carried out by membrane filter technique. We isolated 74 (93.6%) non-O157 STEC strains from 41 calves, 33 goats and 5 (6.3%) patients' stools, however, no O157 serotype was detected in our study. Resistance was observed most commonly to tobramycin (66.2%), kanamycin (48.6%), and amikacin (29.7%) and le...
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Acinetobacter baumannii (AB) is one of the most common causes of nosocomial infections. Therefore, it is of interest to design and develop drugs against Acinetobacter baumannii. A strain of AB showing MIC 32 μg/ml against colistin was... more
Acinetobacter baumannii (AB) is one of the most common causes of nosocomial infections. Therefore, it is of interest to design and develop drugs against Acinetobacter baumannii. A strain of AB showing MIC 32 μg/ml against colistin was isolated from a hospital environment in Iran. Hence, we document data to glean insights from the molecular docking analysis of colistin with the PmrA protein from this bacterium.
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In this study the mechanism of chromium (Cr) and cop-per (Cu) resistance in Pseudomonas aeruginosa was investigated. For this reason, 50 isolates of this micro-organism were separated from 345 burn patients hos-pitalized in burn unit of... more
In this study the mechanism of chromium (Cr) and cop-per (Cu) resistance in Pseudomonas aeruginosa was investigated. For this reason, 50 isolates of this micro-organism were separated from 345 burn patients hos-pitalized in burn unit of Kerman hospital, Iran, during
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Objective(s): Pseudomonas aeruginosa is one of the most important nosocomial pathogens causing a high rate of mortality among hospitalized patients. Herein, we report the prevalence of antibiotic resistance genes, class 1 integrons, major... more
Objective(s): Pseudomonas aeruginosa is one of the most important nosocomial pathogens causing a high rate of mortality among hospitalized patients. Herein, we report the prevalence of antibiotic resistance genes, class 1 integrons, major virulence genes and clonal relationship among multidrug- resistant (MDR) P. aeruginosa, isolated from four referral hospitals in the southeast of Iran. Materials and Methods: In this study, 208 isolates of P. aeruginosa were collected from four referral hospitals in southeast of Iran. Disk diffusion method was used to determine susceptibility to 13 antibacterial agents. AmpC was detected by phenotypic method and β-lactamase genes, virulence genes and class 1 integrons were detected by PCR. Clonal relationship of the isolates was determined by RAPD-PCR. Results: All the isolates were susceptible to polymyxin-B and colistin. Overall, 40.4% of the isolates were MDR, among which resistance to third generation cephalosporins, aminoglycosides, and carbap...
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This book briefly describes the basic molecular bacteriology including bacterial chromosome, molecular techniques used in bacteriology, quorum sensing, Bacterial signal transduction, gene transfer among bacteria in the natural... more
This book briefly describes the basic molecular
bacteriology including bacterial chromosome, molecular
techniques used in bacteriology, quorum sensing, Bacterial signal
transduction, gene transfer among bacteria in the natural
environment, mitochondrial DNA, Index and References……...
ISBN1449542832
EAN‐139781449542832
Primary Category Science / General
Publication Date October 4 2009
Language English
Authored by Dr Mohammad Rza ‐ Shakibaie Ph.D.
bacteriology including bacterial chromosome, molecular
techniques used in bacteriology, quorum sensing, Bacterial signal
transduction, gene transfer among bacteria in the natural
environment, mitochondrial DNA, Index and References……...
ISBN1449542832
EAN‐139781449542832
Primary Category Science / General
Publication Date October 4 2009
Language English
Authored by Dr Mohammad Rza ‐ Shakibaie Ph.D.
Research Interests:
Introduction: Acinetobacter baumannii (AB) is a Gram-negative bacteria associated with various hospital infections. The present study deals with in silico analysis of the biofilm-associated protein (Bap) in this pathogen. Method:... more
Introduction: Acinetobacter baumannii (AB) is a Gram-negative bacteria associated with various hospital infections. The present study deals with in silico analysis of the biofilm-associated protein (Bap) in this pathogen. Method: Sixty-eight multi-drug resistant (MDR) AB were isolated from two hospitals in Kerman, Iran. Biofilm-formation was investigated using the microtiter method and PCR followed by sequencing to detect the bap gene in the strongest biofilmforming isolate. The physicochemical parameters of Bap protein were determined by the ProtParam tool using the ExPasy program. The 3D models from the primary amino acid sequence were constructed using the I-TASSER modeling platform based on multiple-threading alignments by LOMETS. Nevertheless, to ensure the correct initial structure, the protein was minimized in energy through the 3DRefine software of the deep learning system. For the accuracy of predicted models, we calculated the orientation of dihedral angles, including the phi (φ) and psi (ψ) and backbone conformation using the PROCHECK module of the PDB Sum server. The domains and key amino acids involved in protein structure were studied by the Pfam and Interpro softwares. Results: Analysis of the amino acid content of the Bap protein revealed the absence of Arg and Cys in the protein structure. The Bap protein exhibited 99.6% identity with other Bap sequences in the GenBank database. Stereochemical simulation identified 19 antiparallel β-sheets with two small αhelices. The N-terminal of Bap protein formed oligomers that mediate cellular adhesion. Conclusion: This study adds considerable information about Bap protein 3D structure, its conformation, domain analysis, and amino acids involved in cellular attachment.
