Publications by authors named "Ebrahim Kouhsari"

32 Publications

Comparison of toxin-antitoxin expression among drug-susceptible and drug-resistant clinical isolates of Mycobacterium tuberculosis.

Adv Respir Med 2021 ;89(2):110-114

Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran.

Introduction: Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), is a significant global public health threat. Besides extensive multidrug resistance, MTB possesses several properties for long-term viability in the host as well as stress adaptation and resistance in harsh conditions. The role of toxin-antitoxin (TA) systems in disseminating and maintaining antimicrobial resistance in bacterial populations has also been demonstrated. This study aimed to evaluate differences in expression of MazEF (a well-known TA system) related genes (mazE3, mazF3, mazE6, and mazF6) amongst drug-susceptible and resistant MTB isolates in Iran.

Material And Methods: A total of 20 confirmed clinical isolates of MTB including 10 drug-susceptible and 10 drug-resistant (nine MDR, and one XDR) species were included in this study. M. tuberculosis H37Rv was used as the standard strain. RNA extraction, cDNA synthesis, and relative quantitative real-time PCR were performed according to the standard procedures.

Results: Our analysis indicated significant enhanced expression of the mazE6 antitoxin gene in drug-susceptible isolates compared to drug-resistant isolates and the standard strain. The expression of the mazF6 toxin gene was also increased in drug-susceptible isolates compared with the standard strain. In drug-resistant isolates, the expression levels of mazF3 and mazF6 genes were significantly higher than that in the susceptible isolates and the standard strain.

Conclusions: In this study, there was significant overexpression of mazE6 in drug-susceptible isolates. As well, mazF3 and F6 were overexpressed in drug-resistant isolates when compared with the standard strain. The changes in expression levels of MazEF6 associated genes were greater than that of MazEF3 in both groups of isolates.
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http://dx.doi.org/10.5603/ARM.a2021.0033DOI Listing
January 2021

Clonal Lineage Analysis of Shigella flexneri Isolates Circulating in Ahvaz, Iran.

Clin Lab 2021 Apr;67(4)

Background: Shigellosis is a significant public health challenge particularly in developing countries, and the spread of antibiotic resistance genes through integron structures has become an important problem in the treatment of Shigellosis. The aim of this study was to investigate the genetic association of Shigella flexneri antibiotic resistant clones collected from Ahvaz between 2013 and 2015 by pulse field gel electrophoresis (PFGE) method.

Methods: A total of 45 S. flexneri isolates, which were resistant to ampicillin and cotrimoxazole, were obtained from patients with Shigellosis referred to Ahvaz hospitals during 2013 - 2015. PCR was performed to evaluate the frequency of Sul1, int1, blaOXA, and int2 genes. In addition, pulse field gel electrophoresis method was used to investigate the genetic relationship between 40 S. flexneri isolates.

Results: PCR results showed that the highest frequency was related to the sul1 gene with 80% (36 isolates) and the lowest frequency was related to class 2 integron with 15.5% (7 isolates); 31.11% (14 isolates) of the isolates were sul1 and int1. Also, 13.33% (6 isolates) had blaOXA and int1 genes, simultaneously. But none of the isolates had class 1 integrons and class 2 integrons at the same time. PFGE results showed 25 different pulsotype patterns, of which 16 isolates had their own unique pattern and were divided into 16 pulsotypes, and 27 isolates were divided into 9 pulsotypes.

Conclusions: int2 and sul1 resistance genes had an upward trend from 2013 to 2015 and the results of PFGE indicated a different origin of S. flexneri clones.
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http://dx.doi.org/10.7754/Clin.Lab.2020.200830DOI Listing
April 2021

Bedaquiline: Current status and future perspectives.

J Glob Antimicrob Resist 2021 Mar 5;25:48-59. Epub 2021 Mar 5.

Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

The development of drug-resistant tuberculosis (TB) is a major threat worldwide. Based on World Health Organization (WHO) reports, it is estimated that more than 500 000 new cases of drug-resistant TB occur annually. In addition, there are alarming reports of increasing multidrug-resistant TB (MDR-TB) and the emergence of extensively drug-resistant TB (XDR-TB) from different countries of the world. Therefore, new options for TB therapy are required. Bedaquiline (BDQ), a novel anti-TB drug, has significant minimum inhibitory concentrations (MICs) both against drug-susceptible and drug-resistant TB. Moreover, BDQ was recently approved for therapy of MDR-TB. The current narrative review summarises the available data on BDQ resistance, describes its antimicrobial properties, and provides new perspectives on clinical use of this novel anti-TB agent.
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http://dx.doi.org/10.1016/j.jgar.2021.02.017DOI Listing
March 2021

Neutrophil-to-Lymphocyte Ratio as a Poor Prognostic Factor in Iranian COVID-19 Patients.

Clin Lab 2021 Feb;67(2)

Background: We aimed to accumulate evidence that suggests the potential role of neutrophil-to-lymphocyte ratio (NLR) in determining the prognostic factor for COVID-19 patients.

Methods: A cohort of COVID-19 hospitalized patients at the Ilam University of Medical Sciences was analyzed. Logistic regression models were performed to identify the potential role of NLR in determining the prognostic factor for COVID-19 patients.

Results: The total number of in-hospital mortality was 43/328 (13.1%). Multivariate analysis identified that there was a 26% higher risk of in-hospital death for each unit increase in NLR (Odds ratio [OR] = 1.08; 95% confidence interval [95% CI], 1.01 to 1.14; p = 0.0147). Multivariate analysis identified that there was an 8% higher risk of in-hospital death for each unit increase in NLR (Odds ratio [OR] = 1.08; 95% confidence interval [95% CI], 1.01 to 1.14; p = 0.0147). Compared with patients in the NLR < 5 group, the NLR of patients in the NLR ≥ 5 group had a 16-fold higher risk of mortality (OR = 16.04; 95% CI, 1.14 to 224.95; p = 0.0395) after adjustment for potential confounders.

