Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 02 1 10 Samaneh Saedi Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran Azadeh Safarchi Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran Mojtaba Noofeli Department of Human Bacterial Vaccine, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran Keyvan Tadayon Department of Aerobic Bacterial Research and Vaccine Production, Razi Vaccine & Serum Research Institute, Karaj, Iran Alfred Chin Yen Tay The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, Western Australia, Australia; Shenzhen Dapeng New District Kuichong People Hospital, Shenzhen, Guangdong, China Binit Lamichhane The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Nedlands, Western Australia, Australia Hamzeh Rahimi Department of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran Fereshteh Shahcheraghi Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran 2020 01 13 2020 01 15 Background and Objectives: The re-emergence of pertussis still is being reported all over the world. Pathogen adaptation and antigenic divergence of circulating isolates from vaccine strains are the main reasons of infection resurgence. Waning immunity is also an important factor contributing to resurgence of pertussis. Materials and Methods: The genetic diversity and evolutionary characteristics of circulating Iranian isolates of Bordetella pertussis during February 2015 to October 2018 was investigated by pulsed-field gel electrophoresis (PFGE) and subsequently ptxA, ptxP and fim3 alleles were characterized. The next generation genome sequencing was then used to compare the genomics of ptxP1 and ptxP3 of selected isolates from PFGE dendrogram. Results: PFGE differentiated 62 clinical isolates and vaccine and reference strains into 19 PFGE profiles, indicating the higher level of heterogeneity in the population during 2015-2018. The predominant B. pertussis genotype harbored pertussis toxin promoter allele, ptxP3 and the expansion of ptxA1 isolates, were also observed in our population. Conclusion: No changes in allelic profile of predominant clone in recent years was observed but antigenic divergence between recently circulating isolates and the vaccine strain has been progressed and significantly was higher than previous studies. The comparative genomic analysis of the ptxP3 and ptxP1 isolates indicate that changes in ptxP3 genome structure including 32 unique SNPs and three unique indels may have contributed to the expansion of the ptxP3 clone. We compared ptxP3 and ptxP1 isolates in pathogenicity-associated genes and found five of them were specific for the ptxP3 isolates. The polymorphisms in pathogenicity-associated genes suggest structural adaptations for these virulence factors. https://ijm.tums.ac.ir/index.php/ijm/article/view/2450 https://ijm.tums.ac.ir/index.php/ijm/article/download/2450/1215

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 03 70 72 Khosrow Agin Department of Pulmonary and Heart Ward, Loqman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran Iman Rezaee Clinical Virology Research Center, Tehran University of Medical Sciences, Tehran, Iran Zahra Heydarifard Clinical Virology Research Center, Tehran University of Medical Sciences, Tehran, Iran Seyed-Mohammad Jazayeri Clinical Virology Research Center, Tehran University of Medical Sciences, Tehran, Iran 2019 07 16 2020 01 19 A pregnant woman presented by cough and dyspenia. Employing a respiratory multiplex real-time PCR, Human bocavirus (HBoV), Haemophilus influenza and Staphylococcus aureus were positive at cycle thresholds (CTs) of 21, 35 and 33.5, respectively. The patient was diagnosed for bacterial respiratory infection superimposed by bocavirus due to a relative high CT value. Patient’s condition improved using bronchodilators and corticosteroid without any further antibiotic treatment. HBoV is not exclusively a bystander pathogen in some patients. https://ijm.tums.ac.ir/index.php/ijm/article/view/2255 https://ijm.tums.ac.ir/index.php/ijm/article/download/2255/1224

