Microbiology
Zahra Gholipour; Abbas Ali Imani Fooladi; Kazem Parivar; Raheleh Halabian
Abstract
Background & Objective: Superantigens are bacterial toxins that induce a massive immune response in the host. Superantigen staphylococcal enterotoxin B (SEB) can form a ternary complex with its receptors, MHC class II (MHCII) and TCR, and can be used in tumor-targeting therapy, particularly when ...
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Background & Objective: Superantigens are bacterial toxins that induce a massive immune response in the host. Superantigen staphylococcal enterotoxin B (SEB) can form a ternary complex with its receptors, MHC class II (MHCII) and TCR, and can be used in tumor-targeting therapy, particularly when cooperating with a specific vector. In this study, SEB was fused to interleukin-13 (IL13), which forms a complex with IL13 receptor α2 (IL13Rα2) overexpressed in glioblastoma multiforme (GBM) cells for therapeutic goals.Methods We designed four fusion proteins based on the arrangement of SEB (N- or C-terminal domain) and provided a flexible inter-domain linker (no or yes), resulting in the formation of SEB-IL13, SEB-L-IL13, IL13-SEB, and IL13-L-SEB, respectively. These fusion proteins were then evaluated for their various physicochemical properties and structural characteristics. Bioinformatics tools were employed to predict, refine, and validate the three-dimensional structure of the fusion proteins. In addition, the fusion proteins were docked with IL13Rα2, MHCII, and TCR receptors through the HADDOCK 2.4 server. The candidate fusion protein was subjected to molecular dynamics simulation.Results: There were differences among the designed fusion proteins. The model with the N-terminal domain of IL13 and containing an inter-domain linker (IL13-L-SEB) was stable and had a long half-life. The docking analysis revealed that the IL13-L-SEB fusion protein had a higher binding affinity to the IL13Rα2, MHCII, and TCR receptors. Finally, using molecular dynamics simulation through iMODS, acceptable results were obtained for the IL13-L-SEB docked complexes.Conclusion: The results suggest IL13-L-SEB is a promising novel fusion protein for cancer therapeutic application.
Microbiology
Arezoo Salami; Mahsa Falahatinejad; Mahsa Abdorahimi; Mohammadreza Salehi; Farzad Aala; Alireza Abdollahi; Hana Saffar; Sadegh Khodavaisy
Abstract
There has been a rise in COVID-19-associated mucormycosis (CAM) cases, particularly in low-income countries. We describe a case of primary cutaneous mucormycosis after recovering from COVID-19 in a kidney transplant recipient who had a known case of diabetes mellitus. The patient developed cutaneous ...
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There has been a rise in COVID-19-associated mucormycosis (CAM) cases, particularly in low-income countries. We describe a case of primary cutaneous mucormycosis after recovering from COVID-19 in a kidney transplant recipient who had a known case of diabetes mellitus. The patient developed cutaneous ulcers due to Rhizopus oryzae in the right hand. She did not recall any trauma or injury at the affected site. Based on the appearance of the wound we suspected that healthcare-associated mucormycosis could be the causative agent. Due to the initial misdiagnosis as a bacterial infection, the appropriate treatment was delayed, and the lesions progressed rapidly to necrotic ulcers with jagged margins that deteriorated during hospitalization. She underwent consecutive surgical interventions and received broad-spectrum antifungal therapy. Finally, the patient deceased after 32 days of hospital stay. We reviewed the previous case reports of cutaneous mucormycosis occurring in COVID-19 patients and described patient characteristics, predisposing factors, location of ulcers, clinical presentation, management, and outcome. This report and existing published literature indicate a poor outcome for cutaneous mucormycosis in COVID-19 patients and the importance of early diagnosis, aggressive multidisciplinary management, and regular follow-up as a life-saving measure, especially in immunocompromised patients.
Microbiology
Meysam Manouchehrifar; Farzad Khademi; Hadi Peeri Doghaheh; shahram Habibzadeh; Mohsen Arzanlou
Abstract
Background & Objective: Staphylococcus aureus causes various hospital- and community-acquired infections. This study aimed to investigate the phenotypic and genotypic characteristics of erythromycin and inducible clindamycin resistance, virulence gene profiles, and spa types of S. aureus isolates ...
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Background & Objective: Staphylococcus aureus causes various hospital- and community-acquired infections. This study aimed to investigate the phenotypic and genotypic characteristics of erythromycin and inducible clindamycin resistance, virulence gene profiles, and spa types of S. aureus isolates collected from patients in Ardabil Province, Iran.Methods: A total of 118 clinical S. aureus isolates, including 50 (42.4%) methicillin-resistant S. aureus (MRSA) and 68 (57.6%) methicillin-susceptible S. aureus (MSSA) strains, were investigated. Resistance patterns were determined by the disk diffusion method and minimum inhibitory concentration (MIC) test. Inducible macrolide-lincosamide-streptogramin B (iMLSB) resistance was detected using D-test method. The polymerase chain reaction (PCR) was used to identify the virulence and resistance-encoding genes. Additionally, the spa types of the isolates were determined using the PCR, followed by sequencing.Results: In total, 49.1% (58/118) and 44% (52/118) of the isolates were resistant to erythromycin and clindamycin, respectively. Overall, 13.5% (16/118) of the isolates showed the iMLSB resistance phenotype. The ermC gene (72.4% [42]) was the most frequent erythromycin resistance-encoding gene, followed by ermA (60.3% [35]), ermB (60.3% [35]), ermTR (51.7% [30]), and msrA (15.5% [9]) genes among erythromycin-resistant isolates. The virulence genes hla, hld, sea, LukS PV, tst, seb, sed, eta, sec, and etb were detected in 93.2%, 74.5%, 70.3%, 32.2%, 29.6%, 17%, 8.5%, 8.5%, 5.9%, and 4.2% of the isolates, respectively. Ten different spa types were identified for 58 erythromycin-resistant S. aureus strains, of which t030 and t078 types were the most common types.Conclusion: A high frequency of macrolide- and lincosamide-resistant S. aureus isolates with different genetic backgrounds of resistance and virulence may be found in patients in Ardabil Province, Iran.
