2020 CiteScore: 1.7
CHAIRMAN AND EDITOR:
Mohammad Mehdi Feizabadi
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.
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is a newly emerged virus which belongs to Coronaviridae family within the betacoronavirus genus. Previous reports demonstrated that other betacoronaviruses were responsible for adverse outcomes during pregnancy in human. Due to inadequate data, the consequences of a SARS-CoV-2 infection during pregnancy is still a public health concern in the second year of SARS-CoV-2 circulation in human population. Herein, we aimed to review the probable risk of intrauterine vertical transmission of SARS-CoV-2 infection to the fetus, its adverse outcomes during pregnancy for both mother and the fetus and maternal risk factors which affect the severity Coronavirus disease 2019 (COVID-19.
Inflammation acts like a double-edged sword and can be harmful if not appropriately controlled. COVID-19 is created through a novel species of coronavirus SARS-CoV-2 (2019-nCoV). Elevated levels of inflammatory factors such as interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), etc. lead to Acute Respiratory Distress Syndrome (ARDS) and severe complications of infection in the lungs of coronavirus-infected patients. Astaxanthin is a natural and potent carotenoid with powerful antioxidant activity as well as an anti-inflammatory agent that supports good health. The effects of astaxanthin on the regulation of cyclooxygenase-2 (COX-2) pathways and the reduction and suppression of cytokines and other inflammatory agents such as IL-6 and TNF-α have already been identified. Therefore, these unique features can make this natural compound an excellent option to minimize inflammation and its consequences.
Background and Objectives: Ceftaroline (CPT) is a novel cephalosporin with potent activity against methicillin-resistant Staphylococcus aureus (MRSA). Despite its recent introduction, CPT resistance in MRSA has been described worldwide. We aimed in the current study to evaluate the in vitro activity of CPT against 91 clinical MRSA and 3 MSSA isolates.
Materials and Methods: Susceptibility of isolates to CPT was tested using E-test and disk diffusion (DD) method. The nucleotide sequence of the mecA gene and molecular types of isolates with reduced susceptibility to CPT were further studied to identify resistance conferring mutations in PBP2a and the genetic relatedness of the isolates respectively.
Results: Overall, 92.5% of isolates were found to be CPT susceptible (MICs≤1mg/l) and 7 MRSA isolates were characterized with MIC=2mg/l and categorized as susceptible dose dependent. Compared to E-test, DD revealed a categorical agreement rate of 93.6% and the obtained rates for minor, major /very major error were found to be 6.3% and 0% respectively. The MRSA isolates with increased CPT MICs (n=7), belonged to spa types t030 (n=6) and t13927 (n=1) and all carried N146K substitution in PBP2a allosteric domain, except for one isolate which harbored a wild-type PBP2a.
Conclusion: While resistance to CPT was not detected we found increased CPT MICs in 7.69% of MRSA isolates. Reduced susceptibility to CPT in the absence of mecA mutations is indicative of contribution of secondary chromosomal mutations in resistance development.
Background and Objectives: The oral cavity harbors numerous Streptococcus mutans strains which display remarkable genotypic and phenotypic diversity. This study evaluated the genotypic and phenotypic diversity of 209 S. mutans strains isolated from 336 patients with dental caries and compared with the universal reference strain, UA159.
Materials and Methods: Selective cultivation on mitis-salivaries-bacitracin agar and species-specific polymerase chain reaction (PCR) was carried out to isolate and identify the 209 S. mutans isolates from 336 patients with dental caries. Arbitrarily primed polymerase chain reaction (AP-PCR), PCR amplification of specific gene, acid production and biofilm formation capacity were performed to evaluate the genotypic and phenotypic variation. Student’s t-test and Chi-square test were used for analysis of variables and a probability (P) of <0.05 was considered as significant.
Results: Our study revealed a high degree of genotypic and phenotypic variability among the clinical strains. We observed significant differences in colony morphology, generation time, biofilm formation, and acid production while growing in culture medium. All the clinical isolates were able to lower pH while growing in Todd-Hewitt broth. Consistent with phenotypic variations, we also observed genotypic variation by AP-PCR and gene specific PCR. AP-PCR analysis suggested that most of the patients with dental caries have distinct type of S. mutans strains. Genes related to various two component systems were highly conserved among the isolated strains, however, bacteriocin encoding genes such as nlmAB, nlmC were absent in nearly half of the clinical isolates.
