Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 Prevalence of Salmonella Bloodstream Infection and Antimicrobial Resistance in Lagos, Nigeria. 1 14 1908 10.52547/iem.9.1.1 EN Funmilayo M.Akinkunmi Department of Microbiology, Faculty of Science, Lagos State University, P.O. Box 0001 Lasu post office, Ojo, Lagos, Nigeria Samuel O.Ajoseh Department of Microbiology, Faculty of Science, Lagos State University, P.O. Box 0001 Lasu post office, Ojo, Lagos, Nigeria Christopher Fakorede Department of Microbiology, Faculty of Science, Lagos State University, P.O. Box 0001 Lasu post office, Ojo, Lagos, Nigeria Rebecca Abegunrin Department of Microbiology, Faculty of Science, Lagos State University, P.O. Box 0001 Lasu post office, Ojo, Lagos, Nigeria Wasiu Salami Department of Microbiology, Faculty of Science, Lagos State University, P.O. Box 0001 Lasu post office, Ojo, Lagos, Nigeria Aminat Lawal Department of Microbiology, Faculty of Science, Lagos State University, P.O. Box 0001 Lasu post office, Ojo, Lagos, Nigeria Kabiru Akinyemi Department of Microbiology, Faculty of Science, Lagos State University, P.O. Box 0001 Lasu post office, Ojo, Lagos, Nigeria Journal Article Backgrounds: The burden of bacteremia in febrile cases is still poorly understood in Nigeria as in many sub-Saharan African countries due to diagnostic limitations. This study aimed to determine the prevalence of Salmonella bloodstream infections and antimicrobial resistance patterns of bacterial isolates recovered from febrile patients in Lagos, Nigeria. Materials & Methods: A total of 300 blood samples were collected from febrile patients attending four medical centers in Lagos during August 2020 to July 2021. Clinical isolates were identified using API 20E kit. qPCR was used to detect Salmonella isolates in positive blood culture samples using a specific primer set. All isolates were subjected to antimicrobial susceptibility tests using standard procedures. Findings: Totally, 55 bacterial isolates belonging to six bacterial genera were identified, including Salmonella (n=4, 7.27%), Klebsiella species (n=23, 41.82%), Escherichia coli (n=6, 10.91%), Proteus species (n=13, 23.64%), Serratia species (n=7, 12.73%), and Citrobacter species (n=2, 3.64%). In this study, the detection rate of Salmonella isolates in positive blood culture samples using qPCR and invA gene primer set was 100%. Salmonella isolates were 100% resistant to ceftazidime, cefotaxime, and doripenem. Multidrug resistance (MDR) was observed in Salmonella and other bacterial isolates. Conclusion: In this study, qPCR using the invA primer set was found to be highly specific for Salmonella detection. All the bloodstream bacterial pathogens in this study were MDR; thus, there is a need for continuous evaluation of antibiotics in medical settings. Further molecular studies on these bacterial isolates is essential.

https://iem.modares.ac.ir/article_1908_65699726a3c601b9f31bf04019c8593c.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 Characteristics of Prophage Patterns and Virulence Gene Profiles among Methicillin-Resistant Staphylococcus aureus Isolates from Patients with Diabetic Foot Infections in a Referral Hospital in Tehran, Iran 15 23 1909 10.52547/iem.9.1.15 EN Fateh Rahimi Department of Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran 0000-0002-2098-2502 Sanaz Khashei Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran 0000-0001-8076-9896 Journal Article Backgrounds: Diabetic patients are at risk of developing serious foot infections with methicillin-resistant Staphylococcus aureus (MRSA) strains, which are associated with high morbidity and mortality. This study aimed to investigate the frequency of different prophage types and virulence factors among MRSA strains isolated from patients with diabetic foot infections (DFIs) in a referral hospital in Tehran, Iran during 2019 and 2020. Materials & Methods: A total of 238 S. aureus isolates were collected and confirmed using specific primers. The presence of staphylococcal enterotoxins (sea-seq) and hlb, sak, eta, etb, and tsst-1 genes among MRSA isolates was tested using separate polymerase chain reaction (PCR) assays. Also, multiplex PCR was employed for prophage typing of MRSA isolates. Findings: A total of 73 (31%) isolates were confirmed as MRSA, among which four prophage types and 13 different prophage patterns were identified, and prophage type SGF and prophage pattern 7 consisting of SGB, SGF, SGFa, and SGFb types were the dominant ones. Also, 11 enterotoxin-encoding genes and four virulence factor genes were detected among the isolates. All MRSA isolates were positive for sea, sek, seq, and hlb genes. Moreover, out of 12 different enterotoxin patterns, most MRSA isolates were classified into enterotoxin pattern 1, harboring three enterotoxin genes (sea, sek, and seq). Conclusion: This study results indicated the presence of different prophage types and virulence factor genes among MRSA strains isolated from DFI patients, which enable them to produce a variety of diseases.