Microbiology
Samaneh Salarvand; Alireza Abdollahi; Pegah Afarinesh Khaki; Mahsa Norouzi Shadehi; Mohammad Taghi Beigh Mohammadi; Seyed Amir Miratashi Yazdi; Elham Nazar
Abstract
Background & Objective: Antibiotic resistance, especially in the form of multidrug-resistant (MDR), is a big problem, especially in intensive care units (ICUs). This study aimed to evaluate antibiotic resistance and MDR patterns among patients hospitalized in the ICUs in one of the large referral ...
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Background & Objective: Antibiotic resistance, especially in the form of multidrug-resistant (MDR), is a big problem, especially in intensive care units (ICUs). This study aimed to evaluate antibiotic resistance and MDR patterns among patients hospitalized in the ICUs in one of the large referral centers in Iran.Methods: The present study was conducted at Imam Khomeini Hospital in Tehran (a great referral hospital), which admits critically ill patients requiring ICU services. To determine the rate of positive cultures for resistant strains, the patient’s blood specimens were sent to the laboratory of the hospital for inoculation on proper culture media within 2 hours of extraction. Antimicrobial susceptibility tests were done using the Bauer–Kirby disk diffusion method.Results: A total of 1,755 samples were collected from the patients to assess microbial strains and antibiotic resistance. The most common microbial strains detected in the cultures extracted from peripheral blood samples were Klebsiella pneumonia (22.1%), Staphylococcus epidermidis (7.9%) and another coagulase-negative Staphylococcus (15.0%). The antibiogram test showed antibiotic resistance in 1,509 cases, leading to a resistance prevalence rate of 85.9%. The most common antimicrobial resistance observed was against cotrimoxazole (61.7%), ciprofloxacin (51.3%), imipenem (50.0%), and ampicillin (49.6%). The rate of MDR was found to be 96.3%.Conclusion: In Iran’s ICUs, a significantly high level of antibiotic resistance may be seen especially the MDR pattern, which indicates the need to change the pattern of prescribing and managing these drugs in ICU centers.
Microbiology
zahra Mottaghiyan; Davoud Esmaeili; Mohammad Hossein Ahmadi; Mohammad Niakan
Abstract
Background & Objective: Acinetobacter baumannii strains harboring Meallobetalactamases (MBL) pose a significant threat in the context of nosocomial infections. The present investigation was undertaken with the objective of devising a Multiplex PCR methodology for the concurrent detection of MBL genes ...
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Background & Objective: Acinetobacter baumannii strains harboring Meallobetalactamases (MBL) pose a significant threat in the context of nosocomial infections. The present investigation was undertaken with the objective of devising a Multiplex PCR methodology for the concurrent detection of MBL genes within A. baumannii strains prevalent in Tehran City, Iran.Methods: Between October 2020 and February 2021, 100 strains of A. baumannii were procured from burn specimens of hospitalized patients at Motahhari Hospital in Tehran. The identification of A. baumannii strains involved conventional biochemical techniques, coupled with confirmation of the presence of the bla OXA-51 gene. Antibiotic susceptibility was assessed using the Kirby–Bauer disc diffusion test. MBL-producing strains were characterized through a phenotypic approach employing the combined disk test, alongside Multiplex PCR for the simultaneous identification of bla VIM, bla IMP, bla GIM, and bla NDM genes. Statistical analyses were conducted using the chi-square test, with SPSS version 20.0 employed for data processing.Results: Among 100 strains examined, 96.1% exhibited positivity for MBL, as determined by the combined disk test. The study revealed a predominance of extensively drug-resistant (XDR) strains, with colistin demonstrating the highest level of sensitivity. The genotypic assay unveiled that Multiplex PCR identified bla VIM, bla NDM, and bla IMP in 20 strains, bla VIM and bla NDM in 30 strains, and exclusively the bla NDM gene in 45 strains. Notably, the Multiplex PCR technique exhibited the capacity to concurrently detect MBL genes (bla VIM, bla IMP, bla GIM, bla NDM) in 2 strains.Conclusion: The current investigation underscores prevalence of the bla NDM gene within clinical strains of A. baumannii. Furthermore, Multiplex PCR emerges as a robust and highly sensitive technique for rapid discernment of the MBL genes within in A. baumannii strains.
Microbiology
Farzad Mohammadi Ebli; Zoheir Heshmatipour; Khadijeh Daneshjou; Seyed Davood Siadat
Abstract
Background & Objective: Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus pyogenes are among the most important causes of infection in human. Inventing rapid methods to identify these species can help in providing appropriate and effective treatment options. Therefore, the current ...
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Background & Objective: Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus pyogenes are among the most important causes of infection in human. Inventing rapid methods to identify these species can help in providing appropriate and effective treatment options. Therefore, the current study aimed to develop a multiplex touch-down PCR method to identify rapidly the aforementioned species patients' sputum samples, simultaneously.Methods: A total of 50 sputum samples of patients with respiratory infections resistant to treatment were collected. After DNA extraction and primer design, the complete capsule (CAP) region II, capsular polysaccharide biosynthesis (cpsA) and the structural regulator of transcription (spy) genes were amplified for detecting H. influenzae, S. pneumoniae and S. pyogenes by multiplex touch-down PCR.Results: Among 50 samples prepared from patients with different diseases, 27 samples were positive for amplified genes. The frequency of presence of pathogens in the collected samples included 14% H. influenzae, 20% S. pneumoniae and 20% S. pyogenes. Also, in some patients, the simultaneous presence of two or three pathogens were observed.Conclusion: In general, it can be concluded that the PCR touchdown method developed in the present study is an effective and fast method for the simultaneous identification of H. influenzae, S. pneumoniae and S. pyogenes pathogens in clinical samples of patients.