Conclusion: Our results support that S. mutans clinical isolates have wide genotypic diversity and show variation in growth kinetics, acid production, acid tolerance and biofilm formation capacity and indicates the presence of diverse mechanism to initiate and establish the biofilm lifestyle which leads to tooth decay.
Background and Objectives: It is well known that Staphylococcus aureus biofilm plays an important role in adenoiditis and biofilm resistance frequently results in failure of therapy. The goal of this study was to evaluate the biofilm production of S. aureus isolates obtained from adenoid specimens and assess the relationship between biofilm formation ability and ica operon genes.
Materials and Methods: A total of 112 adenoid samples were obtained from patients under 15 years old with adenoid hypertrophy. All S. aureus isolates were initially identified by standard microbiological tests and amplification of nuc by polymerase chain reaction (PCR) technique. Biofilm formation of S. aureus isolates was evaluated and icaADBC genes were detected by PCR technique.
Results: There were 46 isolates (41%) identified as S. aureus. The ability to produce biofilm was detected among total S. aureus isolates. Molecular study of ica operon revealed that 2 (6.3%) and 19 (59.4%) isolates carried icaA and icaD, respectively. The prevalence of icaA + icaD was seen among 11 (34.4%) S. aureus isolates, while icaC and icaB were not detected.
Conclusion: Our findings indicated that icaABCD operon are associated with biofilm formation in S. aureus isolates, however the absence of these genes may not necessarily exclude this property.
Background and Objectives: Neisseria meningitidis, Escherichia coli K1, Streptococcus agalactiae, and Streptococcus pneumoniae cause 90% of bacterial meningitis. Almost all infected people die or have irreversible neurological complications. Therefore, it is essential to have a diagnostic kit with the ability to quickly detect these fatal infections.
Materials and Methods: The project involved 212 patients from whom cerebrospinal fluid samples were obtained. After total genome extraction and performing multiplex quantitative polymerase chain reaction (qPCR), the presence or absence of each infectious factor was determined by comparing with standard strains.
Results: The specificity, sensitivity, positive predictive value, and negative predictive value calculated were 100%, 92.9%, 50%, and 100%, respectively. So, due to the high specificity and sensitivity of the designed primers, they can be used instead of bacterial culture that takes at least 24 to 48 hours.
Conclusion: The remarkable benefit of this method is associated with the speed (up to 3 hours) at which the procedure could be completed. It is also worth noting that this method can reduce the personnel unintentional errors which may occur in the laboratory. On the other hand, as this method simultaneously identifies four common factors that cause bacterial meningitis, it could be used as an auxiliary method diagnostic technique in laboratories particularly in cases of emergency medicine.
Background and Objectives: Non-fermentative Gram-negative Bacilli (NFGNB) is known as a major cause of healthcare-associated infections with high levels of antibiotic resistance. The aim of this study was to investigate the antibiotic resistance profiles and molecular characteristics of metallo-beta-lactamase (MBL)-producing NFGNB.
Materials and Methods: In this cross-sectional study, the antibiotic resistance profile of 122 clinical NFGNB isolates was determined by the Kirby-Bauer disk diffusion and microdilution broth methods. Bacterial isolates were investigated for the detection of MBLs production using the combination disk diffusion Test (CDDT). The existence of blaIMP, blaVIM, and blaNDM genes in all carbapenem-resistant isolates was determined employing polymerase chain reaction (PCR) assays.