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 02 11 17 Tran Hanh Department of Obstetrics, Nghe An Obstetrics and Pediatrics Hospital, Nghe An, Vietnam Vu Du Department of Treatment on Demand, National Hospital of Obstetrics and Gynecology, Hanoi, Vietnam Pham Hien Department of Treatment on Demand, National Hospital of Pediatrics, Hanoi, Vietnam Duong Chinh Department of Neurology, Nghe An Friendship General Hospital, Nghe An, Vietnam Cao Loi Department of Science and Training, National Institute of Malaria Parasitology and Entomology, Hanoi, Vietnam Nguyen Dung Department of Anesthesiology and Critical Care, 108 Military Centre Hospital, Hanoi, Vietnam Do Anh Department of Medical Parasitology, Military Medical University, Hanoi, Vietnam Tran Thi Anh Department of Paediatric, Vinh Medical University, Nghe An, Vietnam 2019 10 14 2019 12 22 Background and Objectives: Identification of GBS serotypes provides helpful information for appropriate the development of suitable vaccines; however, no reports from Vietnam have been published. This study has been performed to find the prevalence and serotypes of group B Streptococcus isolated from vagina of pregnant women in Nghe An province, Vietnam. Materials and Methods: Vaginal swabs were collected from pregnant women at 35-37 weeks of gestation at the Nghe An Obstetrics and Pediatrics Hospital, Vietnam between May 2018 and July 2019. The swabs were cultured on 5% sheep blood agar for isolation of GBS. All isolates were identified using the Gram staining, CAMP test and specific PCR. GBS strains were serotyped using the multiplex PCR assays. Results: The prevalence of vaginal GBS colonization was 9.20% of 750 participants. Among the isolates, serotypes III (39.13%) and V (31.89%) were the most frequent, followed by serotypes Ia (11.59%), VI (11.59%), Ib (2.90%), II (1.45%) and VII (1.45%), respectively. Serotypes IV, VIII and IX were not found. Conclusion: The prevalence of GBS in the Nghe An province of central Vietnam was similar to reports from other parts of the world. The predominat GBS serotypes (III, V, Ia and VI) were slightly different from those previously described from other regions around the world. The high frequency of serotype VI was a notable feature of the strains from pregnant women in Vietnam. https://ijm.tums.ac.ir/index.php/ijm/article/view/2363 https://ijm.tums.ac.ir/index.php/ijm/article/download/2363/1216

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 03 18 24 EN Mohammad Moradi Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran Shahla Mansouri Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran Nouzar Nakhaee Department of Community Medicine, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran Farhad Sarafzadeh Department of Infectious Diseases, Afzalipour Hospital, Kerman University of Medical Sciences, Kerman, Iran Ebrahim Rezazadeh Zarandi Immunology of Infection of Diseases Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran 2018 10 16 2020 01 12 Background and Objectives: Antibiotics prescribed for infections have diverse effects on microbiota and the pathogen Clostridium difficile (C. difficile) as the most important antibiotic-associated diarrhea. This study aims to determine the gene expression of toxins A and B at the transcription level in the sub-MIC of vancomycin (VAN), clindamycin (CLI), and ceftazidime (CAZ) alone and in combination. Materials and Methods: The MIC and fractional inhibitory concentration (FIC) of two C. difficile samples (a clinical isolate and ATCC 9689) were determined by microdilution and checkerboard microdilution methods, respectively. The total RNA was extracted from the medium inoculated with ~106 CFU/mL of fresh bacteria in the pre-reduced medium containing ½ MIC of antibiotics alone and ½ FIC of antibiotics in combination. Real-time PCR was performed by sybrGreen methods in triplicate, and the data were analyzed by the comparative ∆∆CT method. Results: All antibiotics except CAZ (alone and in combination) decreased the gene expression of toxins A and B within 24 hours. VAN and CLI reduced toxin gene expression within 24 and 48 hours. However, CAZ alone and in combination with VAN as well as CLI increased the gene expression of toxins A and B. Conclusion: The results confirmed toxin gene transcription and toxin production are associated with the type of isolates and antibiotics, as well as the combined form of antibiotics. This could be the reason which can explain the occurrence of C. difficile infection among patients who were treated with the third generation of cephalosporins alone and in combination with another antibiotic in the form of combinational therapy. https://ijm.tums.ac.ir/index.php/ijm/article/view/1911 https://ijm.tums.ac.ir/index.php/ijm/article/download/1911/1217

