The Iranian Journal of Microbiology (IJM) is the offi­cial scientific quarterly publication of the Iranian Society of Microbiology which is published by Tehran University of Medical Sciences.  The areas that are covered by IJM are medical, veterinary, food and water, applied and  environmental microbiology. It ac­cepts Original Papers, Review Articles, Short Communications and Let­ters to the Editor in the fields of Microbiology.

Current Issue

Vol 15 No 4 (2023)

Original Article(s)

  • XML | PDF | downloads: 103 | views: 112 | pages: 482-491

    Background and Objectives: Methicillin resistance is acquired by the bacterium due to mecA gene which codes for penicillin-binding protein (PBP2a) having low affinity for β-lactam antibiotics. mecA gene is located on a mobile genetic element called staphylococcal cassette chromosome mec (SCCmec). SCCmec genomic island comprises two site-specific recombinase genes namely ccrA and ccrB [cassette chromosome recombinase] accountable for mobility. Currently, SCCmec elements are classified into types I, II, III, IV and V based on the nature of the mec and ccr gene complexes and are further classified into subtypes according to variances in their J region DNA. SSCmec type IV has been found in community-acquired isolates with various genetic backgrounds. The present study was undertaken to categorize the types of SCCmec types and subtypes I, II, III, IVa, b, c, d, and V and PVL genes among clinical MRSA isolates from COVID-19 confirmed cases.
    Materials and Methods: Based on the Microbiological and Molecular (mecA gene PCR amplification) confirmation of MRSA isolated from 500 MRSA SCCmec clinical samples, 144 cultures were selected for multiplex analysis. The multiplex PCR method developed by Zhang et al. was adapted with some experimental alterations to determine the specific type of these isolates.
    Results: Of the total 500 MRSA, 144 MRSA (60 were CA-MRSA and 84 were HA-MRSA) were selected for characterization of novel multiplex PCR assay for SSCmec Types I to V in MRSA. Molecular characterization of multiplex PCR analysis revealed results compare to the phenotypic results. Of the 60 CA-MRSA; in 56 MRSA strains type IVa was found and significantly defined as CA-MRSA while 4 strains showed mixed gens subtypes. Type II, III, IA, and V were present in overall 84 HA-MRSA. Molecular subtyping was significantly correlated to define molecularly as CA-MRSA and HA-MRSA however 15 (10%) strains showed mixed genes which indicates the alarming finding of changing epidemiology of CA-MRSA and HA-MRSA as well.
    Conclusion: We have all witnessed of COVID-19 pandemic, and its mortality was mostly associated with co-morbid conditions and secondary infections of MDR pathogens. Rapid detections of causative agents of these superbugs with their changing epidemiology by investing in typing and subtyping clones are obligatory. We have described an assay designed for targeting SSCmec types and subtypes I, II, III, IVa,V according to the current updated SCCmec typing system. Changing patterns of molecular epidemiology has been observed by this newly described assay.

  • XML | PDF | downloads: 73 | views: 154 | pages: 492-502

    Background and Objectives: Antibiotic resistance is a significant problem that restricts the options for treating bacterial pneumonia. This research aimed to determine the bacterial causes of pneumonia and antibiotic resistance among hospitalized patients in southwest Ethiopia.
    Materials and Methods: We collected and analyzed 150 sputum samples from individuals with community-acquired pneumonia from April 1st to October 30th, 2019. Standard bacteriological procedures were used to identify the bacteria. Kirby Bauer's disk diffusion method was used to assess the bacteria's susceptibility patterns. Production of carbapenemase and extended-spectrum-lactamase were confirmed phenotypically. Odds ratios and the chi-square test were computed.
    Results: On the whole, bacterial pathogens were verified in 50% of the sputum samples. The predominant bacterial isolates were Klebsiella species, followed by Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae. About 77.5% of isolates were multidrug resistant. Moreover, 40.5% and 10.8% of the isolates were ESBL and carbapenemase producers, respectively. Aging, tobacco smoking, previous history of pneumonia, heart disease, and chronic respiratory disease had association with sputum culture-positivity.
    Conclusion: As a result, it is important to regularly monitor the bacterial etiologies and their patterns of resistance. Additionally, sociodemographic and clinical characteristics should all be taken into account while managing patients with pneumonia empirically in this context.