Results: High resistance in Pseudomonas aeruginosa was reported to cefotaxime and minocycline, whereas Acinetobacter baumannii isolates were highly resistant to all antibiotics except colistin. Multidrug resistance (MDR)-NFGNB (66% vs. 12.5%, P=0.0004) and extensively drug resistant (XDR)-NFGNB (55.7% vs. 12.5%, P=0.001) isolates were significantly more common in hospitalized patients than in outpatients. The production of MBL was seen in 40% of P. aeruginosa and 93.3% of A. baumannii isolates. It was found that 33.3% and 46.7% of carbapenem-resistant P. aeruginosa isolates, and 13.3% and 28.9% of carbapenem-resistant A. baumannii isolates were harboring blaIMP-1 and blaVIM-1 genes, respectively. The incidence of MDR (98.2% vs. 28.3%, P<0.001) and XDR (96.4% vs. 11.7%, P<0.001) in MBL-producing NFGNB isolates was significantly higher than non-MBL-producing isolates.
Conclusion: This study demonstrated a higher rate of resistance among NFGNB isolates with an additional burden of MBL production within them, warranting a need for robust microbiological surveillance and accurate detection of MBL producers among the NFGNB.
Background and Objectives: Enzootic abortion in sheep and goats, also called ovine enzootic abortion (OEA) or enzootic abortion of ewes (EAE), is caused by Chlamydia abortus. The disease has a major economic impact as it represents the most important cause of lamb loss in sheep in parts of Europe, North America and Africa. This serious and potentially life-threatening zoonosis can also affect pregnant women after contact with lambing ewes, leading to severe febrile illness in pregnancy and loss of the foetus.
Materials and Methods: The present study was conducted to the Phylogenetic and Molecular Analysis based on Genes 16S-rRNA, OmpA and POMP of C. abortus in milk samples collected from sheep and goats in West Azerbaijan province, Iran. During 2018, a total number of 360 milk samples were collected from sheep (n = 180) and goats (n = 180) of different regions of the province. All milk samples were subjected to DNA extraction and examined by PCR.
Results: Among 360 milk samples collected from sheep and goats, 31 (8.611%; 95% CI=6.13-11.96) were positive for Chlamydia spp. The helicase, 16S-rRNA and ompA genes were examined and resulted in 8, 31, 31 of positive samples respectively. The accession numbers have been deposited in GenBank (NCBI) (MT367602 and MT367603).
Conclusion: Phylogenetic analysis based on the gene of helicase showed that most of the isolates shared similarity > 99.97%.
Background and Objectives: Legionnaires’ disease continues to be a public health concern. Colonized water distribution systems are often implicated in Legionella transmission, despite the use of various disinfection strategies, the bacterium is capable to persist and survive in water systems. The aim of this study was to investigate the persistence of Legionella pneumophila to sodium chloride over time at different temperatures and analysing the role of biofilms in the survival of this bacteria.
Materials and Methods: L. pneumophila serogroup 1 and L. pneumophila serogroup 2-15 were used to study the effect of sodium chloride on planktonic and sessile cells. The tested concentrations were: 0.5%, 1%, 2%, 3%, 4%, 6% and 8% (W/V) NaCl. Biofilms were grown on 24-well microplates.
Results: At 20°C, L. pneumophila planktonic cells were able to survive in sodium chloride concentrations up to 2%. However, at 37°C, a sodium chloride concentration over 1.5%, reduced systematically the numbers of bacterial cells. Biofilms were grown for 20 days in the absence and presence of sodium chloride. The results show that bacterial strains were able to survive and regrow after the sodium chloride shock (2-3%). Moreover, it seems that this effect is less expressed with the age of the biofilm; old biofilms were more persistent than the young ones.
Conclusion: Results from this study demonstrate that the sodium chloride disinfection strategy was effective on Legionella pneumophila planktonic cells but not on biofilms, which demonstrate the role of biofilms in the persistence and recolonization of L. pneumophila in water distribution systems.
Background and Objectives: There are conflicting studies on the prevalence of mediastinal lymphadenopathy (LAP) and its relationship to the prognosis of COVID-19 disease. The prevalence varied from 3.4 to 66 percent and more prevalent in patients who died. This study aimed to investigate the mediastinal lymphadenopathy and the disease progression in COVID-19 patients.
Materials and Methods: In this case-control study, 195 COVID-19 patients were divided into two groups, with the mediastinal lymphadenopathy and without it. In these groups, demographic characteristics, underlying diseases, laboratory results, and outcomes were compared.