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 03 25 31 Malihe Honarmand Kashi Department of Biology, Islamic Azad University of North Tehran Branch, Tehran, Iran Nader Mosavari Department of PPD Tuberculin, Razi Vaccine and Serum Research Institute, Agriculture Research, Education and Extension Organization, Karaj, Iran Mitra Salehi Department of Biology, Islamic Azad University of North Tehran Branch, Tehran, Iran Naheed Mojgani Department of PPD Tuberculin, Razi Vaccine and Serum Research Institute, Agriculture Research, Education and Extension Organization, Karaj, Iran 2019 07 13 2020 01 19 Background and Objectives: Bovine tuberculosis diagnosis is usually performed by various tests with specific limitations. Mycobacterium bovis culture filtrate contains antigenic proteins that could be used to improve the sensitivity of bovine tuberculosis diagnosis. The objective of this study was to identify and purify antigenic proteins from culture filtrates of M. bovis strain AN5 for use in immunological assays. Materials and Methods: Secreted proteins were purified from the heat-treated culture filtrate of M. bovis strain AN5. Proteins were precipitated with ammonium sulfate, fractionated by Sephadex G50 chromatography. The protein concentrations and the approximate molecular weight were determined by lowry method and 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), respectively. Immunological methods, including dot-blotting and western blotting, assessed the quality of the isolated proteins. Results: The quantity of antigenic proteins in the culture medium was measured at far more than 15% of the amount of proteins secreted into medium. Three main chromatographic fractions obtained and showed concentrations of proteins ranging from 14 to 60 μg/μl with molecular weights in the 10 to 180 kDa range. The purified antigens showed positive reactions to the infected cattle serum throughout dot-blotting. Western blotting revealed a total of 15 to 70 kDa molecular weight proteins. Conclusion: Immunoblotting analysis made it possible to detect and recognize novel antigens that are useful for bovine tuberculosis diagnosis improvement. This is significant since non-specific reactions were not observed when we utilized serum of cattle experimentally infected with M. bovis as a polyclonal antibody. https://ijm.tums.ac.ir/index.php/ijm/article/view/2249 https://ijm.tums.ac.ir/index.php/ijm/article/download/2249/1218

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 03 32 36 Fatemeh Akhavan Tafti Department of Microbiology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran AND Institute for Advanced Research and Education in Transfusion Medicine, Yazd, Iran Gilda Eslami Department of Parasitology and Mycology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran AND Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran Hengameh Zandi Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran AND Department of Microbiology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran Kazem Barzegar Department of English Language, School of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services Yazd, Iran 2019 08 04 2019 09 22 Background and Objectives: Burn wound infections have emerged as an important cause of morbidity and mortality in patients due to prolonged hospital stay. Pseudomonas aeruginosa, is the second cause of bacterial burn wound infections. Resistance mechanisms among P. aeruginosa are intrinsic or acquired. Intrinsic resistance mechanisms among P. aeruginosa isolates are inducible AmpC cephalosporinase, decrease of specific porin OprD, and overexpression of RND efflux pump. The aim of this study was detection of mutations in nalC gene in carbapenem resistant P. aeruginosa isolated from burn wounds. Materials and Methods: In this cross-sectional study, 180 burn-wound specimens were collected. Suspected lactose-negative colonies were identified by conventional biochemical methods. Kirby-Bauer and Etest methods were used for susceptibility testing. PCR and sequencing techniques were used for the detection of nalC mutation. Results: Out of 180 specimens received in the laboratory, 54 of isolates were isolated and identified as P. aeroginosa (30%). Of these isolates 20 (37%) were resistant to at least two carbapenems simultaneously. From these carbapenem resistant isolates, 19 (95%), 14 (70%), 14 (70%), 19 (95%) and 16 (80%) were resistant to imipenem, cefepime, piperacillin, ceftizoxime and gentamicin, respectively. Only 1 (2%) isolate was sensitive to all carbapenems and did not has mutation in nalC gene, 20 (37%) isolates were resistant to at least two carbapenems, and had mutations in nalC gene (Gly71►Glu and Ser209►Arg). Conclusion: As the results showed, mutation in efflux pump was observed in carbapenem resistant isolate and this confirmed that the indiscriminate use of antibiotics for treatment or prophylaxis can increase mutation in efflux pump. https://ijm.tums.ac.ir/index.php/ijm/article/view/2281 https://ijm.tums.ac.ir/index.php/ijm/article/download/2281/1219