  • XML | PDF | downloads: 66 | views: 141 | pages: 503-512

    Background and Objectives: Extraintestinal pathogenic Escherichia coli (ExPEC) is a recently recognized and highly diverse pathotype of E. coli. Its significance as a pathogen has increased due to the emergence of hypervirulent and multidrug-resistant (MDR) strains. The aim of this study was to characterize ExPEC isolates from humans based on their phylogenetic group, virulence factor profile, and antimicrobial susceptibility.
    Materials and Methods: The isolates were collected from patients with extraintestinal infections caused by E. coli, including urinary tract infections, bacteremia, and surgical site infections. The E. coli phylogenetic groups were determined using multiplex PCR. Additionally, the isolates were evaluated for their biofilm-forming abilities, susceptibility to antimicrobial agents, and presence of virulence genes.
    Results: In this study, the isolates were classified into four phylogenetic groups: A (48.3%), B2 (25.8%), D (19.35%), and B1 (6.45%). All isolates exhibited at least one of the ten analyzed virulence factors. However, there was no direct evidence linking a specific phylogenetic group to a particular virulence factor. Nevertheless, the presence of the fimH, fyuA, ompT, traT, and kpsMTII virulence genes was correlated with the production of strong biofilms, multidrug resistance (MDR), and the production of alpha hemolysin.
    Conclusion: This study provides a description of the phylogenetic groups in ExPEC and their potential association with virulence factor profiles and antimicrobial susceptibility.

  • XML | PDF | downloads: 52 | views: 96 | pages: 513-520

    Background and Objectives: Gardnerella vaginalis is one of the most important causes of prevalent genital infections that pose serious risks. This study aimed to determine the prevalence of Gardnerella vaginalis and antibiotic resistance pattern of isolates of patients referred to the gynecology clinic of Shahriar Noor Hospital by PCR and culture methods.
    Materials and Methods: The study was conducted on 500 patients who had suffered from a vaginal infection. The demographic data of patients were studied. For diagnosis of Gardnerella vaginalis isolates, cultivation in anaerobic conditions, biochemical tests, PCR and Gardnerella vaginalis antibiotic susceptibility test to metronidazole and clindamycin were performed. Data analysis was performed utilizing SPSS statistical software version 19 and the Chi-square test.
    Results: Among the 500 patients, 173 were diagnosed with Gardnerella vaginitis. There was a significant relationship between age group, level of education, and contraceptive method with Gardnerella vaginosis incidence. Performing antibiotic susceptibility tests showed that the resistance of Gardnerella vaginalis isolated strains to metronidazole and clindamycin was 86.12% and 17.34%, respectively.
    Conclusion: The high prevalence of Gardnerella vaginalis infections confirms the critical role of the bacterium in the occurrence of bacterial vaginosis. Therefore, it is necessary to check the prevalence of bacterial infections to recommend the correct medical treatment in different societies.