Background: There is limited information on the 3D prediction and modeling of the colistin resistance-associated proteins PmrA/B TCS in Acinetobacter baumannii. We aimed to evaluate the stereochemical structure and domain characterization... more
Background: There is limited information on the 3D prediction and modeling of the colistin resistance-associated proteins PmrA/B TCS in Acinetobacter baumannii. We aimed to evaluate the stereochemical structure and domain characterization of PmrA/B in an A. baumannii isolate resistant to high-level colistin, using bioinformatics tools. Methods: The species of the isolate and its susceptibility to colistin were confirmed by PCR-sequencing and MIC assay, respectively. For 3D prediction of the PmrA/B, we used 16 template models with the highest quality (e-value <1 × 10−50). Results: Prediction of the PmrA structure revealed a monomeric non-redundant protein consisting of 28 α-helices and 22 β-sheets. The PmrA DNA-binding motif displayed three antiparallel α-helices, followed by three β-sheets, and was bond to the major groove of DNA by intermolecular van der Waals bonds through amino acids Lys, Asp, His, and Arg, respectively. Superimposition of the deduced PmrA 3D structure with the closely related PmrA protein model (GenBank no. WP_071210493.1) revealed no distortion in conformation, due to Glu→Lys substitution at position 218. Similarly, the PmrB protein structure displayed 24 α-helices and 13 β-sheets. In our case, His251 acted as a phosphate receptor in the HisKA domain. The amino acid substitutions were mainly observed at the putative N-terminus region of the protein. Furthermore, two substitutions (Lys21→Ser and Ser28→Arg) in the transmembrane domain were detected. Conclusion: The DNA-binding motif of PmrA is highly conserved, though the N-terminal fragment of PmrB showed a high rate of base substitutions. This research provides valuable insights into the mechanism of Col-R in A. baumannii.
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Background: There is limited information on the 3D prediction and modeling of the colistin resistance-associated proteins PmrA/B TCS in Acinetobacter baumannii. We aimed to evaluate the stereochemical structure and domain characterization... more
Background: There is limited information on the 3D prediction and modeling of the colistin resistance-associated proteins PmrA/B TCS in Acinetobacter baumannii. We aimed to evaluate the stereochemical structure and domain characterization of PmrA/B in an A. baumannii isolate resistant to high-level colistin, using bioinformatics tools. Methods: The species of the isolate and its susceptibility to colistin were confirmed by PCR-sequencing and MIC assay, respectively. For 3D prediction of the PmrA/B, we used 16 template models with the highest quality (e-value <1 × 10−50). Results: Prediction of the PmrA structure revealed a monomeric non-redundant protein consisting of 28 α-helices and 22 β-sheets. The PmrA DNA-binding motif displayed three antiparallel α-helices, followed by three β-sheets, and was bond to the major groove of DNA by intermolecular van der Waals bonds through amino acids Lys, Asp, His, and Arg, respectively. Superimposition of the deduced PmrA 3D structure with the closely related PmrA protein model (GenBank no. WP_071210493.1) revealed no distortion in conformation, due to Glu→Lys substitution at position 218. Similarly, the PmrB protein structure displayed 24 α-helices and 13 β-sheets. In our case, His251 acted as a phosphate receptor in the HisKA domain. The amino acid substitutions were mainly observed at the putative N-terminus region of the protein. Furthermore, two substitutions (Lys21→Ser and Ser28→Arg) in the transmembrane domain were detected. Conclusion: The DNA-binding motif of PmrA is highly conserved, though the N-terminal fragment of PmrB showed a high rate of base substitutions. This research provides valuable insights into the mechanism of Col-R in A. baumannii.
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Background: The aim of this study was to evaluate the susceptibility of catheter-related Klebsiella pneumoniae isolates to two biocides (benzalkonium chloride and Deconex) under biofilm and planktonic conditions. Methods: A total of 85... more
Background: The aim of this study was to evaluate the susceptibility of catheter-related Klebsiella pneumoniae isolates to two biocides (benzalkonium chloride and
Deconex) under biofilm and planktonic conditions.
Methods: A total of 85 strains of K. pneumoniae were isolated from catheters of inpatients hospitalized in four hospitals in Kerman, Iran. Susceptibility to antibiotics and
biocides under biofilm and planktonic growths was performed using the microdilution method. Antibiofilm activity of the biocides was determined by microtiter assay.
