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Soheila Habibi Ghahfarokhi, 1 Mehrdad Mosadegh, 1 Ali Ahmadi, 2 Mohammad Reza Pourmand, 1 Mohammad Azarsa, 3 Mohammad Rahbar, 4 Bahram Nikmanesh 5 1Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; 2Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran; 3Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran; 4Department of Microbiology, Reference Health Laboratories Research Center, Ministry of Health and Medical Education, Tehran, Iran; 5Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, IranCorrespondence: Mohammad Reza PourmandDepartment of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Poursina St., Keshavarz Blvd., Tehran 1417613151, IranTel/Fax +98 21-88-95-4910Email mpourmand@tums.ac.irIntroduction: Encapsulated Streptococcus pneumoniae strains cause high morbidity and mortality, mainly in countries with no pneumococcal conjugate vaccines (PCVs) immunization program. This study investigated the epidemiological changes of S. pneumoniae isolates including serotype distribution and antimicrobial susceptibility in Tehran, Iran.Methods: A total of 80 S. pneumoniae samples were collected from patients admitted to Shariati hospital over two periods. Half of the isolates were collected from February to September 2017 and the other half from July 2018 to March 2019. The antimicrobial susceptibility testing and PCV-13 serotype coverage of S. pneumoniae isolates were evaluated among patients with invasive and non-invasive infections.Results: The most common serotypes were 23F (17.5%), 14 (16.3%), 3 (16.3%) 19F (12.5%), and 19A (12.5%) in the present study. The vaccine coverage rates of PCV-7, PCV-10 and PCV-13 were 52.6%, 52.6%, and 83.7%, respectively. S. pneumoniae isolates with the serotype of the PCV-13 showed an increasing trend during the study. Nearly half of the S. pneumoniae strains were MDR, while MDR serotype 19A increased (40%) during the study periods. A small minority of isolates (16%) belonged to non-vaccine serotypes, 65% of which were assigned to MDR. In general, the frequency of penicillin resistant and MDR strains were estimated about 27.5% and 51%, respectively. An increase was observed in resistance to erythromycin and co-trimoxazole.Conclusion: The results showed that majority of the circulating serotypes in our study are related to PCV-13 serotypes. The use of conjugate vaccine in the immunization program and surveillance of antimicrobial resistance can be effective in reducing the pneumococcal clinical burden.Keywords: Streptococcus pneumoniae, serotype, pneumococcal conjugate vaccine, PCV, antibiotic susceptibility, multi-drug resistance, MDR

Roghayeh Samadi,1 Zohreh Ghalavand,1 Reza Mirnejad,2 Bahram Nikmanesh,3 Gita Eslami1 1Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2Molecular Biology Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran; 3Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, IranCorrespondence: Gita EslamiDepartment of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, IranTel +98-2123872556Email g_eslami@yahoo.comIntroduction: Methicillin-resistant Staphylococcus aureus (MRSA) causes high rates of mortality and a substantial burden to health systems worldwide. Here, we investigated the antimicrobial susceptibility and molecular characteristics of MRSA isolated from children referred to Children’s Medical Center in Tehran.Materials and methods: A total of 98 MRSA isolates were collected from children. Antimicrobial resistance patterns were determined using the disk diffusion and E-test methods. The presence of biofilm encoding genes and the pvl gene were determined by PCR. We used the microtiter plate method to assess the ability of biofilm formation. The MRSA isolates were further analyzed using PFGE and SCCmec typing.Results: Antibiotic susceptibility testing showed that the highest and the lowest antibiotic resistance percentage were related to erythromycin (62%) and minocycline (10%), respectively. Overall, 63% of MRSA isolates were biofilm producers. Resistance to two antibiotics such as erythromycin (72% vs 28%, P=0.01) and clindamycin (71% vs 29%, P=0.04) was higher among biofilm producers than non-biofilm producers. All strains had biofilm-forming genes and the prevalence of pvl gene was 41%. Most MRSA isolates belonged to SCCmec IVa (75%) and SCCmec III (18%). In PFGE technique, 5 common types and 2 single types were identified; Common type 1 with 37 isolates was dominant clone.Conclusion: We thus report preliminary data on the prevalence and distribution of MRSA genotypes in Tehran Children’s Hospital. These findings characterize the MRSA colonization dynamics in child patients in Iran and may aid the design of strategies to prevent MRSA infection and dissemination.Keywords: MRSA, biofilm formation, antibiotic resistance, SCCmec typing, PFGE