Microbiology
Shabnam khavandi; Mohsen Arzanlou; Roghayeh Teimourpour; Hadi Peeridogaheh
Abstract
Background & Objective: Carbapenem-resistant is Gram-negative bacteria representing a worldwide public health problem. The present study aims to survey the phenotypic and genotypic characteristics of carbapenem-resistant Escherichia coli isolates collected from hospitalized patients and outpatients ...
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Background & Objective: Carbapenem-resistant is Gram-negative bacteria representing a worldwide public health problem. The present study aims to survey the phenotypic and genotypic characteristics of carbapenem-resistant Escherichia coli isolates collected from hospitalized patients and outpatients in Ardabil province, Iran.Methods: Two hundred samples were collected from the patients who had already been referred to the hospitals in Ardabil, Iran, from January to June 2017. Each patient's social and demographic data were recorded in the first step. The resistance profile of all E. coli isolates against imipenem and meropenem antibiotics were determined using the Kirby-Bauer disk diffusion method. Moreover, the broth microdilution method determined the Minimum Inhibitory Concentration (MIC) of E. coli isolates to imipenem. The Carbapenem Inactivation Method (CIM) and Carba NP test were employed for screening carbapenem-resistant strains. The frequency of carbapenem-encoding genes was determined using Polymerase Chain Reaction (PCR) method. The Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR analysis was used to evaluate the genetic relatedness of E. coli isolates.Results: Out of 200 urine samples, 66% (n = 132) of the samples were collected from women. The patients' age varied from 1 month to 93 years. Results of the disk diffusion method revealed that 33% (n=66/200) of E. coli isolates were resistant to imipenem. However, imipenem resistance was detected in 37% (n = 74/200) of the E. coli isolates using broth microdilution method. All E. coli isolates were negative in CIM and Carba NP tests. Moreover, we could not detect any carbapenemase encoding genes among E. coli isolates. The ERIC-PCR method revealed the E. coli strains were classified into 39 clusters with 80% similarity.Conclusion: It appears that E. coli is the most common cause of urinary tract infection in Ardabil province.
Microbiology
Forough Goodarzi; Masoumeh Hallajzadeh; Mohammad Sholeh; Malihe Talebi; Vahid Pirhajati Mahabadi; Nour Amirmozafari
Abstract
Background & Objective: This study aims to isolate a lytic bacteriophage against planktonic Enterococcus faecalis V583 culture and evaluate its ability to disrupt and inhibit biofilm.Methods: An anti-E. faecalis phage was isolated from sewage and visualized by electron microscopy, the vB_EfsS_V583 ...
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Background & Objective: This study aims to isolate a lytic bacteriophage against planktonic Enterococcus faecalis V583 culture and evaluate its ability to disrupt and inhibit biofilm.Methods: An anti-E. faecalis phage was isolated from sewage and visualized by electron microscopy, the vB_EfsS_V583 (V583) host range was determined by spot test on 13 E. faecalis clinical strains. Inhibition and degradation experiments were designed to investigate the effect of phage on biofilm. In the inhibition and degradation assay, biofilms were formed in the presence and absence of phage, respectively. Finally, crystal violet method tested the effect of phage on biofilm.Results: Phage V583 belongs to the Siphoviridae family and can infect all E. faecalis strains. Antibacterial activity has been shown to degrade and inhibit biofilm produced by V583. The study results showed that phage v583 is more efficient in biofilm inhibition than biofilm degradation. In both assays, phage-treated wells' absorption is less than untreated wells. These results were confirmed by Colony-forming unit reduction in the treated biofilm.Conclusion: The anti-biofilm activity showed that phage therapy using phage V583 might be an alternative tool to remove E. faecalis biofilms.
Microbiology
Mohammad Pourahmadi; Kimia Pourahmadi; Farzan Modaresi; Shekoufeh Atashpoor; Azita Azad; Alireza Ranjbaran; Abdolmajid Ghasemian
Abstract
Background & Objective: The spread and development of drug-resistant bacterial strains has prompted the hunt for novel antibacterial polypeptides undergoing conformational changes to confer rapid bactericidal effects. The aim of this study was to evaluate the effect of novel BMAP27-Melittin conjugated ...
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Background & Objective: The spread and development of drug-resistant bacterial strains has prompted the hunt for novel antibacterial polypeptides undergoing conformational changes to confer rapid bactericidal effects. The aim of this study was to evaluate the effect of novel BMAP27-Melittin conjugated peptide- nanoparticle (NP) against Streptococcus mutans as the primary pathogen from subgingival plaques.Methods: Sixty subgingival plaque samples were collected, and 39 S. mutans isolates were identified. The BMAP27-Melittin conjugated peptide was purchased from GenScript Company, USA. Minimum Inhibitory Concentration (MIC), Minimum Bactericidal Concentration (MBC), Biofilm Inhibitory Concentration (BIC), and Biofilm Eradication Concentration (BEC) of BMAP27-Melittin-NP were calculated using the microtiter method.Results: Thirty-nine infected subjects were reported, including 24 males and 15 females (P=0.299). MIC, MBC, BIC, and BEC of BMAP27-Melittin–NP against S. mutans were 1.8, 2.9, 2.1, and 3.8μg/mL, respectively. The mean MBC, BEC, and BIC values were significantly lower among clinical isolates than S. mutans ATCC 35688 standard strain (P=0.032, 0.001, and 0.001, respectively).Conclusion: BMAP27-Melittin-NP demonstrated significant antibacterial and anti-biofilm effects against clinical isolates of S. mutans which can be considered a promising compound to prevent or treat dental caries and eradicate the oral infections.