Conclusions: NLR is an independent risk factor of mortality COVID-19 patients.
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http://dx.doi.org/10.7754/Clin.Lab.2020.200726DOI Listing
February 2021

Clinical, epidemiological, laboratory, and radiological characteristics of novel Coronavirus (2019-nCoV) in retrospective studies: A systemic review and meta-analysis.

Indian J Med Microbiol 2021 Jan 4;39(1):104-115. Epub 2020 Nov 4.

Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran. Electronic address:

Background: In December 2019, a novel pneumonia related to the 2019 coronavirus unexpectedly developed in Wuhan, China. We aimed to review data of the novel Coronavirus (2019-nCoV) by analyzing all the published retrospective studies on the clinical, epidemiological, laboratory, and radiological characteristics of patients with 2019-nCoV.

Methods: We searched in four bibliographic databases PubMed, Scopus, Embase, and Web of Science) for studies March 10, 2020 focused on the clinical, epidemiological, laboratory, and radiological characteristics of patients with 2019-nCoV for meta-analysis. The Newcastle-Ottawa Scale was used to quality assessment, and publication bias was analyzed by Egger's test. In the meta-analysis, a random-effects model with Stata/SE software, v.14.1 (StataCorp, College Station, TX) was used to obtain a pooled incidence rate.

Results: Fifty studies were included in this systematic review and meta-analysis with 8815 patients and the mean age was 46 years and 4647 (52.7%) were male. The pooled incidences rate of clinical symptoms were: fever (83%, 95% CI: 0.77, 0.89), cough (59%, 95% CI: 0.48, 0.69), myalgia or fatigue (31%, 95% CI: 0.23, 0.39), sputum production (29%, 95% CI: 0.21, 0.39), and dyspnea (19%, 95% CI: 0.12, 0.26). The pooled incidence rate of acute respiratory distress syndrome (ARDS) was (22%, 95% CI: 0.00, 0.60).

Conclusion: The results of this systemic review and meta-analysis present a quantitative pooled incidence rate of different characters of 2019-nCoV and has great potential to develop diagnosis and patient's stratification in 2019-nCoV. However, this conclusions of this study still requisite to be warranted by more careful design, larger sample size multivariate studies to corroborate the results of this meta-analysis.
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http://dx.doi.org/10.1016/j.ijmmb.2020.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7667392PMC
January 2021

Tigecycline antibacterial activity, clinical effectiveness, and mechanisms and epidemiology of resistance: narrative review.

Eur J Clin Microbiol Infect Dis 2021 Jan 5. Epub 2021 Jan 5.

Department of Laboratory Sciences, School of Allied Medical Sciences, Ilam University of Medical sciences, Ilam, Iran.

Tigecycline is unique glycylcycline class of semisynthetic antimicrobial agents developed for the treatment of polymicrobial infections caused by multidrug-resistant Gram-positive and Gram-negative pathogens. Tigecycline evades the main tetracycline resistance genetic mechanisms, such as tetracycline-specific efflux pump acquisition and ribosomal protection, via the addition of a glycyclamide moiety to the 9-position of minocycline. The use of the parenteral form of tigecycline is approved for complicated skin and skin structure infections (excluding diabetes foot infection), complicated intra-abdominal infections, and community-acquired bacterial pneumonia in adults. New evidence also suggests the effectiveness of tigecycline for the treatment of severe Clostridioides difficile infections. Tigecycline showed in vitro susceptibility to Coxiella spp., Rickettsia spp., and multidrug-resistant Neisseria gonnorrhoeae strains which indicate the possible use of tigecycline in the treatment of infections caused by these pathogens. Except for intrinsic, or often reported resistance in some Gram-negatives, tigecycline is effective against a wide range of multidrug-resistant nosocomial pathogens. Herein, we summarize the currently available data on tigecycline pharmacokinetics and pharmacodynamics, its mechanism of action, the epidemiology of tigecycline resistance, and its clinical effectiveness.
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http://dx.doi.org/10.1007/s10096-020-04121-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7785128PMC
January 2021

The Prevalence of Shiga toxin-1 in non-Shigella dysenteriae isolates collected from diarrhea samples in patients, Ahvaz, Iran.

Infect Disord Drug Targets 2020 Dec 7. Epub 2020 Dec 7.

Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam. Iran.

Background: Acute diarrhea is a major public health problem particularly in developing countries. Shigellosis is one of the substantial causative agents of microbial dysentery and still has a remarkable prevalence particularly in areas with poor hygienic infrastructures. The probable existence of the deadly Shiga toxin (Stx) protein in some Shigella strains would manifest life-threatening clinical symptoms of the infection.

Methods: The aim of this study was to determine the presence of Shigella toxin 1 (Stx1) in isolated from patients with diarrhea. Totally, 227 Shigella species including 60 S. flexneri, 157 S. sonnei, and 10 S. boydii were collected from diarrheal patients in tropical infectious diseases research center of Ahvaz, Iran, during 2013-2015. The isolates were collected mostly from the intensive care unit, infectious disease, and surgery settings. The isolates were identified and the polymerase chain reaction (PCR) was performed to detect the stx gene.

Results: The results indicated that none of them encode the stx1 gene.

Conclusion: Isolates of this study were not capable of stx1 encoding. Future investigations should consider the relations between other Shigella species and Shigella toxin in Iran.
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http://dx.doi.org/10.2174/1871526520666201207122924DOI Listing
December 2020

The potential use of theranostic bacteria in cancer.

J Cell Physiol 2021 Jun 10;236(6):4184-4194. Epub 2020 Nov 10.

Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran.