Background and Objective: Yersinia is a gram-negative bacillus that cause diarrhea through consumption of contaminated food and water. This study was performed to identify the atypical Yersinia virulence markers isolated from children with diarrhea. Methods: This descriptive cross -sectional study was done on 384 fecal samples of 0- 14 years old children admitted at children medical center from August 2011 to August of 2012. Fecal samples, for the enrichment, after 21 days of incubation in alkaline buffer with pH=7.2 at 4degree C, on days 7, 14 and 21 samples were cultured on CIN agar and Mac agar and then confirm the differentiation atypical Yersinia from other typical Yersinia species from fermentation of different sugars. Isolates were tested for marker of virulence including calcium dependence, auto agglutination, Congo red uptake and binding of crystal violet. Results: Out of 384 stool samples, 4 (1.04%) were infected with Yersinia (Yersinia frederikseni, Yersinia kristensenii and Yersinia enterocolitica). Out of these three, only two samples in association was positive with virulence markers. Conclusion: Phenotypic markers can be used to study the properties of phenotypic strains of Yersinia.

Background and Objective: Yersinia enterocolitica is a worldwide pathogen belong to genus Yersinia. The association between acute childhood diarrhea and other diseases caused by Yersinia enterocolitica has been established by several researchers. Due to the lack of sufficient information on other pathogenic Yersinia species, this study was done to determine the prevalence and the pattern of antibiotic susceptibility of atypical Yersinia spp isolated from children, less than 14 years old. Methods: This descriptive cross - sectional study was carried on 384 children with diarrhea whom referred to the Tehran children medical center, Tehran, Iran during August 2011 to August 2012. 384 fecal specimens of children were transferd to the laboratory and cold enrichment in alkaline buffer with pH of 7.2 for 21 days. The samples were cultured in Cefsulodin-Irgasan-Novobiocin Agar (CIN) differential media in 7, 14, and 21 days. The identification of Yersinia species were carried out by conventional procedure. Antibiotic susceptibility test to Ciprofloxacin, Co-trimoxazole, Tetracycline, Chloramphenicol, Erythromycin, Ampicillin, Gentamicin, Penicillin were determined by standard disk diffusion method. Results: Out of 384 fecal samples, 3 (0.7%) were infected with Yersinia. Three species of Yersinia were Y.enterocolitica, Y.Kristensenii and Y.frederiksenii. All three strains were sensitive to Cotrimoxazole, Tetracycline, Chloramphenicol, Ciprofloxacin and Gentamicin. Conclusion: This study showed that atypical Yersinia play important role in diarrhea. Therefore, more attention should be noticed to atypical Yersinia species in addition to Yersinia enterocolitica.

Background: Septicaemia is a leading cause of morbidity and mortality of infant's and childerens espicially in first week of their life, both in developed and underdeveloped countries.The aim of this research was to study of bacterial agents causing septicaemia and to determine their antibiotic suseptibility patternes. Materials and Methods : This was a descriptive study, it was performed during eight months from October 2011 till May 2011. In total 216 blood culture samples of children suspected of septicaemia in children health centre hospital were send to the laboratory for investigation. The bacterial identification was carried out by culturing and conventional biomedical tests. The antibiotic sensitivity tests were performed by disk diffusion method. These data are analyzed by SPSS and the results Expressed as relative frequencies. Results: Out of 216 tested samples 55(25.6%) were positive and 161 (74.54%) negative. The dominated bacteria was Escherichia coli (31.42%), followed by Staphylococcus aureus (22.86 %), Klebsiella pneumonia (20%)), Staphylococcus epidermidis (14.28%), Streptococcus pneumonia (2.86%), Salmonella typhi (2.86%), Enterobacter cloacae (2.86%) and Stenotrophomonas maltophilia (2.86%). In general gram-negative bacteria were isolated more than gram-positive. Staphylococcus bacteria were more resistant to antibiotics than other isolated bacteria, and were 100% resistant to penicillin. The enterobacteriaceae were more sensitive to norfloxacin, amikacin, tobramycin, and they were 100% resistant to ampicillin. Conclusion: The results obtained in this study showed that gram-negative bacteria are more responsible in septicaemia in children ward, and norfloxacin is the more effective antibiotic in comparison with others. [ABSTRACT FROM AUTHOR]