  • XML | PDF | downloads: 47 | views: 69 | pages: 521-532

    Background and Objectives: he occurrence and characteristics of Extended Spectrum- and AmpC-β-lactamase producing Enterobacterales (ESBL-PE and AmpC-PE) in an urban wastewater treatment plant (WWTP) were investigated.
    Materials and Methods: A total of 30 wastewater samples were collected from all sections of WWTP. Enterobacterales were isolated and identified using standard microbiological tests. The antibiotic resistance profile was determined by the Kirby–Bauer disk diffusion method. Phenotypic screening for ESBL-PE and AmpC-PE isolates was performed by double-disk synergy and boronic acid disk potentiation tests, respectively. The isolates were examined for AmpC- and ESBL-encoding genes by PCR and sequencing methods.
    Results: Among 146 Enterobacterales isolates, 8.9% (n=13) [ESBL-only; 5.48% (n=8) and ESBL + AmpC; 3.42% (n=5)] were ESBL-producers and 15.75% (n=23) [AmpC-only; 12.33% (n=18) and ESBL + AmpC; 3.42% (n=5)] AmpC-producers. Hafnia spp. with 33.33% (n=1/3) and E. coli with 20.58% (n=7/34) [ESBL-only; 17.64% (n=6/34) and ESBL + AmpC; 2.94% (n=1/34)] were the most common ESBL-producing bacteria. Enterobacter spp. with 37.50% (n=6/16) of isolates were the most common AmpC-producing organisms. ESBL- and/or AmpC-producing isolates were identified in all parts of the WWTP including 80% (n=8/10) of samples taken from effluent. Among ESBL-producing isolates, blaCTX-M, blaTEM, and blaSHV ESBL-encoding genes were found in 61.5% (n=8), 15.3% (n=2), and 7.7% (n=1) of isolates, respectively. All CTX-M-type enzymes belonged to the CTX-M-1 group and CTX-M-15 subgroup. blaTEM and blaSHV type genes belonged to blaTEM-20 and blaHSV-12 subtypes, respectively. blaDHA with 73.9% (n=17/23), and blaCIT and blaFOX with 30.4% (n=7/23) each, were the most common AmpC-encoding genes among AmpC-producing isolates. Overall, 75% of ESBL-producing and 55.5% of AmpC-producing isolates exhibited multi-drug resistance phenotypes. The organisms were most resistant against ampicillin (82.2%) nalidixic acid (43.8%) and cephalexin (41.1%).
    Conclusion: ESBL- and AmpC-producing Enterobacterales spp. with diverse genetic resistance backgrounds in WWTP effluent poses a significant risk to public health.

  • XML | PDF | downloads: 42 | views: 53 | pages: 533-540

    Background and Objectives: Instead of antibiotics, propolis is a promising alternative for treating bacterial diseases. The aim of this study was to evaluate the effect of propolis ethanol extract (PEE) on Yersinia ruckeri (Y. ruckeri), a fish pathogen, by examining its impact on the cell wall, cytoplasmic membrane, and gene expression.
    Materials and Methods: The effect of propolis on the bacterial cell wall, membrane, and DNA using scanning electron microscopy (SEM) was investigated. Its effect on the NAD+/NADH ratio, reactive oxygen species (ROS) production, as well as the expression of a virulence factor (yrp1) was also determined.
    Results: It was demonstrated that PEE has multiple antibacterial mechanisms against Y. ruckeri involving cell wall damage, membrane lysis, and a decrease in gene expression.
    Conclusion: The obtained results indicated that the mode of propolis action against Y. ruckeri is both structural and functional, while others showed propolis only could inactivate bacteria in a structural way.

  • XML | PDF | downloads: 63 | views: 77 | pages: 541-549

    Background and Objectives: Plasma radiation is a widely used technique for sterilization or decontamination in various industries, as well as in some healthcare settings such as dentistry. The primary aim of this study was to assess the potential of plasma radiation to create a new population of Staphylococcus aureus cells with distinct characteristics that could lead to novel healthcare challenges.
    Materials and Methods: A homemade non-thermal plasma apparatus was applied and the effects of plasma treatment on S. aureus ATCC25923 was assessed. Plasma radiation was applied under controlled conditions to ensure that some bacterial cells remained viable. The treatment was repeated 10 times, with each round followed by a recovery phase to collect any surviving bacterial cells. To assess the potential changes in the bacterial population, we examined the antibiotic susceptibility pattern, micro-structural characteristics using scanning electron microscopy (SEM), and total protein profile using the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) technique.
    Results: The experimental results revealed slight variations in the antibiotic susceptibility patterns of certain cell wall agents (imipenem, cephalothin, and cefepime), as well as in the MALDI-TOF spectra. However, no changes were observed in the SEM images.
    Conclusion: The insufficient application of non-thermal plasma in bacterial decontamination may lead to physiological changes that could enrich or select certain subpopulations of S. aureus.