Microbiology
Azar valizadeh; Fra Khosravi; hamid sedighian; Elham Behzadi; Elaheh Parizad; Abbas Ali Imani Fooladi
Abstract
Background & Objective: Despite the vaccination with the BCG vaccine, tuberculosis (TB) remains one of the major health problems in the world. The aim of this study was to evaluate our newly designed vaccine using IL-22 as an adjuvant in comparison with the common BCG vaccine.Methods: The gene constructs ...
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Background & Objective: Despite the vaccination with the BCG vaccine, tuberculosis (TB) remains one of the major health problems in the world. The aim of this study was to evaluate our newly designed vaccine using IL-22 as an adjuvant in comparison with the common BCG vaccine.Methods: The gene constructs were cloned into the expression vector of pET28a and then into the recombinant vector of PET28a – HSPX, and PPE44 was transformed into Escherichia coli BL21 (DE3). Finally, the immunogenicity of recombinant proteins with and without BCG and IL-22 in BALB/c mice was investigated.Results: The key cytokines INF-γ and TNF-α were elevated more greatly in BCG immunized group than in PHF immunized group.Immunization with PHF showed a significant increase in IL-4 levels versus the BCG group. Adding IL-22 to the vaccine formulations indicated a tiny increase in IL-4 levels compared to their related vaccine groups.Specific total IgG1 in the experimental groups showed an increase in comparison with control groups, but in the vaccinated groups, no significant differences were observed, and the presence of IL-22 in the vaccine formulations indicated a slight decrease compared with the related mere vaccine groups. Results of specific total IgG2a in the experimental groups revealed that only in the PHF group formulated with IL-22 a significant increase occurs compared with all other experimental groups.Conclusion: It seems that BCG, as the only licensed vaccine for TB infection, could be more potent than a recombinant vaccine in the induction of cellular and humoral immune responses.
Microbiology
Mohammadreza Salehi; Shahram Mahmoudi; Omid Rezahosseini; Sayed Jamal Hashemi; Kazem Ahmadikia; Farzad Aala; Nasim Khajavirad; Neda Alijani; Alireza Izadi; Muhammad Ibrahim Getso; Alireza Abdollahi; Arezoo Salami; Seyedeh Rana Khatami; Alireza Adibimehr; Mojtaba Hedayat Yaghoobi; Mohammadmahdi Sabahi; Behshad Pazooki; Farhad Yazdi; Jayran Zebardast; Arash Seifi; Malihe Hasan Nezhad; Masoud Mardani; Sadegh Khodavaisy
Abstract
Cerebral mucormycosis (CM) is a life-threatening manifestation of mucormycosis, an angioinvasive fungal infection caused by Mucorales. We sought to systematically review all available case reports to describe epidemiologic features, clinical manifestations, predisposing factors, and diagnostic and treatment ...
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Cerebral mucormycosis (CM) is a life-threatening manifestation of mucormycosis, an angioinvasive fungal infection caused by Mucorales. We sought to systematically review all available case reports to describe epidemiologic features, clinical manifestations, predisposing factors, and diagnostic and treatment strategies of CM. A systematic search was conducted using a combination of the following keywords: "Mucor", "Zygomycetes", "mucormycosis", "cereb*", "brain", "central nervous system", and "intracranial", separately and in combination until December 31st 2018. Data sources included PubMed, Scopus, EMBASE, Web of Science, Science Direct, and Proquest without limiting the time of publication. We included 287 articles corresponding to 345 cases of CM. Out of the 345 cases, 206 (60%) were male with a median age of 44 years; 130 (38%) were reported from North America; 87 (25%) from Asia; and 84 (24%) from Europe. The median time from onset of symptoms to presentation was 3-7 days (65/345, 65%). The highest mortality was observed among patients with diabetes mellitus (P=0.003). Debridement of infected brain tissue was associated with improved survival in CM cases (OR 1.5; 95% CI 01.3-1.8; P<0.0001). The use of liposomal amphotericin B (L-AMB) was significantly associated with patients' recovery (OR 2.09; 95% CI 1.2-3.4; P=0.003). The combination of L-AMB and posaconazole (12.5%) was more effective than the monotherapy treatment of CM cases (P=0.009). Clinicians should consider DM as an important risk factor for CM. Moreover, surgical debridement and antifungal combination therapy could be an effective approach in the management of CM patients.
Microbiology
Samaneh Abolbashari; MohammadTaghi Shakeri; Maryam Hami; Aida Gholoobi; Amin Hooshyar Chechaklou; Mohammad Sadegh Damavandi; Aref Movaqar; Razieh Yousefi; Zahra Meshkat; Saeedeh Hajebi Khaniki
Abstract
Background & Objective: Polyomaviruses types BK and JC and Cytomegalovirus (CMV) have been shown to be related to kidney transplantation complications. This study aimed to assess the prevalence of these viruses in patients receiving kidney transplantation.Methods: This cross-sectional study was performed ...
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Background & Objective: Polyomaviruses types BK and JC and Cytomegalovirus (CMV) have been shown to be related to kidney transplantation complications. This study aimed to assess the prevalence of these viruses in patients receiving kidney transplantation.Methods: This cross-sectional study was performed on 40 kidney transplant recipients and 44 donors. Urine samples were used for the extraction of viral DNA. The prevalence of JC and BK viruses and their viral loads were determined by real-time polymerase chain reaction.Results: JC and BK viruses were identified in 31% and 92.3% of all subjects, respectively. The frequency of JC and BK cases was not statistically different between the recipient and donor groups (P>0.05). All patients in the donor group and 96.8% of the recipients were positive for CMV IgG antibody. The mean viral load of BK in donors and recipients was 4.5×1010 and 3.3×1011 copies, respectively. The mean viral load of JC was 8.6×107 copies in donors and 2.9×108 copies in recipients. The distribution of BKV was significantly higher in recipients than donors (P=0.001), while no difference was observed between the two studied groups for JCV.Conclusion: This study showed a relatively high prevalence of BK and JC viruria in both renal transplant donors and recipients. The viral load for BKV, but not JCV, was higher in recipients than in donors.