Background: In this study, attempts were made to evaluate the frequency of high-level gentamicin-resistant (HLGR) and vancomycin-resistant enterococci (VRE) and the prevalence and antibiotic resistance profile of enterococcal species isolated from pediatric patients referred to Children's Medical Center Hospital, Tehran, over five years., Materials and Methods: A total of 404 enterococcal isolates from different patients referred to the Children's Medical Center between March 2016 and March 2021 were included in this cross-sectional study. Antimicrobial susceptibility testing was performed using standard methods according to the guidelines of the Clinical Laboratories Standards Institute (CLSI)., Results: Approximately one-third of the enterococcal strains were isolated from urology and intensive care units. 17.3% of the isolates were obtained from outpatient sources. However, 82.7% of the isolates were sourced from inpatient settings. We found that the rates of resistance to ampicillin, penicillin, and vancomycin were twice as high in inpatients as in outpatients. Of the total isolates, 87.4% and 49.3% were identified as HLGR and VRE, respectively. In addition, we identified 2% of the VRE isolates that were not susceptible to linezolid. Nitrofurantoin showed excellent activity against enterococcal isolates in the urine, with a susceptibility rate of 92.5%., Conclusion: The present study reports the highest range of VRE isolated from pediatric patients in Iran. Despite the predominance of HLGR enterococci in our region, vancomycin remains effective against such strains. This study is among the few to demonstrate the incidence of linezolid-insensitive VRE in pediatric patients. Therefore, it is important to evaluate effective infection control measures to prevent linezolid and vancomycin resistance in enterococci., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2024 Bahram Nikmanesh et al.)

Here, we described the efficacy of colistin sub-minimum inhibitory concentrations (sub-MICs) on biofilm-forming activity, host epithelial cell adherence, and invasion capacity of Acinetobacter baumannii strains collected from children admitted to the Children's Medical Center Hospital. Biofilm formation potency of A. baumannii clinical isolates was measured using a 96-well microtiter plate assay. Distribution of biofilm-related genes, including bap , abaI , ompA , csuE , and bla PER-1 , was detected by PCR. The mRNA expression level of ompA and csuE was measured by qPCR in the presence of ¼ and ½ MICs of colistin. A. baumannii adhesion and invasion to eukaryotic host cells were phenotypically assayed at sub-MICs of colistin. Eighty percent (56/70) and 35.7% (25/70) of A. baumannii isolates were multidrug-resistant (MDR) and extensively drug-resistant (XDR) phenotypes, respectively. The strong, moderate, and weak biofilm producers of A. baumannii were 37.1% (26/70), 32.8%, (23/70), and 22.8% (16/70), respectively. The frequencies of biofilm-associated genes were 100% for abaI , ompA , and csuE , followed by 22.8% (16/70) and 24.3% (17/70) for bap and bla PER-1 , respectively. The downregulation of csuE and ompA expression levels was observed in the sub-MIC of colistin. In vitro cell culture study showed a decreased capability of A. baumannii to adhere to the human epithelial cells at sub-inhibitory doses of colistin; however, none of the isolates could invade HEp-2 cells. Our study showed that the genes encoding biofilm-associated proteins undergo downregulation in expression levels after exposure to sub-MICs of colistin in A. baumannii . Longitudinal in vivo studies are needed to fully understand the clinical aspects of pathogenicity mechanisms and evolutionary dynamics of drug resistance.IMPORTANCESince the toxicity of colistin is dose dependent, there is a focus on strategies that reduce the dose while maintaining the therapeutic effect of the drug. Our findings about sub-inhibitory doses of colistin provide a novel insight into the logical use of colistin to treat and control Acinetobacter baumannii -related infections in clinical practice., Competing Interests: The authors declare no conflict of interest.

Candidemia caused by rare and uncommon Candida species is becoming more prevalent in pediatric healthcare settings, resulting in significant morbidity and mortality. One such species, Candida palmioleophila , is resistant to fluconazole but highly susceptible to echinocandins. Here, we report the first documented case of C. palmioleophila candidemia in Iran that occurred in a male infant with biliary atresia who had been hospitalized for 2 months. The patient's blood and urine cultures were positive for both yeast and bacterial species. Through DNA sequence analysis, the yeast isolate was identified as C. palmioleophila . In vitro antifungal susceptibility testing of the isolate against amphotericin B, fluconazole, itraconazole, voriconazole, isavuconazole, posaconazole, and nystatin revealed MIC values of 2, 16, 0.25, 0.0625, 0.125, 0.25, and 4 μg/mL, respectively, and minimum effective concentration for caspofungin was 0.031 μg/mL. Despite receiving antibacterial and antifungal therapies, the patient unfortunately expired due to bradycardia and hypoxemia. Proper identification and epidemiological surveillance studies are needed to understand the exact prevalence of these emerging yeast pathogens. Previously reported cases of C. palmioleophila infection, primarily associated with bloodstream infections and catheter-related candidemia, were reviewed., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Aboutalebian, Nikmanesh, Mohammadpour, Charsizadeh and Mirhendi.)