https://iem.modares.ac.ir/article_1909_0609154fa35b3194026346c9cac2a248.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 Isolation and Molecular Identification of Streptomyces spp. Producing Antibacterial Compounds from Iranian Soil 25 34 1910 10.52547/iem.9.1.25 EN Roya Moravej Department of biology, Sanandaj branch, Islamic azad university, Sanandaj, Iran Sahar Honarmand Jahromi Department of Microbiology, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran Peyman Azad Department of biology, Sanandaj branch, Islamic azad university, Sanandaj, Iran Journal Article Backgrounds: This study was conducted with the aim of isolation and molecular identification of Streptomyces spp. producing antibacterial compounds from Iranian soil. Materials & Methods: In this study, 50 soil samples were collected from different areas of Sanandaj city. Soil samples were cultured on starch casein media. Streptomyces species were characterized using morphological and biochemical assays. Molecular identification was performed by 16S rRNA sequencing. Antimicrobial activity was evaluated using perpendicular streak and agar well diffusion methods. Findings: To identify active Streptomyces strains in terms of producing antibacterial agents, screening was performed in two stages. Among 20 Streptomyces strains isolated from soil samples, six isolates were selected in the primary screening stage based on their ability to limit the growth of pathogens. Of the two solvents used in the secondary screening stage, ethyl acetate was the most suitable solvent for extracting effective metabolites of Streptomyces. Among the six isolates selected based on their antimicrobial activity, two isolates with the highest antibacterial activity were selected for the sequencing process. By analyzing the dendrogram and the data obtained from the NCBI database, it was found that one isolate (Yellow 4A) was 98% similar to S. fradiae, and the other isolate (Green 4A) was 98% similar to S. coelicolor. Conclusion: The use of proper strategies to identify potential new Streptomyces species with antibacterial properties may bring a bright future in the treatment of resistant pathogens. However, more studies are required to detect active metabolites of the mentioned isolates.

https://iem.modares.ac.ir/article_1910_ab7314887865c4265e896c6e209d1cd6.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 Impact of IL-35 and presepsin on immunological, hematological, and biochemical parameters in COVID-19 patients 35 42 1911 10.52547/iem.9.1.35 EN Falah Hasan Obayes AL-Khikani Department of biology, Sanandaj branch, Islamic azad university, Sanandaj, Iran Zeytoon Abdulridha Alkhafaji Department of Microbiology, College of Medicine, University of Babylon, Hilla, Iraq. Journal Article Backgrounds: Immune-inflammatory responses appear to play a key role in severe SARS-CoV-2 infections. Interleukin-35 (IL-35) and presepsin (PSN) are inhibitory cytokine and pro-inflammatory interleukin, which play a crucial role in the immune system modulation, respectively. Therefore, the study of IL-35 and PSN interaction with other parameters may be critical for managing patients with COVID-19. Materials & Methods: A total of 125 severe/critical COVID-19 patients and 60 healthy persons as a control group were enrolled in this work. These patients were admitted to Marjan medical city and Al-Sadeq hospital in Iraq during February to August 2022 and diagnosed as severe cases depending on the SpO2 percentage according to the guidelines released by the National Health World. Anti- and pro-inflammatory cytokines (IL-35 and PSN) were detected by ELISA technique. Findings: Presepsin showed a positive correlation with admission to the respiratory care unit (RCU) (r= .022, p= .011). A negative correlation was found between presepsin and C- reactive protein (CRP) (r= .21, p= .018). Both PSN and IL-35 in biochemical tests showed a positive strong effect on glucose levels in COVID-19 patients (r= .234, p= .008 and r= .241, p= .007, respectively). IL-35 had a positive impact on alkaline phosphatase (ALP) (r= .28, p= .002). Hemoglobin (Hb) level showed a positive correlation with presepsin (r= .2, p= .02). Conclusion: This study confirms the growing evidence showing the direct role of regulatory pro-inflammatory cytokines in the development and control of COVID-19 through the interaction with other parameters.