Conventional chemotherapy approaches have not been fully successful in the treatment of cancer, due to limitations imposed by the pathophysiology of solid tumors, leading to nonspecific drug uptake by healthy cells, poor bioavailability, and toxicity. Thus, novel therapeutic modalities for more efficient cancer treatment are urgently required. Living bacteria can be used as a theranostic approach for the simultaneous diagnosis and therapy of tumors. Herein, we summarize the currently available literature focused on the advantages and challenges for the use of theranostic bacteria in cancer therapy.
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http://dx.doi.org/10.1002/jcp.30152DOI Listing
June 2021

Multiple-Locus Variable-Number Tandem-Repeat Analysis Genotyping of Brucella Isolates from Iran.

Clin Lab 2020 Oct;66(10)

Background: Brucellosis is considered a main health concern in humans and animals. Neither familiar molecular methods nor the classical biotyping techniques are acceptable for subtyping Brucella spp. Loci containing variable number tandem repeats (VNTRs) have recently demonstrated their practicality in typing isolates from human and animal origin despite the excessive genetic homogeneity in the genus Brucella.

Methods: The genotypic characteristics of sixty-six Brucella melitensis and thirty-four Brucella abortus isolates from veterinary samples and human brucellosis cases in Iran during 2014 - 2018. They were analyzed using multiple-locus variable-number tandem-repeat analysis (MLVA) which consisted of sixteen primer pairs and designed and classified as belonging to one of the three panels: panel 1 (MLVA-8: eight loci including Bruce06, Bruce08, Bruce11, Bruce12, Bruce42, Bruce43, Bruce45, and Bruce55), panel 2A (three loci including Bruce18, Bruce19, and Bruce21), and panel 2B (five loci including Bruce04, Bruce07, Bruce09, Bruce16, and Bruce30); MLVA-11 (panels 1 and 2A), and MLVA-16 (panels 1, 2A, and 2B) using BioNumerics software (Version 7.6).

Results: Using panel 1, 2A, and 2B (MLVA-16), 59 genotypes with a genetic similarity coefficient ranging from 91 to 100% were obtained from the 100 Brucella spp. isolates. For all isolates, only genotype 36 and genotype 26 were obtained using panels 1 and 2A, respectively. The B. abortus isolates showed variations at 9 different genotypes, while B. melitensis isolates have been dispersed in 50 different genotypes. Bruce16 and Bruce4 showed the highest discriminatory power.

Conclusions: The MLVA-16 assay appeared to be a useful and important molecular genotyping tool that is capable of proving epidemiological linkages in outbreak and trace-back investigations and is helpful in improving the effectiveness of brucellosis control programs.
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http://dx.doi.org/10.7754/Clin.Lab.2020.200119DOI Listing
October 2020

Antimicrobial resistance in Clostridioides (Clostridium) difficile derived from humans: a systematic review and meta-analysis.

Antimicrob Resist Infect Control 2020 09 25;9(1):158. Epub 2020 Sep 25.

Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran.

Background: Clostridioides (Clostridium) difficile is an important pathogen of healthcare- associated diarrhea, however, an increase in the occurrence of C. difficile infection (CDI) outside hospital settings has been reported. The accumulation of antimicrobial resistance in C. difficile can increase the risk of CDI development and/or its spread. The limited number of antimicrobials for the treatment of CDI is matter of some concern.

Objectives: In order to summarize the data on antimicrobial resistance to C. difficile derived from humans, a systematic review and meta-analysis were performed.

Methods: We searched five bibliographic databases: (MEDLINE [PubMed], Scopus, Embase, Cochrane Library and Web of Science) for studies that focused on antimicrobial susceptibility testing in C. difficile and were published between 1992 and 2019. The weighted pooled resistance (WPR) for each antimicrobial agent was calculated using a random- effects model.

Results: A total of 111 studies were included. The WPR for metronidazole and vancomycin was 1.0% (95% CI 0-3%) and 1% (95% CI 0-2%) for the breakpoint > 2 mg/L and 0% (95% CI 0%) for breakpoint ≥32 μg/ml. Rifampin and tigecycline had a WPRs of 37.0% (95% CI 18-58%) and 1% (95% CI 0-3%), respectively. The WPRs for the other antimicrobials were as follows: ciprofloxacin 95% (95% CI 85-100%), moxifloxacin 32% (95% CI 25-40%), clindamycin 59% (95% CI 53-65%), amoxicillin/clavulanate 0% (0-0%), piperacillin/tazobactam 0% (0-0%) and ceftriaxone 47% (95% CI 29-65%). Tetracycline had a WPR 20% (95% CI 14-27%) and meropenem showed 0% (95% CI 0-1%); resistance to fidaxomicin was reported in one isolate (0.08%).

Conclusion: Resistance to metronidazole, vancomycin, fidaxomicin, meropenem and piperacillin/tazobactam is reported rarely. From the alternative CDI drug treatments, tigecycline had a lower resistance rate than rifampin. The high-risk antimicrobials for CDI development showed a high level of resistance, the highest was seen in the second generation of fluoroquinolones and clindamycin; amoxicillin/clavulanate showed almost no resistance. Tetracycline resistance was present in one fifth of human clinical C. difficile isolates.
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http://dx.doi.org/10.1186/s13756-020-00815-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7517813PMC
September 2020

Involvement of the AcrAB efflux pump in ciprofloxacin resistance in clinical Klebsiella pneumoniae isolates.

Infect Disord Drug Targets 2020 Sep 5. Epub 2020 Sep 5.

Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran. Iran.

Background: Increasing prevalence of multiple antibiotic resistance in Klebsiella pneumoniae strains confines the therapeutic options used to treat bacterial infections.

Objective: We aimed in this study to investigate the role of AcrAB, qepA efflux pump, and AAC(6')-Ib-cr enzyme in ciprofloxacin resistance and to detect the RAPD-PCR fingerprint of K. pneumoniae isolates.

Methods: In total, 117 K. pneumoniae isolates were collected from hospitalized patients in three hospitals in Tehran, Iran from August 2013 to March 2014. Antimicrobial susceptibility tests were performed by the disk diffusion method. Molecular identification and expression level of encoding quinolone resistance genes, acrA, acrB, qepA, and aac(6')-Ib-cr, was performed by PCR and real-time PCR assays, respectively. All the K. pneumoniae isolates containing these genes was used simultaneously for RAPD-PCR typing.