  • XML | PDF | downloads: 49 | views: 59 | pages: 550-556

    Background and Objectives: In the present study, the anti-biofilm activity of Lactobacillus rhamnosus GG and Nisin was investigated on biofilm-forming abilities of Staphylococcus epidermidis strains and the expression of the biofilm-associated genes.
    Materials and Methods: In this study, the standard strain of L. rhamnosus GG (ATCC 53103) and Nisin were used to assess their anti-microbial and anti-biofilm effects on S. epidermidis (RP62A).
    Results: The MIC and MBC analysis showed that Nisin at 256 μg/mL and 512 μg/mL, and L. rhamnosus GG at 1×107 CFU/mL and 1×108 CFU/mL have anti-microbial activity compared to the negative control respectively. L. rhamnosus GG bacteria and Nisin inhibited the biofilm formation of S. epidermidis based on optical density of at 570 nm (P <0.001). The relative mRNA expression of aap, icaA, and icaD genes was significantly reduced compared to the negative control after treating S. epidermidis with sub-MIC of Nisin (0.44, 0.25 and 0.6 fold, respectively) (P>0.05). In addition, the relative expression of aap and icaA genes, but not icaD (P>0.05), was significantly lower than the negative control (0.62 and 0.7 fold, respectively) (P>0.05), after exposure to the sub MIC of L. rhamnosus GG.
    Conclusion: Nisin and L. rhamnosus GG exhibit potent activity against biofilm-forming abilities of S. epidermidis and these agents could be utilized as an anti-biofilm agents against S. epidermidis infections.

  • XML | PDF | downloads: 35 | views: 48 | pages: 557-564

    Background and Objectives: The increasing number of methicillin-resistant Staphylococcus aureus persuade the need for preventive measures. Glucomannan is a polysaccharide choice for developing immunological strategies. This study aimed to investigate changes in gene expression and phagocytic activity of macrophage cells in the presence of glucomannan.
    Materials and Methods: The effect of different concentrations of glucomannan (25, 50, and 100 µg/mL) on the phagocytic activity of macrophage cells was measured using the colony count method. The expression of Tumor Necrosis Factor-alpha (TNF-α) and Inducible Nitric Oxide Synthase (iNOS) genes was evaluated by Real-Time PCR.
    Results: The concentrations of glucomannan significantly reduced the bacterial Colony-Forming Unit (CFU) and increased the phagocytic activity of macrophage cells. The maximum effect of glucomannan on iNOS and TNF-Α genes expression was 100 µg/mL.
    Conclusion: Glucomannan should be considered an adjuvant that stimulates the immune system. It may increase the expression of TNF-α and iNOS genes and the phagocytic activity of macrophage cells against methicillin-resistant Staphylococcus aureus.

  • XML | PDF | downloads: 69 | views: 60 | pages: 565-573

    Background and Objectives: This study aimed to develop a natural nanoemulsion with antibacterial and anticancer properties.
    Materials and Methods: The chemical composition of the Origanum majorana essential oil was investigated using GC–MS analysis. Besides, the successful loading of the essential oil in the nanoemulsion was confirmed using ATR-FTIR analysis. Moreover, nanoemulsion’s anticancer, antioxidant, and antibacterial activities were investigated.
    Results: Terpinen-4-o1 (46.90%) was identified as the major compound in the essential oil. The nanoemulsion with a 149 ± 5 nm droplet size and zeta potential of -11 ± 1 mV was prepared. The cytotoxic effect of the nanoemulsion against A-375 human melanoma cells (IC50 = 139 µg/mL) showed significantly more potency than A-549 human lung cancer cells (IC50 = 318 µg/mL). Interestingly, growth of Staphylococcus aureus (Gram-positive) and E. coli (Gram-negative) bacteria after treatment with 4800 µg/mL of nanoemulsion were obtained at 12 ± 2 and 6 ± 1%, respectively. However, the IC50 value of nanoemulsion against E. coli (580 µg/mL) was not significantly different (P > 0.05) from S. aureus (611 µg/mL).
    Conclusion: A straightforward preparation method, high stability, and multi-biological effects are the main advantages of the prepared nanoemulsion. Therefore it could be considered for further investigation in vivo studies or complementary medicine.