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 03 37 42 Mohammad Sekhavati Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Ashraf Mohabati Mobarez Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran Seyed Davar Siadat Microbiology Research Center (MRC) Pasteur, Institute of Iran, Tehran, Iran Mojtaba Noofeli Department of Human Bacterial Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran 2019 07 27 2019 09 22 Background and Objectives: There are many pertussis outbreaks which is mainly due to the reduction in the immunity of acellular pertussis (aP) vaccines. Therefore, there is a crucial necessity to develop a new generation of pertussis vaccine. Preceding researches have shown that Bordetella pertussis outer membrane vesicles (OMVs) have appropriate specifications, making them a suitable vaccine candidate against pertussis. Materials and Methods: The OMVs were separated by a new serial ultra centrifugation technique. Transmission electron microscopy (TEM) examination, SDS-PAGE, Western blotting and ELISA assay were used to characterize the OMVs. Results: TEM studies showed the size of the extracted OMVs at 40-200 nm. The presence of pertussis toxin, filamentous hemagglutinin, and pertactin was verified using Western blot and ELISA assay. Conclusion: The presented technique is a simple and effective way to obtain OMVs from Bordetella pertussis. So it can be utilized as an appropriate procedure in the development of an OMV-based vaccine against pertussis. https://ijm.tums.ac.ir/index.php/ijm/article/view/2267 https://ijm.tums.ac.ir/index.php/ijm/article/download/2267/1220

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 03 43 51 Mahmoud Osanloo Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran Abbas Abdollahi Department of Microbiology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran Alireza Valizadeh Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran Niloufar Abedinpour Department of Medicine, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran 2019 09 14 2020 01 03 Background and Objectives: Plant-derived essential oils (EOs) shave many usages in health and medicine, such as antibacterial agents. The aim of this study was the improvement of antibacterial activities of two EOs using nanotechnology. Materials and Methods: Antibacterial activity was investigated on four important human pathogenic bacteria using the 96-well plate microdilution method, a quantitative approach. Eleven formulations were prepared using each of the EOs. Eventually, the best nanoformulation with the smallest particle size and polydispersive indices (PDI and SPAN) was selected using each EO for further investigations. Moreover, two microemulsions with similar ingredients and the same portion in comparison with two selected nanoemulsions were also prepared. Antibacterial activity of each EO was compared with its micro- and nano-emulsions. Results: The antibacterial efficacy of Zataria multiflora EO (ZMEO) was significantly better than Mentha piperita EO (MPEO). Besides, the antibacterial activity of nanoemulsion of ZMEO with a particle size of 129 ± 12 nm was significantly better than no- and micro-formulated forms of ZMEO. Interestingly, the efficiency of MPEO nanoemulsion (160 ± 25 nm) was also significantly better than MPEO and its micro-formulated form. Conclusion: Regardless of the intrinsic antibacterial property of two examined EOs, by formulating to nanoemulsion, their efficiencies were improved. Nanoemulsion of ZMEO introduced as an inexpensive, potent and green antibacterial agent. https://ijm.tums.ac.ir/index.php/ijm/article/view/2325 https://ijm.tums.ac.ir/index.php/ijm/article/download/2325/1221