Acute appendicitis represents one of the most common causes of emergency abdominal surgery worldwide. Meanwhile, Enterobius vermicularis has been suggested as one of the probable causes of appendicitis. In this study, the morphological characteristics of the remnant pinworms and pathologic changes were explored in old-archived FFPE tissues of appendectomies. Moreover, we provide the first molecular identification, genetic, and haplotype variation of this nematode from the old-archived FFPE tissue section of appendectomy using the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. Seventeen FFPE appendectomies with E. vermicularis infection, stored over 12-22 years, were collected from two different geographical areas of Iran. In the histopathological examination, tissue changes were observed in thirteen cases (76.4%) and inflammation in four blocks (23.5%). After DNA extraction, the cox1 gene was amplified in twelve (70.6%) cases using the nested polymerase chain reaction (PCR). Phylogenetic analysis and a median-joining network of 78 available cox1 sequences of E. vermicularis revealed 59 haplotypes. We identified five haplotypes that fell into type B. All Haplotypes are novel except for two haplotypes, Hap32 and Hap37, identical to E. vermicularis sequences from Iran, Greece, and Germany. The ranges of diversity distance and haplotype diversity within the isolates were 0-1.9% and HD:0.643-0.667, subsequently. Overall, the absence of inflammation or even tissue changes in some sections can suggest the possible non-inflammatory role of E. vermicularis in appendicitis. Although FFPE material suffers from PCR inhibition, we could successfully use nested PCR to characterize E. vermicularis in old-archived appendectomy blocks and suggest this method as a complementary diagnosis technique in pathology. While the predominant type was B in the Middle East and Europe, further studies on a larger sample size from different geographical regions could probably confirm the results obtained in the present study., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Haghshenas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background and Purpose: Given the high mortality rate of invasive candidiasis in hospitalized pediatric patients, it is crucial to establish a predictive system to achieve early diagnosis and treatment of patients who are likely to benefit from early antifungal treatment. This study aimed to assess the Candida colonization index, species distribution, and antifungal susceptibility pattern of Candida strains isolated from pediatric patients with high Candida colonization index (CI)., Materials and Methods: This study was carried out at the Children's Medical Center in Tehran-Iran. In total, 661 samples were collected from 83 patients. The Candida CI was calculated according to the descriptions of previous studies. The isolates were identified using polymerase chain reaction-based techniques. The Clinical and Laboratory Standard Institute protocol M60 was used to conduct the antifungal susceptibility test., Results: A colonization index greater than 0.5 was confirmed in 29 cases (58% of positive samples) with two children developing candidemia. Candida albicans (n=53, 49.5%) was the most common Candida species in patients with CI > 0.5. Except for acute lymphoblastic leukemia, no risk factors were linked to a high index in colonized children ( P > 0.05). Twelve isolates (7.01%) were multi-azole resistant with high MICs against both isavuconazole and ravuconazole and seven strains (4.09%) were echinocandins resistant., Conclusion: In pediatric intensive care units, patients are at risk of fungal infection, particularly candidemia. In this study, more than half of the children with positive yeast cultures had CI > 0.5, and 6.8% developed candidemia., Competing Interests: There is no conflict of interest., (Copyright: © 2021, Published by Mazandaran University of Medical Sciences on behalf of Iranian Society of Medical Mycology and Invasive Fungi Research Center.)

Background and Purpose: This study aimed to evaluate the species distribution and susceptibility pattern of the strains isolated from Candida colonization in pediatric patients staying at pediatric intensive care unit (ICU) and infant ICU of Children's Medical Center in Tehran, Iran., Materials and Methods: This study was conducted in the Children's Medical Center in Tehran, Iran. In total, 440 samples from 56 patients with oral cavity, skin surrounded catheters, and ear, throat, nasal, and urine cultures were collected. All patients were evaluated in terms of Candida colonization on the admission day as well as the days 7, 14, and 28 according to the previous studies. CHROMagar Candida medium was applied for primary/multiple species identification and the isolates were identified by using polymerase chain reaction-based methods to the species-specific complex level. The antifungal susceptibility test was performed according to the Clinical and Laboratory Standards protocol published as M27-A3 and M60 documents., Results: In total, 136 yeast samples from 26 individuals (30.9%) out of 440 samples were considered colonization. The most prevalent species in IICU was C. albicans (27%, n=20) followed by C. krusei (24 %, n=18) and C. parapsilosis (16%, n=12). In PICU, the predominant species was C. krusei (40%, n=24) followed by C. parapsilosis (18%, n=11) and C. dubliniensis (16%, n=10). Among the 40 tested isolates from both units, fluconazole-resistant isolates (n=11, 8.15%) were determined according to the new breakpoints. In the case of echinocandins, 2 isolates, including C. albicans (n=1) and C. krusei (n=1) were resistant against both caspofungin and anidulafungin (totally 1.48%)., Conclusion: In the present study, since C. krusei is intrinsically-resistance against fluconazole, emphasizing the importance of species-level identification of Candida isolates is outstanding. However, according to the antifungal susceptibility testing results, only 7.2% of the strains were resistant to fluconazole. It would be beneficial to monitor the ICU patients who are at high risk of invasive Candida infection., Competing Interests: There is no conflict of interest., (Copyright: © 2021, Published by Mazandaran University of Medical Sciences on behalf of Iranian Society of Medical Mycology and Invasive Fungi Research Center.)