Results: The median age in the LAP group was higher than the opposite group (62 vs. 58.5; p= 0.037). SpO2 (85% vs. 90%; P <0.001), lymphocyte count (760 vs. 969; p= 0.02), Neutrophil-to-Lymphocyte Ratio (5.53 vs. 4.41; p= 0.02), and ESR (36 vs. 29; p= 0.03) were significantly correlated with the presence of lymphadenopathy, using the Mann-Whitney Wilcoxon rank test. ICU admission (65.71% vs. 36.87; p= 0.003), mechanical ventilation (31.42% vs. 13.75%; p= 0.022), disease severity (65.71% vs. 40%; p <0.01), length of hospital stay (9 vs. 7; p= 0.039) and mortality rate (40% vs. 21.25%; p= 0.034) were more predominantly observed in the LAP group, using the χ2 test. There was no apparent difference in sex and the underlying diseases among the two groups.
Conclusion: This observation showed a relatively high prevalence of mediastinal lymphadenopathy in COVID-19 patients, which was more common in the elderly with low oxygen saturation. Therefore, LAP may lead to further intensive care needs, more use of mechanical ventilation, high severity of disease, and mortality rate.
Background and Objectives: Human Enterovirus 71 (EV-A71) is the causative agent for many dermal to neurological diseases especially polio-like paralysis outbreaks around the world. This study, the first of this kind in Iran, aimed to find neutralizing antibodies against EV-A71 in serum of healthy individuals in different age groups based on neutralization test (NT).
Materials and Methods: In this cross-sectional study, 547 serum samples were collected from healthy individuals who were referring for routine checkup tests (aged from under 6 months to over 31 years old) to Imam-Khomeini Hospital in Tehran during January-December 2015. Serum samples were examined by NT in cell culture to detect neutralizing antibodies against EV-A71. In the next step, some of the positive samples were subjected to complete titration to determine the exact titer of anti-EV-A71 antibodies.
Results: Of 547 samples, 310 (56.7%) were positive for EV-A71 neutralizing antibody. The presence of the antibody increased with age (p<0.001), and there was a significant statistical relationship between sex and the presence of antibody (p=0.009).
Conclusion: Our results demonstrated an apparent but limited circulation of EV-A71 in our society. After the worldwide eradication of poliovirus, EV-A71 which can cause polio-likes syndrome, might be the new challenge for our health care system as regard more in depth research is however needed.
Background and Objectives: Human T-lymphotropic virus type-1 (HTLV-1) belongs to retrovirus family that causes the neurological disorder HTLV-1 adult T-cell leukemia/lymphoma (ATLL). Since 1980, seven subtypes of the virus have been recognized. HTLV-1 is prevalent and endemic in some regions, such as Africa, Japan, South America and Iran as the endemic regions of the HTLV-1 in the Middle East. To study HTLV-1 subtypes and routes of virus spread in Iran, phylogenetic and phylodynamic analyses were performed and for as much as no previous phylogenetic studies were conducted in Tehran, we do this survey. To this purpose, the Tax region of HTLV-1 was used.
Materials and Methods: In this study 100 samples were collected from blood donors in Tehran. All samples were screened for anti-HTLV-I antibodies by ELISA. Then, genomic DNA was extracted from all positive samples (10 people), and for confirmation of infection, ordinary PCR was performed for both the HBZ and LTR regions. Moreover, the Tax region was amplified and purified PCR products were sequenced and analyzed, and finally, a phylogenetic tree was constructed using Mega X software.
Results: Phylogenetic analysis confirmed that isolates from Iran, Japan, Brazil, and Africa are located within the extensive ‘‘transcontinental’’ subgroup A clade of HTLV-1 Cosmopolitan subtype a. The Japanese sequences are the closest to the Iranian sequences and have the most genetic similarity with them.
Conclusion: Through phylogenetic and phylodynamic analyses HTLV-1 strain in Tehran were characterized in Iran. The appearance of HTLV-1 in Iran was probably happened by the ancient Silk Road which linked China to Antioch.
Background and Objectives: Pneumocystis jirovecii pneumonia (PJP) is a serious infection that usually affects those with a weak immune system. Since the prevalence of this infection in Iran and in the world is not clearly defined, the present study aimed to evaluate the incidence, clinical spectrum, and demographic characteristics of PJP among HIV and non-HIV immunocompromised patients.