Microbiology
Abdolreza Javadi; Shahriar Dabiri; Manzumeh Shamsi Meymandi; Mohammad Hashemi-Bahremani; Hussein Soleimantabar; Bahram Dabiri; Houman Vosough; Maryam Gheidi Sharan; Farnoosh Sedaghati
Abstract
Background & Objective: Coronavirus disease 2019 (COVID-19) is progressively spreading, and many researchers have focused on the prognostic value of laboratory analyses. This study reviewed routine blood parameters, upper respiratory viral load, and chest imaging in recovered and expired COVID-19 ...
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Background & Objective: Coronavirus disease 2019 (COVID-19) is progressively spreading, and many researchers have focused on the prognostic value of laboratory analyses. This study reviewed routine blood parameters, upper respiratory viral load, and chest imaging in recovered and expired COVID-19 patients and evaluated possible correlations.Methods: In this retrograde study, 138 COVID-19 cases were enrolled. Chest tomography scores of patients, routine hematologic and biochemical parameters, and respiratory viral loads were measured. Furthermore, their correlation with severity of disease and the outcome was investigated during a week of admission.Results: The mean age of participants was 58.6±16; 36.2% of whom were diagnosed as critical, 8.7% expired, and 46% showed less than 50% lung opacity. The expiring rate was only correlated to the severity of illness and viral load. During admission, hemoglobin concentration was decreased in critical patients (from 11.49±0.27 to 10.59±0.36, P=0.042) and also among CT-scan scoring groups (P=0.000), while neutrophils (P=0.04), WBC (P=0.03), and platelets (P=0.000) count were increased. In patients with more than 50% lung opacity, leukocyte counts were decreased, but neutrophil and platelets counts showed raise (all P<0.05), while other hematologic parameters did not change. CRP and LDH demonstrated no increase based on the severity of the illness, RT-PCR viral loads and/or outcome. However, both CRP and LDH were increased in patients with more than 50% lobal opacity (CRP: 69.3±9.9 to 1021.1±7.5 and LDH:589.5±93.2 to 1128.6±15.81, P<0.05).Conclusion: We found that hemoglobin, white blood cells, neutrophil, lymphocytes, and platelets count together with chest tomography score might be beneficial for expedition the diagnosis, assessmen the severity of the disease, and outcome in the hospitalized cases, while CRP and LDH might be considered as the consequence of lung involvement.
Microbiology
Alireza Abdollahi; Samaneh Salarvand; Vahid Mehrtash; Bita Jafarzadeh; Mohammadreza Salehi; Reza Ghalehtaki; Saeed Nateghi
Abstract
Background & Objective: COVID-19 reverse transcription-polymerase chain reaction (RT-PCR) has been a reference test for diagnosing a disease since the very beginning of the pandemic. COVID-19 serology tests have also been developed and used to estimate the prevalence of individuals who have already ...
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Background & Objective: COVID-19 reverse transcription-polymerase chain reaction (RT-PCR) has been a reference test for diagnosing a disease since the very beginning of the pandemic. COVID-19 serology tests have also been developed and used to estimate the prevalence of individuals who have already been infected. We aimed to evaluate the performance of serology tests for the diagnosis of patients who had been referred to medical centers with acute symptoms.Methods: In this cross-sectional study, 80 individuals suspected of COVID-19 who had been referred to Imam Khomeini Hospital Complex, Tehran, Iran, were examined. Upper respiratory tract specimens for RT-PCR and blood samples for COVID-19 IgM and IgG antibody level tests were collected and the results were compared. Results: The overall proportion in agreement, the agreement between positive results, and the agreement between negative results when comparing RT-PCR and IgM serology test were 40% (kappa = -0.006, P = 0.9), 32%, and 66.6%, respectively, and when comparing RT-PCR and IgG serology test were 46% (kappa = -0.006, P = 0.94), 43.5%, and 55.5%, respectively.Conclusion: The absence of a gold standard method for the diagnosis of COVID-19 makes it very challenging to determine the true sensitivity and specificity of different methods. The study results revealed no agreement between the two methods; so the RT-PCR test for upper respiratory tract specimen cannot be replaced with COVID-19 serology test for the diagnosis of patients with acute symptoms.
Microbiology
Alireza Abdollahi; Samaneh Salarvand; Vahid Mehrtash; Bita Jafarzadeh; Reza Ghalehtaki; Saeed Nateghi
Abstract
Background & Objective: The prevalence of COVID-19 and its severity have been observed to be on a lower level in underdeveloped countries with poorer standards of hygiene. This disparity may be attributed to the higher seroprevalence of other viral diseases which can result in the presence of antibodies ...