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 03 52 61 Fatemeh Shayesteh Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran Asmat Ahmad Department of Bioscience and Biotechnology, Faculty of Science and Technology, University Kebangsaan Malaysia, Selangor, Malaysia Gires Usup Department of Environmental Science and Natural Resources, Faculty of Science and Technology, University Kebangsaan Malaysia, Selangor, Malaysia 2019 11 02 2019 11 29 Background and Objectives: Biofilm formed by Proteus mirabilis strains is one of the most important medical problems especially in the case of device-related urinary tract infections. This study was conducted to evaluate the bacteriocin produced by a marine isolate of Bacillus sp. Sh10, for it's in vitro inhibitory activity against pre-formed biofilm and in interference with the biofilm-forming of two biofilm-producing bacteria (P. mirabilis UCa4 and P. mirabilis UCe1). Materials and Methods: Sensitivity of two biofilm-producing bacteria (P. mirabilis UCa4 and P. mirabilis UCe1) to bacteriocin, was investigated in planktonic and biofilm states by cell viability and crystal violet assay, respectively. Scanning electron microscopy (SEM) was also performed to determine the effect of bacteriocin on the morphology of the cells associated with biofilm. Results: It was found that bacteriocin possessed bactericidal activity to biofilm-forming isolates in the planktonic state. However, bacteriocin interferes with the formation of biofilms and disrupts established biofilms. Bacteriocin reduced biofilm formation in the isolates of P. mirabilis UCa4 and P. mirabilis UCe1 with SMIC50 of 32 and 128 μg/mL, desirable SMIC50 of bacteriocin for biofilm disruption were 128 and 256 μg/mL, respectively. The SEM results indicated that bacteriocin affected the cell morphology of biofilm-associated cells. Conclusion: The present findings indicated that bacteriocin from Bacillus sp. Sh10 has bactericidal properties against biofilm-forming isolates of P. mirabilis UCa4 and P. mirabilis UCe1 and has the ability to inhibit the formation of biofilm and disrupt established biofilm. https://ijm.tums.ac.ir/index.php/ijm/article/view/2387 https://ijm.tums.ac.ir/index.php/ijm/article/download/2387/1222

Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 12 1 2020 03 03 62 69 Dirayah Husain Department of Biology, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia Syahrul Gunawan Department of Biology, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia Sulfahri Sulfahri Department of Biology, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia 2019 10 01 2019 12 17 Background and Objectives: Pathogenic bacterial infection is one of the factors that can cause extensive losses in poultry farming. Pathogenic bacteria that infect domestic chickens (Gallus domesticus) include Escherichia coli. This study has investigated antimicrobial compounds from probiotic bacteria isolated from the digestive tract of domestic chickens originating from Takalar Regency, South Sulawesi, Indonesia. Materials and Methods: Lactic acid bacteria were grown on de Man–Ragosa–Sharpe agar medium for 24 hours. The bacterial isolate with the best inhibitory power was identified as Bacillus subtilis (B. subtilis), based on 16S RNA sequences. Antimicrobial activity of the selected lactic acid bacteria was tested on the pathogenic bacteria, E. coli and Staphylococcus aureus. Using well diffusion method. In this study, in silico study was conducted to examine the structure and binding affinity of lactic acid bacteria against E. coli and S. aureus. Molecular docking experiments were performed using the PyRx 0.8 software. Results: This study showed that the bacteria were B. subtilis strain PATA-5. The response of inhibition of antimicrobial compounds produced by B. subtilis strain PATA-5 maximum in the stationary phase. The bactericidal properties of B. subtilis strain PATA-5 were categorized as strong against Gram-negative E. coli, i.e., 30.5 mm, when compared to Gram-positive S. aureus, i.e., 17.5 mm. Conclusion: B. subtilis strain PATA-5 is capable to produce natural antibiotic cyclic lipopeptides, namely surfactin. https://ijm.tums.ac.ir/index.php/ijm/article/view/2346 https://ijm.tums.ac.ir/index.php/ijm/article/download/2346/1223