Background: Multiple yeast species can cause human disease, involving superficial to deep-seated infections. Treatment of these infections depends on the accurate identification of causative agents; however, reliable methods are not available in many laboratories, especially not in resource-limited settings. Here, a new multiplex assay for rapid and low-cost identification of pathogenic yeasts is described., Methods: A two-step multiplex assay named YEAST PLEX that comprises of four tubes and identifies 17 clinically important common to rare yeasts was designed and evaluated. The set also provides PCR amplicon of unidentified species for direct sequencing. The specificity of YEAST PLEX was tested using 28 reference strains belonging to 17 species and 101 DNA samples of clinically important non-target bacteria, parasites, and fungi as well as human genomic DNA. The method was further analyzed using 203 previously identified and 89 unknown clinical yeast isolates. Moreover, the method was tested for its ability to identify mixed yeast colonies by using 18 mixed suspensions of two or three species., Results: YEAST PLEX was able to identify all the target species without any non-specific PCR products. When compared to PCR-sequencing/MALDI-TOF, the results of YEAST PLEX were in 100% agreement. Regarding the 89 unknown clinical isolates, random isolates were selected and subjected to PCR-sequencing. The results of sequencing were in agreement with those of YEAST PLEX. Furthermore, this method was able to correctly identify all yeasts in mixed suspensions., Conclusion: YEAST PLEX is an accurate, low-cost, and rapid method for identification of yeasts, with applicability, especially in developing countries., (© 2022 The Authors. Journal of Clinical Laboratory Analysis published by Wiley Periodicals LLC.)

Background: β-Lactam antibiotics have been broadly used for the treatment of Acinetobacter baumannii infections, resulting in development of β-lactam inactivating β-lactamases. Here, we described antibiotic resistance rate, prevalence of β-lactamase-encoding genes, and clonal relationships of A. baumannii strains isolated from children referred to Children's Medical Center in Tehran, Iran, during 2019-2020., Methods: A total of 60 non-replicate A. baumannii isolates were recovered from clinical specimens of pediatric patients. Antibiotic susceptibility testing was done by the disc diffusion method. Colistin susceptibility of isolates was performed by the broth microdilution method. β-lactamase-encoding genes were characterized by PCR. The presence of ISAba1 element upstream of the several oxacillinase genes was also checked. Genetic relatedness of isolates was determined by using random amplification of polymorphic DNA (RAPD) typing., Results: The antimicrobial susceptibility tests showed that 83.3% of A. baumannii isolates were MDR, and 40% XDR. Both MDR and XDR A. baumannii isolates were susceptible to colistin. The frequency of bla OXA-51-like , bla OXA-23-like , bla TEM , bla OXA-24-like , bla PER , bla SHV , bla CTX-M , bla OXA-58-like , and bla IMP was 100, 93.33, 60, 36.67, 28.33, 8.33, 5, 3.33, and 1.67%, respectively. Coexistence of ISAba1/bla OXA-23-like and ISAba1/bla OXA-51-like was observed in 65% and 85% of isolates, respectively. RAPD analysis revealed 4 common types and 2 single types of A. baumannii isolates., Conclusions: The multiple clones harboring bla OXA-23-like , ISAba1-bla OXA-51-like , and ISAba1-bla OXA-23-like were responsible for the spread of A. baumannii isolates in our clinical wards. Dissemination of the well-established clones is worrisome and would become therapeutic challenges due to the possible transferring genetic elements associated with resistance., (© 2021. The Author(s).)