https://iem.modares.ac.ir/article_1911_04df4d434d481c5bb723be1b6df1ee65.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 Investigation of Metallobetalactamase (blaIMP & blaVIM) and Carbapenemase (blaKPC & blaGES) Genes in Gram Negative Rods Isolated from Cancer Patients 43 53 1912 10.52547/iem.9.1.43 EN Fahime Maleki Department of Immunology & Microbiology, Arak University of Medical Sciences, Arak, Iran Majid Akbari Infectious Research Center, Arak University of Medical Sciences, Arak, Iran Mohammadmohmmad Arjomandzadegan Vice Chancellor for Research of IDRC Arak University of Medical Sciences, Iran. Azam Ahmadi Assistant professor, IDRC research center Arak University of Medical Sciences. Journal Article Backgrounds: Bacterial infections are the most common complication in cancer patients. Infection with multi-drug resistant bacteria has recently become a worrying phenomenon in cancer patients. This study focused on Gram-negative bacteria isolated from clinical samples of cancer patients. The purpose of this study was to evaluate the presence and prevalence of drug resistance genes, including metallobetalactamase (blaIMP and blaVIM) and carbapenemase (blaKPC and blaGES) genes, in the main bacteria agents of nosocomial infections in cancer patients, such as Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli. Materials & Methods: Common biochemical methods were used to identify bacterial isolates. Antimicrobial susceptibility testing was performed according to the standard method recommended by the Clinical and Laboratory Standards Institute (2019). Polymerase chain reaction (PCR) method was also used to check the presence and prevalence of resistance genes. Findings: During six months, from May to November 2020, 250 clinical samples were collected from cancer patients in Ayatollah Khansari hospital in Arak city, Iran. From which 80 Gram-negative bacilli were isolated, including 33 (41.2%) E. coli, 15 (18.7%) A. baumannii complex, 12 (15%) P. aeruginosa, eight (10%) K. pneumoniae, seven (8.7%) Citrobacter freundii, and five (6.2%) Enterobacter aerogenes isolates. The frequency of blaKPC, blaGES, blaIMP, and blaVIM genes was 39.95, 21.25, 16.25, and 17.45%, respectively. Conclusion: The present study emphasizes the importance of identifying Gram negative rods and their resistance genes (metallobetalactamase and carbapenemase genes) in cancer patients, carrying out preventive instructions to prevent the transmission of resistance genes, and reducing mortality in these patients.

https://iem.modares.ac.ir/article_1912_ff7d0f525b3be596a51fb919492c099c.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 Evaluation of the Relative Frequency of Carbapenemase Genes by Phenotypic and Genotypic Methods in Pseudomonas aeruginosa Isolates from Patients with Open Heart Surgery in Iran 55 62 1913 10.52547/iem.9.1.55 EN Maryam Mokhtari Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran Ali Mojtahedi Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran Nejat Mahdieh Cardiogenetic Research Center, Rajaei Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran Alireza Jafari Urology Research Center, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran Zahra Atrkar Roushan School of Medicine, Guilan University of Medical Sciences, Rasht, Iran Mohammad Javad Arya Anatomical and clinical Pathologist, Fellowship of dermatopathology, Head of Sina Pathobiology Lab, Yazd, Iran. Journal Article Backgrounds: Carbapenem resistance among Pseudomonas aeruginosa strains is alarming. This study aimed to investigate the relative frequency of carbapenem-resistant P. aeruginosa strains by phenotypic and genotypic methods. Materials & Methods: The antibiotic susceptibility pattern of 60 P. aeruginosa isolates was determined by disk diffusion method (Kirby-Bauer). BD Phoenix automated microbiology system was used to identify carbapenem-resistant isolates, and the minimum inhibitory concentration (MIC) was determined using E-Test. In addition, mCIM (modified carbapenem inactivation method) phenotypic test was performed to evaluate carbapenem resistance genes in P. aeruginosa isolates. The prevalence of metallo-beta-lactamase (MβL) genes in carbapenem-resistant P. aeruginosa isolates was determined using conventional polymerase chain reaction (PCR). Findings: The frequency of carbapenem-resistant P. aeruginosa isolates was 36% (22 of 60). The highest resistance was observed to imipenem and meropenem (36.6%), and the highest sensitivity was observed to amikacin (75%). All carbapenem-resistant P. aeruginosa isolates were confirmed by the BD Phoenix automated system (MIC> 8 µg/mL for imipenem and meropenem), E-test (MIC ˂32 µg/mL), and mCIM assay (the growth inhibition zone diameter was 6-8 mm). In carbapenem-resistant P. aeruginosa isolates, the frequency of blaVIM, blaIMP, and blaSPM genes was 9.1% (2 of 22), 4.5% (1 of 22), and 4.5% (1 of 22), respectively. BlaKPC and blaNDM genes were not found in any of the isolates. Conclusion: Based on the present study results, all phenotypic tests used to identify carbapenemase-producing isolates had the same sensitivity (100%) and specificity (100%).