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Background & Objective: The prevalence of COVID-19 and its severity have been observed to be on a lower level in underdeveloped countries with poorer standards of hygiene. This disparity may be attributed to the higher seroprevalence of other viral diseases which can result in the presence of antibodies protective against COVID-19. Two of the widespread diseases in such countries are infection to hepatitis A and E viruses (HAV and HEV). In the present study, we explored the relationship between the level of antibodies against these viruses and the susceptibility to COVID-19.Methods: Ninety patients were studied in two groups of controls and cases each consisting 45 individuals. The cases were patients with the clinical symptoms of COVID-19 and positive RT-PCR test results. The controls were individuals referred to the respiratory triage of Imam Khomeini Hospital Complex and were not demonstrating relevant clinical symptoms of COVID-19 and their RT-PCR test results were negative. Levels of HAV and HEV antibodies were measured and compared in these two groups.Results: The median of HAV antibody level was 13.6 (IQR=11.5-16.9) and 13.2 (IQR =10.7-14.7) in cases and controls, respectively, showing no statistically significant difference (P = 0.1). Likewise, the median of HEV antibody level was 6.7 (IQR=5.3-7.1) and 7.1 (IQR=6.3-7.5) in cases and controls, respectively, which again showed no statistically significant difference (P=0.41).Conclusion: The present study was carried out in a region with a relatively high prevalence of HAV and HEV infections. Contrary to our expectations, no statistically significant relationship was observed between the levels of antibodies against these viruses and the susceptibility to COVID-19. Further studies with larger sample sizes and in other countries are needed to come to a definite conclusion.
Microbiology
Sorour Farzi; Reza Ranjbar; Mohammad Niakan; Mohammad Hossein Ahmadi
Abstract
Background & Objective: Escherichia coli (E. coli) is a leading cause of urinary tract infections becoming resistant against beta-lactams and cephalosporins through different mechanisms, including ESBL production due to the presence of ESBL specific genes, including blaCTX-M and blaTEM. The purpose ...
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Background & Objective: Escherichia coli (E. coli) is a leading cause of urinary tract infections becoming resistant against beta-lactams and cephalosporins through different mechanisms, including ESBL production due to the presence of ESBL specific genes, including blaCTX-M and blaTEM. The purpose of the present study was to detect the uropathogenic E. coli strains producing the ESBL.Methods: A total of 100 isolates of uropathogenic E. coli were randomly selected in a period of 6 months and their resistances to a number of antibiotics including amoxicillin, amikacin, gentamicin, ciprofloxacin, ceftazidime, cefotaxime, ceftriaxone, ceftizoxime, nalidixic acid, and nitrofurantoin were determined. Then, DDT test was used to detect the presence of ESBL. Finally, the presence of blaCTX-M and blaTEM resistance genes was analyzed by PCR method.Results: The resistance profile of bacterial isolates to the antibiotics was as follows: amoxicillin: 16.7%, amikacin: 7.8%, gentamicin: 20.3%, ciprofloxacin: 35.5/%, ceftazidime: 35.0%, cefotaxime: 40.0%, ceftriaxone: 41.3%, nalidixic acid: 64.0%, nitrofurantoin: 9.7%, and ceftizoxime: 100%. Of these, 28 isolates (28%) were reported to be resistant to cefotaxime, ceftazidime, and ceftriaxone. In DDT test, 21 ESBL positive cases (21%) were detected. PCR results showed that the presence of blaCTX-M and blaTEM genes in the isolates were 21% and 20%, respectively. Conclusion: Regarding the production of ESBL by some E. coli isolates, phenotypic detection of ESBL-producing isolates is routinely suggested in the laboratories. Likewise, the treatment regimen should be selected regarding the ESBL production to avoid treatment failure.
Microbiology
Zahra Yousefpour; Fateme Davarzani; Parviz Owlia
Abstract
Background & Objective: The ability of Pseudomonas aeruginosa to form biofilm has an important role in establishment of chronic phase of infections. Biofilm formation can be affected by antibiotics sub-MIC concentrations. The principal aim of the present study was to evaluate the effect of gentamicin ...
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Background & Objective: The ability of Pseudomonas aeruginosa to form biofilm has an important role in establishment of chronic phase of infections. Biofilm formation can be affected by antibiotics sub-MIC concentrations. The principal aim of the present study was to evaluate the effect of gentamicin at sub-MIC concentrations on biofilm formation in 100 Pseudomonas aeruginosa clinical isolates.Methods: Determination of minimal inhibitory concentration of gentamicin for clinical isolates was done using micro broth dilution method. The amount of biofilm formation in the treated and untreated isolates with gentamicin sub-MIC (1/2&1/4MIC) concentrations was evaluated using microtitre plate assay. pelA and pslA genes were detected in clinical isolates by PCR method.Results: 99% of clinical isolates were biofilm producer. Different changes in amountof biofilm formation were observed in the treated clinical isolates with sub-MIC concentrations of gentamicin. Two dominant changes were observed in 80% of clinical isolates. These concentrations had inhibitory effect on biofilm formation in 46.4% of isolates and caused a significant decrease in its amount. While in 31.3% of the isolates, the biofilm formation was significantly increased. The frequency of pelA and pslA genes among clinical isolates was 100%. Conclusion: gentamicin sub-MIC concentrations cause different changes on biofilm formation of Pseudomonas aeruginosa clinical isolates. Therefore, further studies are needed for discovering new treatment strategies and using sub-MIC concentrations of the antibiotic in prevention and treatment of Pseudomonas aeruginosa infections.
Microbiology
Zoheir Heshmatipour; Nasibeh Arabameri; Shima Eftekhar Ardebili; Zeinab Jafari Bidhendi
Abstract
Background & Objective: Pseudomonas aeruginosa is an opportunistic pathogen and one of the most common causes of nosocomial infections. This bacterium's antibiotic resistance to the common fluoroquinolone antibiotics, especially ciprofloxacin, is due to mutations in the gyrA and parC genes. This ...