Results: Colistin and carbapenems were the most efficient antibiotics against the clinical isolates of K. pneumoniae. PCR assay demonstrated that among the 117 isolates, 110 (94%) and 102 (87%) were positive for acrA and acrB gene, and for qepA and aac(6')-Ib-cr genes, 5 (4%) and 100 (85%) isolates were detected, respectively. Determination of AcrAB pump expression in 21% of strains demonstrated an increased expression, and the mean increase expression for acrB genes was 0.5-81. The results of RAPD-PCR reflected that in 95% CI, all isolates belong to a clone.

Conclusion: A high prevalence of genes encoding quinolone resistance in K. pneumoniae was detected in clinical samples. Therefore, control of infection and prevention of drug-resistant bacteria spread need careful management of medication and identification of resistant isolates.
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http://dx.doi.org/10.2174/1871526520999200905121220DOI Listing
September 2020

Tumor cryotherapy using Ice-producing bacteria.

Med Hypotheses 2020 Nov 13;144:110101. Epub 2020 Jul 13.

Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran; Student Research Committee, Ilam University of Medical Sciences, Ilam, Iran; Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran. Electronic address:

One of he approaches to cancer treatment is cryotherapy. In this therapy low temperatures lead to freezing and killing the cancer cells. Low temperature has several side effects on the health of tissues. Using bacteria for treatment of cancer as a therapeutic approach is proposed. One of the bacteria is Pseudomonas syringe with ice-producing properties. In this study, we hypothesized that by insertion of INA gene of P. syringe into anaerobic bacteria can do cryotherapy at a low temperature. This hypothesis is based on the manipulated anaerobic bacteria moves to the side of the tumor from ice crystal.
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http://dx.doi.org/10.1016/j.mehy.2020.110101DOI Listing
November 2020

The increasing antimicrobial resistance of Helicobacter pylori in Iran: A systematic review and meta-analysis.

Helicobacter 2020 Oct 23;25(5):e12730. Epub 2020 Jul 23.

Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran.

Background: Antimicrobial resistance of Helicobacter pylori can result in eradication failure. Metadata on the antimicrobial resistance of H pylori in Iran could help to formulate H pylori eradication strategies in Iran.

Methods: A systematic review was performed after searching in MEDLINE, Scopus, Embase, Web of Science, and the Cochrane Library. A meta-analysis was performed, and a comparison of the rates between children and adults; time periods (1999-2010, 2011-2016, 2017-2019); and the methods used was carried out.

Results: A total of 66 studies investigating 5936 H pylori isolates were analyzed. The weighted pooled resistance (WPR) rates were as follows: clarithromycin 21% (95% CI 16-26), metronidazole 62% (95% 57-67), clarithromycin in combination with metronidazole 16% (95% CI 10-23), ciprofloxacin 24% (95% CI 15-33), levofloxacin 18% (95% CI 9-30), erythromycin 29% (95% CI 12-50), furazolidone 13% (95% CI 4-27), tetracycline 8% (95% CI 5-13), and amoxicillin 15% (95% CI 9-22). During the three time periods, there was an increased resistance to amoxicillin, clarithromycin, ciprofloxacin, furazolidone, and tetracycline (P ˂ .05). Furazolidone and a clarithromycin/metronidazole combination had the higher resistance rates in children (P ˂ .05).

Conclusion: An increasing rate of resistance to amoxicillin, clarithromycin, ciprofloxacin, furazolidone, and tetracycline in Iranian H pylori isolates was identified. In children, the resistance to furazolidone and a combination of clarithromycin and metronidazole is higher compared to adults. As a stable, high resistance to metronidazole was found in children and adults in all Iranian provinces, we suggest that metronidazole should not be included in the Iranian H pylori eradication scheme.
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http://dx.doi.org/10.1111/hel.12730DOI Listing
October 2020

Microbiological detoxification of mycotoxins: Focus on Mechanisms and Advances.

Infect Disord Drug Targets 2020 Jun 16. Epub 2020 Jun 16.

Department of Biochemistry, Biophysics and Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari. Iran.

Some fungal species of the genera Aspergillus, Penicillium, and Fusarium secretes toxic metabolites known as mycotoxins, has become a global concern that is toxic to different species of animals and humans. Biological mycotoxins detoxification has been studied by researchers around the world as a new strategy for the mycotoxin removal. Bacteria, fungi, yeast, molds, and protozoa are the main living organisms appropriate for the mycotoxin detoxification. Enzymatic and degradation sorption are the main mechanisms involved in microbiological detoxification of mycotoxins. Regardless of the method used, proper management tools that consist of before-harvest prevention and after-harvest detoxification, are required. Here, in this review we focus on the microbiological detoxification, and mechanisms involved in decontamination of mycotoxins.
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http://dx.doi.org/10.2174/1871526520666200616145150DOI Listing
June 2020

Evaluation of type II toxin-antitoxin systems, antibiotic resistance profiles, and biofilm quorum sensing genes in Acinetobacter baumannii isolates in Iraq.

Infect Disord Drug Targets 2020 May 25. Epub 2020 May 25.

Department of Biology, College of Science, Mustansiriyah University, Baghdad. Iraq.

Background: Bacterial Toxin-Antitoxin (TAs) systems are extensive two-component elements in the bacterial genome, which involved in many key biological functions including growth arrest, survival, biofilm formation, plasmid maintenance, defense against phages, persistence and virulence.

Aim: This study aimed to assess the molecular determinants involved in TAs, biofilm quorum sensing, and antibiotic resistance profiles in Acinetobacter baumannii isolated from Baghdad`s hospitals in Iraq.