Background and Objectives: Escherichia coli (E. coli) sequence type 131 (ST131) is associated with extended-spectrum beta-lactamase (ESBL) production and fluoroquinolone resistance. This study aimed to investigate the prevalence of ST131, ESBL, and plasmid-mediated quinolone resistance (PMQR) genes in the ciprofloxacin-resistant (CIP R ) and ESBL producers from women with UTI., Materials and Methods: The CIP-resistant ESBL producing (CIP R /ESBL + ) E. coli isolates were screened for ST131-by specific PCR of mdh and gyrB . The ESBL and PMQR genes were screened by single PCR. The ST131 and non-ST131 isolates were selected to determine the mutations of gyrA and parC using PCR and sequencing, and also their genetic background by the Pasteur-MLST scheme., Results: Overall, 55% (33/60) CIP R /ESBL + isolates were identified as ST131 (94% O25b-ST131). Resistance rate to ampicillin-sulbactam (70%), aztreonam (97%) and gentamicin (61%), the prevalence of aac(6')-Ib-cr (66%), bla CTX-M-15 (82%), the profile of qnrS+aac(6')-Ib-cr (30%), and the double mutation in the parC was significantly higher in ST131 than non- ST131 isolates. The coexistence of PMQR and ESBL genes was found in more than 50% of ST131 and non-ST131 isolates. ST131 isolates differentiated into PST43 and PST506., Conclusion: Management of women with UTI caused by the CIP R /ESBL + isolates (ST131) co-harbored PMQR, ESBL, and chromosomal mutations, is important for their effective therapy., (Copyright © 2021 The Authors. Published by Tehran University of Medical Sciences.)

Background: Salmonella is considered as a main cause of community-acquired diarrhea in humans, however, sources of the multi-drug resistant (MDR) strains and their link with the disease are not well known., Aims: This study aimed to investigate the frequency, serogroup diversity, and antimicrobial susceptibility patterns of Salmonella strains in poultry meat and stool samples of patients with community acquired diarrhea in Tehran., Methods: We compared the frequency of non-typhoidal Salmonella serogroups, the similarities of their resistance patterns to 10 antimicrobial compounds, the prevalence of extended spectrum β-lactamase (ESBL) and ampicillinase C (AmpC) genetic determinants, and class 1 and 2 integrons in 100 chicken meat and 400 stool samples of symptomatic patients in Tehran during June 2018 to March 2019., Results: Salmonella was isolated from 75% and 5.5% of the chicken meats and human stool samples, respectively. The chicken meat isolates mainly belonged to serogroup C (88%, 66/75), while the human stool isolates were mainly related to serogroup D (59.1%, 13/22). The MDR phenotype and the most common rates of resistance to antibiotics, including tetracycline, trimethoprim/sulfamethoxazole (TS) and azithromycin, were detected in 4.5% and 45.3%, 59% and 13.6%, 43% and 9.1%, 42% and 9.1% of the human stool and chicken meat samples, respectively. Carriage of bla CTX , bla SHV , and bla PER genes in the meat isolate with ESBL resistance phenotype and bla ACC , bla FOX , and bla CMY-2 among the 7 meat strains with AmpC resistance phenotype was not confirmed using polymerase chain reaction (PCR). High prevalence of class 1 and 2 integrons was characterized and showed a correlation with resistance to TS and chloramphenicol., Conclusion: These findings showed a lack of association between chicken meats and human isolates due to discrepancy between the characterized serogroups and resistance phenotypes.

Background: Candida species cause a wide spectrum of disease entities. Candida africana and Candida dubliniensis -members of Candida albicans complex-are currently gaining both clinical and epidemiologic significance., Materials and Methods: Totally, 150 pediatric isolates that had previously been identified as C. albicans species complex based on a positive germ tube test were included. The isolates were cultured on CHROMagar Candida medium to ensure their purity and the results of germ tube test. For definitive speciation, PCR amplification and size polymorphism of the hyphal wall protein 1 ( HWP1 ) gene was used. The results of HWP1 -PCR were confirmed by sequencing the amplified fragments for randomly selected isolates of C. africana and C. dubliniensis ., Results: All 150 isolates included in this study were reconfirmed as C. albicans complex on chromogenic media. Based on the HWP1 gene size polymorphism, 141 (94%) isolates were identified as C. albicans , 2 (1.33%) as C. africana , and 1 (0.67%) as C. dubliniensis . The remaining 6 (4%) C. albicans complex isolates were a mix of C. albicans and C. africana . All isolates of C. africana and C. dubliniensis have been recovered from cases of candiduria., Conclusion: C. africana , either alone or mixed with C. albicans , could be a cause of candiduria among pediatric patients and should not be ignored., Competing Interests: Conflict of interest: All authors declare no conflicts of interest in this paper., (© 2020 the Author(s), licensee AIMS Press.)