https://iem.modares.ac.ir/article_1913_c44799b04a1c72e3c8593a53e8000c78.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 SARS-CoV-2 Reinfection Rate: A Systematic Review and Meta-analysis 63 70 1914 10.52547/iem.9.1.63 EN Yousef Alimohamadi Health Research Center, Life Style Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran Kiana Bahani Department of Epidemiology and Biostatistics School of public health, Tehran University of Medical Science, Tehran, Iran Kolsoom Alimohammadi Health Research Center, Life Style Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran Mojtaba Sepandi Health Research Center, Life Style Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran Journal Article Backgrounds: Reinfection among COVID-19 patients is still a challenging issue in the medical literature. Therefore, the current meta-analysis was conducted to estimate the pooled incidence rate of reinfection among COVID-19 patients. Materials & Methods: A comprehensive search was conducted in PubMed, Web of Science, and Scopus databases from July 1 to October 1, 2021. Original studies which estimated the incidence rate of COVID-19 reinfection were included. CASP (Critical Appraisal skills program) was used to assess the quality of studies. Data were analyzed by STATA statistical software Version 15 (StataCorp, College Station, TX, USA). Findings: A total of 3803 articles were found, of which 16 articles remained after title, abstract, and full text screening. The minimum and maximum incidence rates of reinfection were 0.001 and 0.73%, respectively. The pooled estimated incidence rate of COVID-19 reinfection was 0.11% (95% confidence interval: 0.02-0.20, p< .001, I2 = 100.0). The highest pooled estimated incidence rate of reinfection was observed in people <50 years old (0.14%) (95% CI: 0.001-0.34, p<.001, I2 = 100). Regarding the time elapsed after the first infection, the highest reinfection rate occurred four months after the first infection (0.12%) (95% CI: 0.001-0.27, p< .001, I2 = 100). Conclusion: The incidence rate of reinfection among COVID-19 patients is expected to be high. However, it seems that the influence of factors including the age of patients and the time elapsed after the first infection must be considered.

https://iem.modares.ac.ir/article_1914_07a4e20a7bbeeb7a736682b26b16ebe8.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 Diagnostic Role of Platelet-Lymphocyte Ratio and Platelet Parameters in COVID-19 Disease 71 78 1915 10.52547/iem.9.1.71 EN Nidhya Ganesan Associate Professor, Department of Pathology, PSG Institute of Medical Sciences and Research, Coimbatore, India Eliz Thomas Associate Professor, Department of Pathology, PSG Institute of Medical Sciences and Research, Coimbatore, India Subba Rao Tadury Madhukar Professor, Department of Pathology, PSG Institute of Medical Sciences and Research, Coimbatore, India Karthikeyan S Associate Professor, Department of Community Medicine, PSG Institute of Medical Sciences and Research, Coimbatore, India Lawanya G Assistant Professor, Department of Pathology, PSG Institute of Medical Sciences and Research, Coimbatore, India Journal Article Backgrounds: This study aimed to analyze the applicability of platelet parameters in assessing the severity of COVID-19 disease. Materials & Methods: Patients with RT-PCR confirmed COVID-19 in the pathology department of a tertiary care hospital in south India from June to December 2020 were included in this study. Clinical details and laboratory parameters of these patients were obtained. The difference between the studied variables in two groups was assessed using independent t-test. The optimum cut-off value of platelet to lymphocyte ratio (PLR) to differentiate between the tested groups was estimated using ROC (receiver operator curve) analysis. Findings: This study was conducted on 218 COVID-19 patients, of whom 17.9% showed thrombocytopenia at the time of admission. Among the hematological parameters, PLR, absolute lymphocyte count (ALC), platelet distribution width (PDW), D-dimer, and erythrocyte sedimentation rate (ESR) were significantly different between the ICU (intensive care unit) and non-ICU groups. Increased PLR values were associated with the disease severity. Conclusion: PLR could be used as an additional biomarker in assessing the severity of COVID-19 disease, and a cut-off value of 210.27 is optimal to differentiate severe COVID-19 disease from its mild and moderate forms with 79% specificity.