Methods: A total of 127 A. baumannii isolates were collected from 2160 different clinical samples. The antimicrobial susceptibility test was performed using disk diffusion test. All isolates were characterized for molecular determinants involved in TAs and biofilm formation using the well-known PCR-based sequencing assay.

Results: A high multi-drug resistant (MDR) (96.06%; 122/127 ) and imipenem resistance (84.25%; 107/127 ) rates were observed from A.baumannii isolates. Results showed the presence of rhlIR gene in three isolates (2.36%), and lasIR gene appeared in two isolates (1.57%) isolates, whilst, mazEF, ccdAB, and relBE genes have not detected among isolates.

Conclusion: A high MDR and imipenem resistance rates within a low prevalence of rhlIR, and lasIR genes could be found in clinical A. baumannii isolates from some of Iraqi hospitals.
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http://dx.doi.org/10.2174/1871526520666200525170318DOI Listing
May 2020

The characterization of bacterial communities of oropharynx microbiota in healthy children by combining culture techniques and sequencing of the 16S rRNA gene.

Microb Pathog 2020 Jun 3;143:104115. Epub 2020 Mar 3.

Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran. Electronic address:

The high incidence of bacterial respiratory infections has led to a focus on evaluating the human respiratory microbiome. Studies based on culture-based and molecular methods have shown an increase in the bacterial community that includes the bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria in the oropharynx of healthy individuals. Therefore, recognizing this microbial compound and subsequently identifying those carriers of specific pathogens can be of great help in predicting future infections and their control. In this prospective study, we sought to characterize the bacterial communities of the respiratory microbiome in healthy children aged between 3 and 6 years old by combining both cultural techniques and sequencing of the 16S rRNA gene. Seventy-seven oropharynx samples using Dacron swabs were collected from 77 healthy children in the kindergartens of Ilam, Iran. Bacterial identification was performed by phenotypic methods and in house developed PCR-based sequencing (the V1-V9 hypervariable region of the bacterial 16S ribosomal RNA gene). In total, 346 bacterial isolates were characterized based on phenotypic and sequencing-based molecular methods. The 3 most predominant phyla were Firmicutes (74%), Proteobacteria (22%), and Actinobacteria (4%). At the level of the genus, Staphylococci (coagulase-positive and coagulase-negative) and Streptococci were dominant. Also, the most commonly identified potentially pathogenic colonisers were S. aureus (75%), Enterobacteriaceae spp. (40.1%), and A. baumannii (15.6%). The present study identified 3 phyla and 9 family of bacteria in the oropharyngeal microbiome. Remarkably, the presence of potential pathogenic bacteria in the nasopharynx of healthy children can predispose them to infectious diseases, and also frequent exposure to human respiratory bacterial pathogens are further risk factors.
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http://dx.doi.org/10.1016/j.micpath.2020.104115DOI Listing
June 2020

Minocycline, focus on mechanisms of resistance, antibacterial activity, and clinical effectiveness: Back to the future.

J Glob Antimicrob Resist 2020 09 12;22:161-174. Epub 2020 Feb 12.

Department of Microbiology and Virology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.

Objectives: The increasing crisis regarding multidrug-resistant (MDR) and extensively drug-resistant microorganisms leads to appealing therapeutic options.

Methods: During the last 30 years, minocycline, a wide-spectrum antimicrobial agent, has been effective against MDR Gram-positive and Gram-negative bacterial infections. As with other tetracyclines, the mechanism of action of minocycline involves attaching to the bacterial 30S ribosomal subunit and preventing protein synthesis.

Results: This antimicrobial agent has been approved for the treatment of acne vulgaris, some sexually transmitted diseases and rheumatoid arthritis. Although many reports have been published, there remains limited information regarding the prevalence, mechanism of resistance and clinical effectiveness of minocycline.

Conclusion: Thus, we summarize here the currently available data concerning pharmacokinetics and pharmacodynamics, mechanism of action and resistance, antibacterial activity and clinical effectiveness of minocycline.
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http://dx.doi.org/10.1016/j.jgar.2020.01.022DOI Listing
September 2020

Comments on the published systematic review and meta-analysis on the increasing antibiotic resistance in Clostridioides difficile.

Anaerobe 2020 02 20;61:102141. Epub 2020 Jan 20.

Department of Microbiology, Faculty of Biology, Shahid Beheshti University, Tehran, Iran; Department of Molecular Biology, Cancer Biomedical Center (CBC), Tehran, Iran.

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http://dx.doi.org/10.1016/j.anaerobe.2019.102141DOI Listing
February 2020

Effect of Sodium Cromoglycate on Acetic Acid-induced Ulcerative Colitis in Mice.

Korean J Gastroenterol 2020 01;75(1):39-45

Department of Pharmacology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.

Background/aims: Ulcerative colitis (UC) is a type of inflammatory bowel disease that mainly involves the colon. Thus far, glucocorticoids and amino-salicylate have been the main treatment.

Methods: To assess drugs with fewer side effects, this study evaluated the effects of sodium cromoglycate (SCG) on acetic acid-induced UC in rats. The treatment groups included SCG receivers (50 and 100 mg/kg, intra-orally) and sulfasalazine (SSZ) receivers (100 mg/kg, intra-orally). The colonic mucosal injury was assessed by clinical, macroscopic, and histopathological examinations.

Results: In the treatment groups with 50 and 100 mg/kg of SCG, the clinical activity score decreased to 2.67±0.18 and 1.73±0.21 (p<0.05), respectively, compared to the UC control group (3.21±0.31), and were higher than that of the group given the standard treatment of 100 mg/kg SSZ (1.10±0.09). The treatment groups with 50 and 100 mg/kg of SCG showed a lower clinical gross lesion score than the UC control group (2.91±0.28 and 2.10±0.43, vs. 4.49±0.61, p<0.05) and were higher than the standard group (0.95±0.18). Treatment with SCG (100 mg/kg) decreased the macroscopic scores significantly compared to the UC control group (p<0.05) on the 8th day.