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Background & Objective: Pseudomonas aeruginosa is an opportunistic pathogen and one of the most common causes of nosocomial infections. This bacterium's antibiotic resistance to the common fluoroquinolone antibiotics, especially ciprofloxacin, is due to mutations in the gyrA and parC genes. This study aimed to investigate the effect of the mutation in (gyrA, parC) on ciprofloxacin resistance in clinical isolates of Pseudomonas aeruginosa.Methods: A total of 140 clinical samples were collected from hospitals. The samples were identified by standard biochemical tests, and the antibiotic resistance was investigated by the disk diffusion method. DNA was extracted from 30 isolates, and PCR was performed. PCR-sequencing was carried out to assess gyrA and parC mutations in drug-resistant isolates. NCBI-Blast and MEGA7 software was used to analyze the nucleotide sequences.Results: 30 clinical isolates were 80% resistant to ciprofloxacin; meanwhile, in 21 samples, mutations were observed. 87/5% of mutations were related to gyrA (Thr83 → Ile), 79/16 % parC (Ser87 → Leu), and 4/18% (Glu91 → Lys). The antibiotic resistance to ciprofloxacin and mutations in gyrA and parC genes in resistant isolates are significantly related to each other (P<0.05). Conclusion: The mutations in the gyrA and parC genes play an essential role in resistance to ciprofloxacin in clinical isolates of Pseudomonas aeruginosa.
Microbiology
Seyed Esmaeil Azimi Khatibani; Shima Tabatabai
Abstract
Background & Objective: Pathology education conventional methods have been disrupted by the Corona-Virus Disease 2019 (COVID-19) outbreak, compelling a re-evaluation of the means of educational interactions from the undergraduate to the postgraduate level. This commentary explores how the COVID-19 ...
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Background & Objective: Pathology education conventional methods have been disrupted by the Corona-Virus Disease 2019 (COVID-19) outbreak, compelling a re-evaluation of the means of educational interactions from the undergraduate to the postgraduate level. This commentary explores how the COVID-19 outbreak has challenged pathology education.Methods: We reviewed the current challenges and determined the potential implications of virtual technologies on modern pathology education for the future of pathology competency learning and assessment.Results & Conclusion: The challenges are partly due to transferring from in-person teaching to a virtual education. Other reasons are shifting away from discipline-based teaching to organ-system based in medical curriculum and additional pressures on pathology faculties, such as increased demand for pathology services, lack of time, and learning resources. Keeping the national standards in pathology education even in the constant disruptions from pandemic outbreaks are current challenges. Pathology expertise will need to use emergent technologies in providing educational material to ensure quality pathology education. However, virtualization of pathology education produces a value of digital pathology and web-based pathology training materials. Medical students could review clinical cases remotely with their supervisors and gain the pathology competencies necessary for clinical practice.We need new innovative strategies, and we suggested the following steps to take advantage of the current opportunity to meet the challenges: evaluating the available digital training materials for formal pathology education, investing in the virtual infrastructure for competency-based pathology education, expanding student/residents exposure to pathology educational cases through virtual platforms; applying digital pathology solutions for virtual pathology education.
Microbiology
Afsaneh Yakhforoshha; Fatemeh SamieeRad
Abstract
This approach to learning is in accordance with the first of six strategies of Harden SPICES model for curriculum development: student-centered against teacher-centered approach (S) (7,8). In total, the results from medical students and the Knowles’ Andragogical Model as a theoretical lens, is ...
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This approach to learning is in accordance with the first of six strategies of Harden SPICES model for curriculum development: student-centered against teacher-centered approach (S) (7,8). In total, the results from medical students and the Knowles’ Andragogical Model as a theoretical lens, is expected to help medical education experts with emphasizing student center approach in the medical education curriculum to prepare future physician for meeting unexpected healthcare crisis demands.
Microbiology
Sina Neshat; Padideh Daneii; Negar Neshat; Sina Raeisi; Saba Raeisi; Seyed Mohammad Malakooti; Noushin Afshar Moghadam
Abstract
Human papillomavirus infection is one of the most common genital infections. More than 100 types of the virus have been identified, most of which can infect the genital mucosa. The virus is associated with cancerous and precancerous lesions of the cervix. Some types, such as human papillomavirus 16 and ...
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Human papillomavirus infection is one of the most common genital infections. More than 100 types of the virus have been identified, most of which can infect the genital mucosa. The virus is associated with cancerous and precancerous lesions of the cervix. Some types, such as human papillomavirus 16 and 18, are highly carcinogenic; some other types, such as human papillomavirus 6 and 11, are mildly carcinogenic, with HPV 31.33 in between. This study describes the relationship between different types of HPV infection and the findings of a Pap smear. In this prospective study, 1,500 samples from patients who admitted to a private Pathology Laboratory in Isfahan were collected during the years 2019-2020. Two samples were collected from each patient, one for Pap smear study and the other for polymerase chain reaction (PCR) test to detect different types of human papillomavirus (HPV) infection. In a study of 1,500 samples, 236 were positive for Papillomavirus (HPV) infection in Pap smear. By examining the genotype of positive examples, it was found that 14.8% of the samples were infected with type 16, and 1.7% were infected with type 82. HPV infection is common in Iran and is almost similar to European countries such as Germany and Spain. We also found that using a polymerase chain reaction (PCR) method to detect HPV viruses in vaginal secretions could be very useful. Our findings also show which disease is most associated with each type of HPV.
Microbiology
Saeed Mirsadraee; Mihan Pourabdollah Toutkaboni; Mehrdad Bakhshayeshkaram; Mitra sadat Rezaei; Elham Askari; Sara Haseli; Nazanin Sadraee
Abstract
Background & Objective: Diagnosis of coronavirus disease 2019 (COVID-19) can be challenging, especially when the realtime quantitative reverse transcription polymerase chain reaction (RT-PCR) is not available or it is negative. In this study, we evaluated imaging and laboratory findings in a ...