Objectives: Staphylococcus aureus can cause several infections. Its capability to form biofilm has been reported to be a vital property involved in the bacteria's pathogenesis. Various genes contributing to biofilm formation have not yet been completely clarified. This study was designed to evaluate the factors influencing adherence and biofilm formation in S. aureus isolated from paediatric patients., Materials and Methods: One hundred and ninety-seven S. aureus isolates were obtained from pediatric patients and confirmed with phenotypic and molecular examinations. Antimicrobial susceptibility testing and biofilm formation were evaluated using standard methods. The genes encoding adhesion and virulence factors were investigated by the PCR method., Results: The most efficient antibiotics against S. aureus isolates were vancomycin and linezolid. Approximately, 54.2% of MSSA and 85.6% of MRSA isolates were biofilm producers according to the microtiter test. Our analysis indicated that MRSA isolates are better able to form biofilm compared with MSSA isolates. All isolates harbored clfA, fnbpA, icaA, icaB, icaC , and icaD , while clfB, fnbB, hlg , and pvl were detected in 99.5%, 42.1%, 97.5%, and 5.6% of isolates, respectively. In addition, a significant difference was found in fnhB gene and biofilm formation., Conclusion: Our findings showed a significant correlation between mecA and pvl genes and MRSA and biofilm formation in S. aureus isolates. Additionally, this study indicated the significant role of the fnhB gene as a major marker for S. aureus biofilm formation. Therefore, further experiments are warranted to exactly elucidate the function of the fnhB gene in the formation of biofilm.

Background: Echinococcus granulosus parasite causes a zoonotic disease which is important for public and veterinary health. Since pumpkin seeds ( Cucurbita sp.) are used as traditional vermifuge in Iran, they may be a potential herbal anthelmintic., Methods: This study was designed in 2016 to evaluate the in vitro scolicidal effect of Cucurbita moschata seeds form northern part of Iran. Hydroalcoholic and petroleum ether extracts were prepared by maceration and soxhlet respectively. Both extracts with four different concentrations (100, 10, 1, 0.1 mg/ml) were incubated against protoscoleces in 5, 15, 30 and 60 min., Results: Maximum mortality was 16% with 1% hydroalcoholic extract in 60 min. The highest mortality with organic extract was 4% with 10% concentration in 60 min ( P =0.015)., Conclusion: Since highest mortality was 16%, the extract did not reach to LD50 (50% mortality). Therefore, the potency of the total extract is not sufficient as potential scolicidal drug., Competing Interests: Conflict of interests The authors declare that there is no conflict of interest., (Copyright© Iranian Society of Parasitology & Tehran University of Medical Sciences.)

Background: Canids are definitive hosts of Echinococcus multilocularis and Echinococcus granulosus. This study aimed to survey these two Echinococcus species in canids of North-Khorasan Province, northeastern Iran, using morphological criteria and genetic characterization of mitochondrial DNA., Methods: The carcasses of 106 canids, namely 61 jackals (Canis aureus), 23 foxes (Vulpes vulpes), 19 dogs (Canis familiaris) and three wolves (Canis lupus) were collected from the study area in 2013-2014 and examined for Echinococcus species. Morphological features were assessed by microscopy of adult worms. For molecular characterization, DNA was extracted, mostly from the adult worms but also from eggs. DNA fragments of the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) mitochondrial genes were amplified and sequenced. Sequences were aligned and compared with reference sequences. Intraspecific and interspecific diversity were calculated and phylogenetic analysis was performed., Results: Overall, 9.4% of the canids (eight jackals and two foxes) were found infected with E. multilocularis by molecular methods, of which seven cases were also confirmed using morphological description of the adult worms. Echinococcus granulosus was found in 6.6% of the canines (four dogs, two jackals and one wolf) as determined by both molecular methods and adult cestode morphology. All E. granulosus isolates were identified as the G1 genotype. Comparative sequence analysis indicated 0-0.7% and 0% intraspecific divergence within E. granulosus isolates and 0% and 0-0.2% within E. multilocularis isolates for cox1 and nad1, respectively., Conclusions: This study revealed the presence of E. multilocularis and E. granulosus in canids of North-Khorasan Province of Iran. Jackals were found infected with both E. multilocularis and E. granulosus, but infection with the former species was higher.