Conclusions: SCG (100mg/kg) decreased significantly the clinical activity score, gross lesion, and percentage-affected area compared to the UC controls on the 8th day.
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http://dx.doi.org/10.4166/kjg.2020.75.1.39DOI Listing
January 2020

Evaluation of Putative Toxin-antitoxins Systems in Clinical in Iran.

Infect Disord Drug Targets 2021 ;21(1):38-42

Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran.

Background: Toxin-antitoxin systems (TAs) are two-component elements, which are extensive in the bacterial genome and have a regulatory role in many cellular activities including, growth arrest, survival, biofilm formation, and bacterial persistence.

Objective: TAs have not well studied in Brucella spp.

Methods: We evaluated the presence of different toxin-antitoxin systems, including relE- rhhlike, Fic- Phd, Cog- Rhh, and cogT- cogAT in 40 clinical Brucella melitensis isolates using PCRbased sequencing assay.

Results: Our results showed the high presence of relE-rhh-like, Fic-Phd, Cog-rhh, and cogTcogAT s TAs genes in B. melitensis isolates that were 96.25%, 92.5%, 96.25%, and 95%, respectively.

Conclusion: A high presence of TAs genes in clinical B. melitensis isolates revealed that the TA system could be an antibacterial target in B. melitensis but more investigation is necessitated to elucidate the exact roles of these genes.
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http://dx.doi.org/10.2174/1871526520666200117113420DOI Listing
January 2021

Rapid Simultaneous Molecular Stool-Based Detection of Toxigenic Clostridioides difficile by Quantitative TaqMan Real-Time PCR Assay.

Clin Lab 2019 Apr;65(4)

Background: Clostridioides difficile is a major cause of nosocomial infectious diarrhea in hospitalized patients throughout the world.

Methods: A multiplex real-time PCR assay was developed and evaluated in comparison with toxigenic culture (TC) (as gold standard method) for direct detection of toxigenic C. difficile in fecal specimens. The multiplex real-time PCR assay simultaneously detected glutamate dehydrogenase (gluD), toxin A (tcdA), toxin B (tcdB), and binary toxin (cdtB) genes in stool samples.

Results: The results of multiplex real-time PCR were compared to those of the TC method in 250 patients suspected of C. difficile infection. The prevalence of positive TC was 13.6%. Forty-two stool samples (16.8%) were determined to be gluD+ using multiplex real-time PCR. These included 35 (83.3%) toxigenic (32 tcdA+, tcdB+ and three tcdB+) and 7 (20.0%) were cdtB+. The multiplex real-time PCR assay had a sensitivity of 91.45%, specificity of 99.54%, and positive and negative predictive values of 97% and 98.6%, respectively, compared to the TC method for diagnosis of C. difficile. The analytical sensitivity of the multiplex real-time PCR assay was estimated to be 102 CFU/g of stools and 0.0200 pg of genomic DNA from culture. The analytical specificity was determined to be 100% by using enteric and non-C. difficile standard bacterial strains.

Conclusions: The molecular method developed in the study was rapid, sensitive, and specific for detection of toxigenic C. difficile. It is applicable to be performed in clinical laboratories and correlated well with the results obtained by TC.
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http://dx.doi.org/10.7754/Clin.Lab.2018.180735DOI Listing
April 2019

Therapeutic bacteria to combat cancer; current advances, challenges, and opportunities.

Cancer Med 2019 06 5;8(6):3167-3181. Epub 2019 Apr 5.

Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.

Successful treatment of cancer remains a challenge, due to the unique pathophysiology of solid tumors, and the predictable emergence of resistance. Traditional methods for cancer therapy including radiotherapy, chemotherapy, and immunotherapy all have their own limitations. A novel approach is bacteriotherapy, either used alone, or in combination with conventional methods, has shown a positive effect on regression of tumors and inhibition of metastasis. Bacteria-assisted tumor-targeted therapy used as therapeutic/gene/drug delivery vehicles has great promise in the treatment of tumors. The use of bacteria only, or in combination with conventional methods was found to be effective in some experimental models of cancer (tumor regression and increased survival rate). In this article, we reviewed the major advantages, challenges, and prospective directions for combinations of bacteria with conventional methods for tumor therapy.
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http://dx.doi.org/10.1002/cam4.2148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558487PMC
June 2019

Extraction and purification of the H9N2 virus nucleoprotein: A simple and practical method.

Med J Islam Repub Iran 2018 21;32:128. Epub 2018 Dec 21.

Department of Botany, Biotechnology and Bioinformatics, Payame Noor University, Tehran, Iran.

Avian Influenza disease annually entails a significant economic loss to the poultry industry around the world. Influenza virus is a polymorphic virus of the orthomyxoviridae family (single-stranded RNA genome), and nucleoprotein (NP) is the structural and internal protein of the virus. The aim of the work was to purify nucleoprotein for further investigations with a simple, low-cost, fast and practical method. In this study, H9N2 influenza virus was isolated in specific pathogen-free embryonated chicken eggs by allantoically inoculating 103 to 105 egg-infective doses (EID50) for 9 to 11 days, purified by 10% (W/V) polyethylene glycol (PEG) 6000 with a sucrose gradient of 60% to 30%. The influenza virus proteins were collected and prepared as fractions by preparative electrophoresis. Finally, the purified NP was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot procedures. The protein analysis with SDS-PAGE and silver nitrate staining indicated that the desired samples contained purified nucleoprotein and lacked other viral proteins. The results of the investigation of lyophilized fractions containing nucleoprotein on the SDS-PAGE revealed the absence of viral RNA in nucleoprotein and its high purity. According to this study, purified nucleoprotein can be used to produce nucleoprotein vaccines, as well as to study structural, molecular and diagnostic and therapeutic materials.
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http://dx.doi.org/10.14196/mjiri.32.128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6387826PMC
December 2018

Molecular typing of Clostridioides difficile isolates from clinical and non-clinical samples in Iran.