  • XML | PDF | downloads: 30 | views: 52 | pages: 574-584

    Background and Objectives: The present study was to evaluate the microbial diversity inhabiting biodeteriorated precious manuscripts of the Holy Quran placed in one of the repositories of the Library of Astan Quds Razavi (AQR), and its relation to the air microbial diversity.
    Materials and Methods: Three non-invasive sampling methods, culture-based techniques, and molecular identification were used to investigate the microorganisms involved in deterioration. To investigate the air microbial quality and its role in the destruction of the repository objects, air samples were taken from six different points inside the repository. Biomodeling studies were designed to verify the impact of microbial isolates.
    Results: 14 fungal isolates were obtained from three deteriorated ancient Quran manuscripts. The most frequently isolated fungi from the different substrates were Aspergillus spp. and Penicillium spp. In the air, the prevalence across fungal genera was rather uniform. 30 species of the identified bacteria were collected from three manuscripts. The results obtained in the present study showed that the bacterial species from different genera belonged to three phyla: Proteobacteria (n = 2), Actinobacteria (n = 4), and Firmicutes (n = 24). The paper strips were artificially colonized by Aspergillus sp., Penicillium chrysogenum, and Talaromyces diversus producing spots which were visible to the naked eye. In the scanning electron microscopy images, the colonization of the selected organism was observed.
    Conclusion: The characteristics of paper inoculated artificially with these microbial isolates confirmed their deteriorating effects. Based on molecular identification, the similarity of fungal and bacterial species isolated from both substrates and air samples suggest the direct relationship between microorganisms from the air and those isolated from the manuscripts.

  • XML | PDF | downloads: 44 | views: 69 | pages: 585-593

    Background and Objectives: Breast cancer is currently the most commonly diagnosed neoplasm in women worldwide. There is evidence that human papillomavirus (HPV) infection may play a key role in breast cancer aggressiveness, but results are conflicting across studies. The aim of this study was to investigate the presence of the HPV viral genome in benign and malignant breast tissue samples and its clinicopathological characteristics of cancer.
    Materials and Methods: In this case-control study, 100 formalin-fixed paraffin-embedded (FFPE) of breast cancer and 100 blocks of non-cancerous breast tissue were selected as a control group from the pathology department of Imam Khomeini Hospital in Ahvaz from 2020-2022. The presence of HPV was detected using nested PCR including MY09/11 primers and sequencing were performed for virus genotyping.
    Results: The present study enrolled 100 subjects each in two cancer and control groups with a mean age of 52.81±13.23 and 35.77±11.65, respectively. The risk of cancer in HPV-infected patients is almost 5 times higher than in HPV-negative individuals, it is not statistically significant (OR =4.99, 95% CI 0.35 to 72.15, p=0.238). The prevalence of HPV in the cancer and control groups was 7% and 1%, respectively and HPVs detected in two groups were of the HPV 16 genotype. Although the chance of ER and PR expression, lymphvascular involvement, perineural invasion, and higher tumor grade was higher in HPV-positive subjects than in HPV-negative subjects, this was not statistically significant (OR>1, p>0.05).
    Conclusion: Based on studies reporting the existence of sequences of different high-risk HPV types (oncogenes) in breast cancer tissues, this study confirmed the hypothesis of a possible infectious cause in the development of breast cancer. So far, however, the results have been controversial and inconclusive. Further studies with large sample sizes are needed to demonstrate the link between HPV and breast cancer.

  • XML | PDF | downloads: 39 | views: 75 | pages: 594-600

    Background and Objectives: Because of the controversial aspects of the CMV virus during pregnancy, it should be considered a serious health threat, especially in developing countries. The present seromolecular study aimed to determine cytomegalovirus prevalence in pregnant women referred to health centers in the north of Iran.
    Materials and Methods: One hundred and twenty-five pregnant women who were referred to health centers in Mazandaran province for regular health checks were randomly selected from Jan 2022 to Oct 2022. To detect the presence of the CMV genome and specific IgM and IgG antibodies against cytomegalovirus, the conventional PCR and ELISA tests were applied respectively.
    Results: All 125 pregnant women that attended the study were from Mazandaran province with a mean age of 30 years ranging from 20 to 42 years. The result showed that 2 (1.6%), 92 (73.6%), and 2 (1.6%) of the cases were positive for IgM, IgG, and IgM/IgG, respectively. The PCR test results indicated that the CMV DNA was present in 10 (8%) pregnant women. Our study shows that all PCR-positive cases were negative for the IgM test. Of the 10 PCR-positive samples 3 were positive and 1 was suspicious for the IgG test.
    Conclusion: Our study revealed that there is an urgent need for vaccination or other strategies to prevent and treat congenital CMV infection. Reducing the burden of congenital CMV infection requires global awareness. Further studies are recommended to obtain accurate estimates of the risk of congenital CMV infection.

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