Biofilm eradication was carried out at different periods of time. The presence of cepA and qacEΔ1 genes were detected by polymerase chain reaction (PCR).
Results: We found that 15% (n = 12) of the isolates showed strong biofilm activity, 40% (n = 35) displayed moderate activity, 30% (n = 26) demonstrated weak activity,
and 15% (n = 12) showed no attachment to microtiter wells. Both the biocides had profound inhibitory activities on planktonic cells (average minimum inhibitory
concentration [MIC] 0.06 ± 0.2 mg/ml for Deconex and 0.03 ± 0.1 mg/ml for benzalkonium chloride). They exerted the least antibiofilm activity at a sub-MIC
concentration of 0.015 mg/ml. The isolates that formed high biofilm also harboured the cepA gene. Furthermore, a considerable increase in MIC to piperacillin/tazobactam,
tetracycline, and cefotaxime was observed for cells grown in biofilm conditions for 24 hours, but all the isolates were sensitive to colistin and tigecycline. These differences
were statistically significant, with a p-value of < 0.05. Most of the biofilms were eradicated from the microtiter plate within 30 minutes’ exposure to these biocides.
Conclusions: As the data indicates, benzalkonium chloride and Deconex have good potential as hospital disinfectants for catheter-related infections caused by K.
pneumoniae in planktonic conditions. Antimicrobial stewardship programs must be performed weekly in our hospitals to improve the quality of antimicrobial use, reduce
the use of antibiotics, and shorten the length of hospital stay without increasing mortality rates.
Deconex) under biofilm and planktonic conditions.
Methods: A total of 85 strains of K. pneumoniae were isolated from catheters of inpatients hospitalized in four hospitals in Kerman, Iran. Susceptibility to antibiotics and
biocides under biofilm and planktonic growths was performed using the microdilution method. Antibiofilm activity of the biocides was determined by microtiter assay.
Biofilm eradication was carried out at different periods of time. The presence of cepA and qacEΔ1 genes were detected by polymerase chain reaction (PCR).
Results: We found that 15% (n = 12) of the isolates showed strong biofilm activity, 40% (n = 35) displayed moderate activity, 30% (n = 26) demonstrated weak activity,
and 15% (n = 12) showed no attachment to microtiter wells. Both the biocides had profound inhibitory activities on planktonic cells (average minimum inhibitory
concentration [MIC] 0.06 ± 0.2 mg/ml for Deconex and 0.03 ± 0.1 mg/ml for benzalkonium chloride). They exerted the least antibiofilm activity at a sub-MIC
concentration of 0.015 mg/ml. The isolates that formed high biofilm also harboured the cepA gene. Furthermore, a considerable increase in MIC to piperacillin/tazobactam,
tetracycline, and cefotaxime was observed for cells grown in biofilm conditions for 24 hours, but all the isolates were sensitive to colistin and tigecycline. These differences
were statistically significant, with a p-value of < 0.05. Most of the biofilms were eradicated from the microtiter plate within 30 minutes’ exposure to these biocides.
Conclusions: As the data indicates, benzalkonium chloride and Deconex have good potential as hospital disinfectants for catheter-related infections caused by K.
pneumoniae in planktonic conditions. Antimicrobial stewardship programs must be performed weekly in our hospitals to improve the quality of antimicrobial use, reduce
the use of antibiotics, and shorten the length of hospital stay without increasing mortality rates.
Research Interests:
Research Interests:
The focal points of the research in our lab are plasmid mediated antibiotic and metal resistance, biofilm formation and its genes in hospital isolates of Acinetobacter. Quorum sensing and signal transduction in Acinetobacter and also... more
The focal points of the research in our lab are plasmid mediated antibiotic and metal resistance, biofilm formation and its genes in hospital isolates of Acinetobacter. Quorum sensing and signal transduction in Acinetobacter and also enhancing bioremediation of heavy metals using genetic engineering organisms, cloning some genes responsible for biofilm formation and also we are using genetic engineered bacteria for decreasing the CO2 emission. All these steps are subject to elaborate control by numerous regulatory proteins and small effectors. We are working on biogenic nanometals for disruption of biofilm and introducing potent nano-drugs. Our goal is to achieve synthesis of a nano-drug with potent antimicrobial and antibiofilm activity and less toxicity. The important factor for my research group also is cost. The nanotechnology allows us to develop a cost effective drug especially for poor countries in Africa. My students are working in the molecular design of nano-drug and delivery system by bioinformatics systems. Recently we studied possibility of existence of antibiotic resistant islands (ARI) in bacterial chromosome like Pathogenicity Island and the genes in these islands can transfer effectively by integrons transposons or by plasmids to other bacterial strains. My team for the first time submitted three genes and integrons class 1 to GenBank NCBI and found new IMP55. Similarly, for the first time we suggested Dr. Shakibaie MR Stages of biofilm formation from platonic