APMIS 2019 Apr;127(4):222-227

Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.

Clostridioides difficile is a major cause of nosocomial infectious diarrhea in hospitalized patients throughout the world. We aimed to characterize C. difficile isolates among hospitalized patients, hospital staffs, and hospital environment samples obtained in three tertiary care hospitals of Iran with regard to their molecular types between June 2016 and November 2017. The toxigenicity of C. difficile isolates was determined by toxigenic culture and multiplex-PCR. Toxigenic C. difficile isolates collected were ribotyped using capillary gel electrophoresis-based PCR and the database of WEBRIBO (http://webribo.ages.at). Of 500 clinical and non-clinical samples, toxigenic C. difficile were identified in 35 of 250 stool samples (14%) and in 3 of 250 swabs (1.2%). The most frequently found ribotypes (RTs) were 039, AI-12, and AI-21 (15.8, 10.52, and 10.52% of all isolates, respectively). Further RTs were: 017, 001, AI-3, AI-15, AI-18, AI-10, AI-4, and PR21195 (as new ribotype). The epidemic RTs (027 and 078) seen in the Europe, North America, and Asia were completely absent in this study.
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http://dx.doi.org/10.1111/apm.12937DOI Listing
April 2019

Antimicrobial resistance, prevalence of resistance genes, and molecular characterization in intestinal Bacteroides fragilis group isolates.

APMIS 2019 Jun 19;127(6):454-461. Epub 2019 Mar 19.

Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.

Since the level of antimicrobial resistance in Bacteroides fragilis has increased, monitoring the antimicrobial susceptibility could be necessary. The objectives of this study were to (i) investigate the prevalence of species, the occurrence of reduced antimicrobial susceptibility (E-test method), and antibiotic resistance genes in the B. fragilis group and (ii) evaluate the prevalence of enterotoxigenic B. fragilis and the distribution of bft gene subtypes in hospitalized patients. As many as 475 isolates out of 250 stool samples were detected to be B. fragilis group by using conventional biochemical tests (API-32A system) and multiplex-PCR. In addition, 48.2%, 13.9%, 76.6%, and 1.2% of B. fragilis group isolates were resistant (according to EUCAST breakpoint) to piperacillin-tazobactam, meropenem, clindamycin, and metronidazole, respectively. Six metronidazole-resistant strains were isolated; B. fragilis (n: 3), B. thetaiotaomicron, B. vulgates, and B. ovatus. The presence of the cfiA, cepA, ermF, and nim genes was observed in 3.8%, 15.9%, 34.1%, and 0.7% of the B. fragilis isolates, respectively. One hundred thirty-two B. fragilis isolates (27.8%)and 21 B  fragilis isolates (15.9%) turned out to be bft gene positive by multiplex-PCR; eleven isolates (52.4%) harbored bft-1, eight isolates (38%) harbored bft-2 isotypes, and two isolates (9.5%) harbored bft-3 isotype (16.66%). These bacteria harbor antimicrobial resistance genes that could be transferred to other susceptible intestinal strains. Further investigations on lineage analysis are needed for a better understanding of these bacteria in Iran.
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http://dx.doi.org/10.1111/apm.12943DOI Listing
June 2019

The emergence of metronidazole and vancomycin reduced susceptibility in Clostridium difficile isolates in Iran.

J Glob Antimicrob Resist 2019 09 28;18:28-33. Epub 2019 Jan 28.

Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran. Electronic address:

Objectives: Clostridium difficile (C. difficile) is the main causative agent of antibiotic-associated diarrhoea (AAD) and pseudomembranous colitis. The accumulation of antimicrobial resistance in C. difficile strains can drive C. difficile infection (CDI) epidemiology. This study was undertaken to evaluate the antimicrobial resistance patterns of toxigenic C. difficile isolates cultured from diarrhoeal stool samples of hospitalised patients with suspected CDI in three tertiary care hospitals in Tehran, Iran.

Methods: Two hundred and fifty diarrhoeal stool samples were investigated by toxigenic culture using cycloserine-cefoxitin-fructose agar and the VERO cell line. Antimicrobial susceptibility to metronidazole, vancomycin, clindamycin, tetracycline, and moxifloxacin was performed by disk diffusion and Etest methods on Brucella Blood Agar supplemented with hemin and vitamin K.

Results: Thirty-five stool samples (14.0%) proved positive using C. difficile toxigenic culture. According to Clinical and Laboratory Standards Institute breakpoints, the following resistance was identified in C. difficile isolates: metronidazole (2 of 35); moxifloxacin (7 of 35); clindamycin (18 of 35); and tetracycline (5 of 35). Using European Committee on Antimicrobial Susceptibility Testing breakpoints, three of 35 isolates showed reduced-susceptibility for vancomycin and 14 of 35 for metronidazole. In addition, the results showed a good correlation between the inhibition zone diameter (disk diffusion) and MIC values (Etest); Pearson correlation coefficient 0.7400.95 (P< 0.001).

Conclusions: Multidrug resistance was observed in Iranian clinical toxigenic C. difficile isolates, including reduced susceptibility to first-line CDI treatment drugs. In addition, disk diffusion can be used as a cost-effective option for the antimicrobial susceptibility testing of C. difficile isolates.
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http://dx.doi.org/10.1016/j.jgar.2019.01.027DOI Listing
September 2019

The diversity of class B and class D carbapenemases in clinical Acinetobacter baumannii isolates.

Infez Med 2018 Dec;26(4):329-335

Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.