https://iem.modares.ac.ir/article_1915_b432f34c5a997c8e7c806a895ecc5e25.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 Thromboembolic Manifestations in Hospitalized COVID-19 Patients in India- A Single-Centre Retrospective Study 79 85 1916 10.52547/iem.9.1.79 EN Yoganathan Chidambaram Assistant Professor, Department of Medicine, PSG Institute of Medical Sciences and Research, Coimbatore, India Clement Jenil Dhas Assistant Professor, Department of Medicine, PSG Institute of Medical Sciences and Research, Coimbatore, India Nekkanti Abilash Assistant Professor, Department of Medicine, PSG Institute of Medical Sciences and Research, Coimbatore, India Velammal Petchiappan Associate Professor, Department of Medicine, PSG Institute of Medical Sciences and Research, Coimbatore, India Murali Alagesan Professor, Department of Medicine, PSG Institute of Medical Sciences and Research, Coimbatore, India Journal Article Backgrounds: This study aimed to evaluate the incidence and clinical profile of thromboembolic disease in COVID-19 patients and analyze its association with D-dimer and Interleukin (IL)-6 levels. Materials & Methods: This was a retrospective, single-center study conducted by analyzing data obtained from the case records of COVID-19 confirmed patients with thromboembolic manifestations in India during January 2020 to February 2022. Patients with conditions such as malignancy, prothrombotic states, and autoimmune diseases were excluded from the analysis. D-dimer and IL-6 levels and thrombotic events were analyzed along with comorbid conditions like diabetes mellitus (DM), hypertension, and dyslipidemia. Chi-square tests were used to evaluate the association of various thrombotic manifestations with D-dimer and IL-6 levels. A p-value of ≤ .05 was considered statistically significant. Findings: The mean age of 88 COVID-19 confirmed cases with thrombotic manifestations was 61.01±15.23 years, and the majority (62.5%) of the cases were male. D-dimer and IL-6 levels were elevated in 78.41 and 80.68% of the cases, respectively. The predominant thrombotic manifestation was pulmonary thromboembolism (PTE) (48.86%), followed by acute coronary syndrome (ACS) (36.36%), cerebrovascular accident (CVA) (22.73%), etc. There was no significant association between various thrombotic manifestations and D-dimer and IL-6 levels. Conclusion: PTE was the predominant thromboembolic manifestation in COVID-19 patients in the current cohort. Elevated D-dimer and IL-6 levels though found in the majority of the patients were not associated with thrombotic events. However, early recognition and treatment could reduce morbidity in COVID-19 patients.

https://iem.modares.ac.ir/article_1916_65fc52ed8f88c81323a418ca94cec2ed.pdf

Tarbiat Modares University Infection Epidemiology and Microbiology 2588-4107 9 1 2023 03 01 Review on Phytochemicals and Pharmacological Activities of Syzygium aromaticum 87 97 1917 10.52547/iem.9.1.87 EN Dr. Yahya Bin Abdullah Alrashdi School of Nursing, College of Pharmacy and Nursing, University of Nizwa, P. O. Box 33, Postal Code 616, Nizwa, Sultanate of Oman Dr. Mohammad Amzad Hossain School of Pharmacy, College of Pharmacy and Nursing, University of Nizwa, P. O. Box 33, Postal Code 616, Nizwa, Sultanate of Oman Journal Article Backgrounds: Syzygium aromaticum L (S. aromaticum, clove) is a plant species belonging to the Myrtaceae family. It is cultivated in many African and Asian countries. Folk medicine practitioners use different parts of this plant to treat gastrointestinal problems, diarrhea, dental pain, ulcer, and other chronic diseases. Experimental data on phytochemicals and pharmacological activities of this plant are scattered or unsystematic. Therefore, this review aimed to explore the available data on phytochemicals and pharmacological activities of S. aromaticum essential oil and extracts with various polarities. Materials & Methods: The literature review showed that only a few studies were conducted on this plant; consequently, there is not enough documented information about its bioactive phytochemicals and pharmacological activities. Findings: Most previous studies reviewed reported significant bioactive phytochemical contents, namely eugenol (49.7%), caryophyllene (18.9%), benzene, and 1-ethyl-3-nitro (11.1%), along with minor amounts of phytochemicals including carotenoids, gallic acid, flavonoids, oxalic acid, tannins, amino acids, fatty acids, and cyanidin glycoside. Sugars, coumarins, oleanolic acid, saponins, glycosides, and lipids were also identified in this species. The methanol extract of this plant and its different polar fractions were shown to exhibit significant antimicrobial, antioxidant, anti-allergic, antidiabetic, antihypertensive, anti-inflammatory, antifungal, and anticancer activities. Furthermore, the plant extracts were also shown to have chemoprotective and hepatoprotective properties. Conclusion: This review provides comprehensive data on botanical aspects, phytochemicals, and pharmacological activities of this plant to researchers to explore traditional/ medicinal uses and commercial drug production from S. aromaticum.

https://iem.modares.ac.ir/article_1917_cb79f8fa58b91d3af6c9c991f63962d3.pdf