Materials and Methods: Bronchoalveolar Lavage (BAL) specimens were obtained from 3 groups of immunocompromised patients, including acquired immunodeficiency syndrome (AIDS) patients, diabetic patients, and patients receiving immunosuppressive therapies. All were hospitalized in pulmonary units. The specimens were examined using microscopic methods (Giemsa and calcofluor white staining) and the nested-PCR technique based on mtLSU-rRNA gene.
Results: A total of 120 BAL samples were collected. From 12.5% (5 from 40) of HIV-infected patients, 5% (2 from 40) of patients receiving immunosuppressive therapies, and 2.5% (1 from 40) of diabetic patients Pneumocystis jiroveci was isolated. There was not any association between the prevalence of PJP and the patient's gender (p= 0.557) and age (p= 0.681). Fever and dyspnea (n=7, 87.5%), nonproductive cough and abnormal auscultation sound (n=5, 62.5%), and also chills and weight loss (n=2, 25%) were the documented clinical symptoms of PJP. Also, the results showed that none of the samples had positive results for P. jiroveci with microscopic tests while using the nested-PCR method 8 samples had positive results.
Conclusion: Since PJP often causes symptoms that are similar to other illnesses, such as the flu or tuberculosis, clinical and laboratory findings should be used simultaneously for making the final decision on drug administration.
Background and Objectives: Monosomy of chromosome 5 associated with utilization of non-canonical sugar L-sorbose is one of the well-studied aneuploidies in Candida albicans. Stress-induced ploidy changes are crucial determinants for pathogenicity and genetic diversity in C. albicans. The five scattered regulatory regions (A, B, C, 135, and 139) comprising of two functionally redundant pathways (SUR1 and SUR2) were found to be responsible for the growth on L-sorbose. So far, three genes such as CSU51, CSU53 and CSU57 have been identified in region A, region 135 and region C, respectively. In this study we have verified the role of region B in this regulatory pathway.
Materials and Methods: We employed a combinatorial gene deletion approach to verify the role of region B followed by co-over expression studies and qRT-PCR to identify the regulatory role of this region.
Results: We confirmed the role of region B in the regulation of SOU1 gene expression. The qRT-PCR results showed that regulation occurs at transcriptional level along with other two regions in SUR1 pathway. A previously uncharacterized open reading frame in region B has been implicated in this regulation and designated as CSU52. Integrating multiple copies of CSU52 in the genome at tandem, suppresses the growth of recipient strain on L-sorbose, establishing it as a repressor of SOU1 gene.
Conclusion: This finding completes the identification of regulators in SUR1 pathway. This result paves the way to study the underlying molecular mechanisms of SOU1 gene regulation that in-turn helps to understand stress induced aneuploidy.
Background and Objectives: Earthworms coexist with various pathogenic microorganisms; thus, their immunity mechanisms have developed through a long process of adaptation, including through endogenous bacterial symbionts. This study aims to identify earthworm endosymbiont bacteria compounds and their antibacterial activity through an in vitro approach supported by an in silico approach.
Materials and Methods: This research was conducted using the in vitro inhibition test through agar diffusion and the in silico test using molecular docking applications, namely, PyRx and Way2Drugs Prediction of Activity Spectra for Substances (PASS).
Results: The in vitro results showed a potent inhibition activity with a clear zone diameter of 21.75 and 15.5 mm for Staphylococcus aureus and Salmonella Typhi, respectively. These results are supported by chromatography and in silico tests, which showed that several compounds in endosymbiotic bacteria, cyclo (phenylalanyl-prolyl) and sedanolide, have high binding affinity values with several antibiotic-related target proteins in both pathogenic bacteria. Cyclo (phenylalanyl-prolyl) has the highest binding affinity of -6.0 to dihydropteroate synthase, -8.2 to topoisomerase, and -8.2 to the outer membrane, whereas sedanolide has the highest binding affinity to DNA gyrase with approximately -7.3. This antibiotic activity was also clarified through the Way2Drugs PASS application.