Wide distrubution of multidrug-resistant Acinetobacter baumannii strains has become a foremost concern in hospital environments. Treatment of infections caused by multidrug resistant strains has conventionally involved the use of β-lactams such as carbapenems. In this study, we report the distribution of carbapenemase genes in A. baumannii isolated from hospitalized patients. The study was conducted on 110 non-repetitive A. baumannii isolates collected from hospitalized patients, over a nine-month period. Clinical isolates were examined by conventional susceptibility testing, using the disk-diffusion method and multiplex polymerase chain reaction to detect acquired carbapenemase genes. All of the isolates were completely resistant to TOB, SXT, IPM, MEM, CTX, CRO, FEP, CAZ, CIP, PTZ, PIP and were susceptible to colistin, but moderately susceptible TET (2.72%), AK (4.54%) and GEN (3.63%). The prevalence of bla-OXA-51like, bla-OXA-23like, bla-OXA-24like, bla-OXA-58like, blaSIM and blaSPM genes was 100%, 96.36%, 35.45%, 7.27%, 7.27% and 3.63%, respectively. bla-GIM and bla-VIM genes were not detected among the strains. Our results suggest that OXA-type carbapenemase genes plus class B β-lactamases contribute to carbapenem resistance in the collected isolates. Therefore, quick identification of these resistant genes using molecular approaches is critical in limiting the spread of infections caused by A. baumannii. Drug administration correction of the physicians, based on antibiotic susceptibility testing and more knowledge on the nosocomial infection control policies as essential need.
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December 2018

Fosfomycin: mechanisms and the increasing prevalence of resistance.

J Med Microbiol 2019 Jan 15;68(1):11-25. Epub 2018 Nov 15.

2​Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.

There are challenges regarding increased global rates of microbial resistance and the emergence of new mechanisms that result in microorganisms becoming resistant to antimicrobial drugs. Fosfomycin is a broad-spectrum bactericidal antibiotic effective against Gram-negative and certain Gram-positive bacteria, such as Staphylococci, that interfere with cell wall synthesis. During the last 40 years, fosfomycin has been evaluated in a wide range of applications and fields. Although numerous studies have been done in this area, there remains limited information regarding the prevalence of resistance. Therefore, in this review, we focus on the available data concerning the mechanisms and increasing resistance regarding fosfomycin.
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http://dx.doi.org/10.1099/jmm.0.000874DOI Listing
January 2019

Epidemiology of multidrug-resistant Acinetobacter baumannii strains in Iran: a systematic review and meta-analysis.

J Chemother 2017 Dec 16;29(6):327-337. Epub 2017 Jun 16.

a Department of Microbiology, Faculty of Medicine , Iran University of Medical Sciences , Tehran , Islamic Republic of Iran.

Acinetobacter baumannii is an important opportunistic pathogen that causes major public health concern especially in hospitalized patients due to the acquisition of multidrug resistance (MDR). The aim of this study was to systematically review published data about the prevalence rate of MDR-A. baumannii (MDR-AB) from different parts of Iran and provide an overall relative frequency (RF) using meta-analysis. All available national and international databanks were searched to find published studies up to June 2016. Quality of studies was assessed by STROB and PRISMA forms. Because of the significant heterogeneity observed, random effects model was used to combine the results. STATA SE version 11.2 was used for statistical analysis. Out of the 9646 results, 37 suitable articles were extracted according to inclusion and exlusion criteria. The pooled prevalence of MDR-AB was estimated 72% annually. Relative frequency of MDR-AB in different studies varied from 22.8 to 100%. Since the prevalence of MDR-AB is higher than many other countries, measures should be taken to keep the emergence and transmission of these strains to a minimum.
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http://dx.doi.org/10.1080/1120009X.2017.1338377DOI Listing
December 2017

In vitro antibacterial activity of poly (amidoamine)-G7 dendrimer.

BMC Infect Dis 2017 06 5;17(1):395. Epub 2017 Jun 5.

Department of Environmental Health Engineering, Developmental Center for Student Research and Technology Talent, School of Public Health, Iran University of Medical Sciences, Tehran, Iran.

Background: Nano-scale dendrimers are synthetic macromolecules that frequently used in medical and health field. Traditional anibiotics are induce bacterial resistence so there is an urgent need for novel antibacterial drug invention. In the present study seventh generation poly (amidoamine) (PAMAM-G7) dendrimer was synthesized and its antibacterial activities were evaluated against representative Gram- negative and Gram-positive bacteria.

Methods: PAMAM-G7 was synthesized with divergent growth method. The structural and surface of PAMAM-G7 were investigated by transmission electron microscopy, scanning electron microscope and fourier transform infrared. Pseudomonas. aeruginosa (n = 15), E. coli (n = 15), Acinetobacter baumanni (n = 15), Shigella dysenteriae (n = 15), Klebsiella pneumoniae (n = 10), Proteus mirabilis (n = 15), Staphylococcus aureus (n = 15) and Bacillus subtilis (n = 10) have been used for antibacterial activity assay. Additionally, representative standard strains for each bacterium were included. Minimum Inhibitory Concentration (MIC) was determined using microdilution method. Subsequently, Minimum Bactericidal Concentration (MBC) was determined by sub-culturing each of the no growth wells onto Mueller Hinton agar medium. The cytotoxicity of PAMAM-G7 dendrimer were evaluated in HCT116 and NIH 3 T3 cells by MTT assay.

Results: The average size of each particle was approximately 20 nm. PAMAM-G7 was potentially to inhibit both Gram positive and gram negative growth. The MIC50 and MIC90 values were determined to be 2-4 μg/ml and 4-8 μg/ml, respectively. The MBC50 and MBC90 values were found to be 64-256 μg/ml and 128-256 μg/ml, respectively. The cytotoxity effect of dendrimer on HCT116 and NIH 3 T3 cells is dependent upon exposure time to and concentration of dendrimers. The most reduction (44.63 and 43%) in cell viability for HCT116 and NIH 3 T3 cells was observed at the highest concentration, 0.85 μM after 72 h treatmentm, respectively.

Conclusions: This study we conclude that PAMAM-G7 dendrimer could be a potential candidate as a novel antibacterial agent.
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http://dx.doi.org/10.1186/s12879-017-2513-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5460590PMC
June 2017