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Background & Objective: Diagnosis of coronavirus disease 2019 (COVID-19) can be challenging, especially when the realtime quantitative reverse transcription polymerase chain reaction (RT-PCR) is not available or it is negative. In this study, we evaluated imaging and laboratory findings in a group of patients with a multidisciplinary diagnosis of COVID-19 pneumonia. Methods: A total of 163 patients with a clinical diagnosis of COVID-19 pneumonia admitted to a specialised respiratory centre in Tehran, Iran were enrolled in this study. The distribution and characteristics of presenting radiological and laboratory findings were evaluated and the relationship to the outcome was investigated. Results: RTPCR was positive in 92 patients. The diagnosis of COVID-19 in RT-PCR negative patients was made on clinical and radiological grounds (n=71). Also, 24 (14.7%) patients died. The common computed tomography (CT) scan findings included ground-glass (94%) and consolidating opacification (12%), mainly in the lower lobes (90%). Peripheral and central lung changes were observed in 90% and 52% of patients, respectively. Lymphopenia, positive CRP, and raised LDH were present in 32%, 65%, and 96% of cases, respectively. A raised LDH of >500U/L was the best predictor of death in these patients (R2=0.6623; OR=24.4). Other markers of outcome were male gender, age (>50 years), lymphopenia, and severe CXR changes. Conclusion: Diagnosis of COVID-19 can be challenging, and a multidisciplinary approach is often needed. Whilst RT-PCR is the standard diagnostic test, a negative test should be interpreted with caution. Blood tests and imaging can be useful in the diagnosis, monitoring, and risk assessment in patients with COVID-19.
Microbiology
Mohammadreza Jalali Nadoushan; Soha Ahmadi; Paniz Jalali Nadoushan
Abstract
As COVID-19 was declared as a pandemic by the World Health Organization (WHO) in March 2020, it is an emerging need to discuss different aspects of this pandemic. In any pandemic, valid and rapid laboratory diagnostic tests are critically important for early diagnosis, which will increase the rate of ...
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As COVID-19 was declared as a pandemic by the World Health Organization (WHO) in March 2020, it is an emerging need to discuss different aspects of this pandemic. In any pandemic, valid and rapid laboratory diagnostic tests are critically important for early diagnosis, which will increase the rate of successful treatment and more importantly prevent the spread of the disease.
Microbiology
Kosar Jalalvand; Nasrin Shayanfar; Freshteh Shahcheraghi; Elahe Amini; Masha Mohammadpour; Pegah Babaheidarian
Abstract
Background & Objective: Carbapenem-resistant Enterobacteriaceae is a growing concern worldwide including Iran. The emergence of this pathogen is worrying as carbapenem is one of the 'last-line' antibiotics for treatment of infections caused by multi drug resistant gram- negative bacteria. The main ...
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Background & Objective: Carbapenem-resistant Enterobacteriaceae is a growing concern worldwide including Iran. The emergence of this pathogen is worrying as carbapenem is one of the 'last-line' antibiotics for treatment of infections caused by multi drug resistant gram- negative bacteria. The main objective of this study was to determine the prevalence of carbapenem-resistant Enterobacteriaceae in a referral hospital in Tehran, Iran. Methods: In this study, all positive isolates of Enterobacteriaceae recorded in blood, urine, and other body fluids were studied during April 2017 to April 2018 in a referral hospital in Tehran. All cases of resistance to carbapenems were first tested by modified Hodge test. All cases with positive or negative test, after gene extraction, were examined genotypically based on the primers designed for the three Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), and OXA-48 genes by conventional PCR method. Result: 108 isolates (13.6%) were resistant to all cephalosporins as well as to imipenem and meropenem. In a genotypic study, including 45 isolates, 13 isolates were positive for OXA-48 gene, 11 isolates for OXA-48 and NDM genes, 11 isolates for OXA-48, NDM and KPC genes, 4 isolates for OXA-48 genes and KPC, 3 isolates for NDM, one isolate for KPC. On the other hand, two isolates were negative for all three genes examined. Conclusion: OXA-48 gene was one of the most common genes resistant to carbapenems in Iran. According to studies, the prevalence of antibiotic resistance in Iran is rising dramatically, which reduces the choice of antibiotics to treat severe infections in the future.
Microbiology
Sara Masoumi Zavaryani; Reza Mirnejad; Vahhab Piranfar; Mehrdad Moosazadeh Moghaddam; Nikta Sajjadi; Somayyeh Saeedi
Abstract
Background & Objective: Enterococcus Species are the common cause of nosocomial infections, which are highly resistant to different antibiotics. Therefore, determination of their antibiotic susceptibility patterns and simultaneous resistance to antibiotics is important for better treatment strategies. ...
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Background & Objective: Enterococcus Species are the common cause of nosocomial infections, which are highly resistant to different antibiotics. Therefore, determination of their antibiotic susceptibility patterns and simultaneous resistance to antibiotics is important for better treatment strategies. Methods: 400 clinical Enterococcus isolates were collected from different hospitals in Tehran, Iran. Standard phenotypic-biochemical tests and PCR were used to identify the Enterococcus species. The antimicrobial susceptibility patterns and simultaneous resistance to selected antibiotics were determined by disk diffusion method according to the CLSI guidelines. All data analysis was performed using Python packages Scipy and Stats models. Result: According to the biochemical and PCR analyses, among 400 Enterococcus species, 72% of samples were Enterococcus faecalis, 10.75% Enterococcus faecium, and 17.25% other Enterococcus species. The results determined antimicrobial resistances of these strains against gentamicin, vancomycin, fosfomycin trometamol, teicoplanin, and quinupristin/dalfopristin. Results confirmed a significant correlation between resistance to vancomycin and resistance to teicoplanin. This correlation remains significant when including only E. faecium or E. faecalis species. We also found a negative correlation between resistance to teicoplanin and quinupristin/dalfopristin. Additionally, Quinupristin/dalfopristin was the least effective antibiotic while vancomycin and teicoplanin were the most effective ones. Conclusion: Based on the results and association between simultaneous resistance to some antibiotics such as vancomycin and teicoplanin, in the case of antibiotic resistance, the choice of a second antibiotic can be very important which can lead to good or bad effects.