Conclusion: Ten active compounds of endosymbiont bacteria, Cyclo (phenylalanyl-prolyl) and sedanolide were potential candidates for antibacterial compounds based on the inhibition test of the agar diffusion method and the results of reverse docking and Way2Drugs PASS.
Background and Objectives: Non-thermal atmospheric-pressure plasma or cold plasma is defined as an ionized gas. This study aimed to investigate the effect of cold plasma on Pseudomonas aeruginosa strains. Also, the expression level of the alp virulence gene before and after treatment with cold plasma was compared with the Housekeeping gene gyrA.
Materials and Methods: P. aeruginosa isolates recovered from hospitalized burn patients at Shahid Motahari Burns Hospital, Tehran, Iran. The Kirby Bauer disk diffusion method was used to determine the antimicrobial susceptibility test. Then, the antibacterial effect of atmospheric non-thermal plasma was evaluated on P. aeruginosa in as in vitro and in vivo studies at different times on Muller Hinton agar and in mouse model (treated by plasma every day/ 90 sec). The histopathological study was evaluated by Hematoxylin-Eosin staining. Data were analyzed using SPSS software by the Chi-square test and Pvalues less than 0.05 considered as statistically significant.
Results: Results indicated that non-thermal atmospheric plasma inhibited the growth of P. aeruginosa. The non-thermal helium plasma accelerates wound healing for 6 days. Results showed that cold plasma decreased virulence gene expression alp after treatment. Therefore, cold plasma can be suggested as a complementary therapeutic protocol to reduce bacterial infection and accelerate wound healing and reduce the expression of virulence genes of pathogens.
Conclusion: Cold plasma showed pathogen inhibitory properties of P. aeruginosa and virulence alkaline protease and wound healing properties in animal models, so this inexpensive and suitable method can be presented to the medical community to disinfect burn wounds and improve wound healing.
Background and Objectives: Microalgae have been widely used as a novel source of bioactive substances. These substances exhibit various biological actions including, antioxidant and antitumor effects material. The present work is carried out to evaluate potential applications of cyanobacterium Oscillatoria simplicissima containing mainly polysaccharides.
Materials and Methods: Crude polysaccharides from marine cyanobacteria Oscillatoria simplicissima and Oscillatoria acutissima were extracted and characterized according to their chemical content and cytotoxic activities. The isolated polysaccharides characterized by the Fourier transmittance infrared spectrum (FT-IR).
Results: These polysaccharides constituted 34.68 mg/g of sugar, 0.011 mg/g of protein, and 28.92 mg/g of sulfate contents. The antioxidant property of the methanol extracts of these green microalgae was evaluated by measuring the free radical scavenging activity by the DPPH assay method. The algal extracts were then evaluated for their suppressive effect on tumor cell growth (A-549, MDA-MB-231, PC-3, HT-29, HepG2, and HeLa) by using the SRB assay. At a concentration of 10 mg/mL, Oscillatoria simplicissima exhibits an antioxidant activity of 45.97%. The cytotoxic activity revealed that Oscillatoria simplicissima polysaccharide shows potent cytotoxic activity against lung cancer (A-549) cell line 49.465 μg/mL.
Conclusion: Microalgal polysaccharides have great therapeutically potential in drug development used as antitumor and antioxidant agents in near future.
The polymerase chain reaction-based open reading frame typing (POT) method is a simple and rapid method for the strain-level discrimination of methicillin-resistant Staphylococcus aureus (MRSA). We investigated the molecular characteristics of S. aureus strains by multilocus sequencing typing (MLST) and POT and the profiles of antibiotic resistance and virulence genes of MRSA isolates in a single center of Tokyo, Japan. Five types by MLST and 19 types by POT were detected in the 25 MRSA isolates. ST5 and a POT1 score of 93 were associated with healthcare-associated MRSA, whereas ST8 and a POT1 score of 106 were associated with community-associated MRSA. Each strain evaluated by POT score was completely associated with similar profiles of antibiotic resistance and virulence genes. These data showed that the POT system was a powerful molecular tool for the epidemiological characterization of MRSA isolates, which correlated with the profiles of antibiotic resistance and virulence genes.