Fungal bio-aerosols are of concern due to their adverse health effects, especially in indoor environments. The aim of this study was to evaluate the relationship between the concentration and type of fungal bio-aerosols in the indoor and outdoor of Children's Medical Center in Tehran, Iran. In the present descriptive-analytical study, the fungal bio-aerosols' concentrations in both indoor and outdoor of the hospital air were measured. The measurements were carried out by the Anderson method using a Quick Take 30 pump at 28.3 L min -1 and 2.5 min sampling that was placed on a Sabouraud dextrose agar with chloramphenicol. The average concentrations of total fungal bio-aerosols in the hospital indoor and outdoor air were 40.48 and 119.6 CFU/m 3 , respectively. Onco-hematology and bone marrow transplantation wards were the most and least contaminated units, respectively (11.09 CFU/m 3 vs 1.47 CFU/m 3 ). The most common fungi isolated from the indoor environment were Penicillium spp. (45.86%) which was followed by Cladosporium spp. (31.92%), Aspergillus section Nigri (6.26%), sterilized mycelia (5.05%), and Aspergillus section Flavi (2.83%). Cladosporium spp. (61.10 CFU/m 3 ) and Penicillium spp. (18.56 CFU/m 3 ) had the highest mean concentrations in outdoor and indoor air, respectively. The indoor-to-outdoor ratio of fungal aerosols was < 1 at most sampling sites, indicating that the indoor fungal bio-aerosols may have originated from the outdoor environment.

Purpose: Helicobacter pylori is one of the most common human infectious agents which may be transmitted via water. This study was designed to test H. pylori presence via molecular methods in various aquatic environments as well as sewage sludge (SS) to understand the role of these environments in the pathogen's transmission., Methods: specific primers for the 16S rRNA and ure A genes of H. pylori were used in a nested and semi-nested PCR, respectively. Detection sensitivity of H. pylori in environmental samples by semi-nested PCR was also compared with real-time PCR. Analysis of fecal coliforms (FC) as pollution indicator bacteria was also performed., Results: H. pylori 16S rRNA gene was detected in 36% (14/39) of wastewater samples and 8% (2/25) of water samples, while amplification of ure A gene yielded only two positive result s . None of the SS samples were positive for H. pylori and real-time PCR could not identify H. pylori in any of the samples. The results showed no correlation between the presence of H. pylori and FC., Conclusions: Our result revealed the widespread presence of H. pylori in wastewater samples which indicates wastewater may be a source for dissemination and transmission of H. pylori infection. Further research is needed to determine the risk of H. pylori in wastewater reuse for irrigation of crops., Competing Interests: Conflict of interestThe authors declare that they have no conflict of interest.

Background: The aim of this mini-review is to highlight the potential applications of next-generation sequencing technology to the field of clinical oncology with respect to genetic diagnosis, cancer classification, predictive biomarkers and personalized medicine., Methods: Scientific databases were searched to collect relative data., Results: Effective systematic analysis of whole-genome sequence and whole-exome sequence of tumors, targeted genome profiling, transcriptome sequencing and tumor-normal comparisons can be performed using NGS in order to diagnosis of several types of cancer., Conclusion: NGS technology can be powerful enough to discover new and infrequent gene alterations, identify hereditary cancer mutation carriers and provide a reliable molecular portrait of wide range of cancers in a quick and cost-effective manner., Competing Interests: Conflict of interest The authors declare that there is no conflict of interests.

Introduction: Staphylococcus aureus is known to be a major cause of skin and soft tissue infections, pneumonia and invasive diseases. In this study, attempts were made to examine the prevalence of tsst-1, eta, etb, and luk-PV genes among methicillin-resistant S. aureus (MRSA) isolated from children in Tehran., Methodology: In the present cross-sectional study, a total of 100 MRSA were isolated from children who were referred to a pediatric hospital during 11-month period of September 2014 to August 2015. Isolates were identified using biochemical tests and then, using PCR, the isolates were tested for the presence of mecA, tsst-1, eta, etb, and luk-PV genes. Susceptibility of isolates to cefoxitin, penicillin, erythromycin, clindamycin, gentamicin, rifampin, minocycline, co-trimoxazole, linezolid, and vancomycin were evaluated using standard methods., Results: It was found that the MRSA isolates had the greatest resistance to clindamycin (72%) and erythromycin (59%), while the lowest rates of resistance were observed to be related to minocycline (6%) and rifampin (12%). All of isolates were sensitive to vancomycin and linezolid. The mecA gene was detected in all the isolates. Moreover, luk-PV and tsst-1 were detected in 18% and 17% of the isolates, respectively. None of the isolates harbored eta and etb genes., Conclusions: Our data provide specifications about the toxin production status of S. aureus isolates from pediatric children. The current study showed increased resistance to different antibiotics in S. aureus isolates. Therefore, to prevent multi-resistance to other antibiotic classes, it is essential to withhold prescriptions and stop unessential use of available antibiotics., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2017 Mozhgan Esmaeili Benvidi, Hamidreza Houri, Zohreh Ghalavand, Bahram Nikmanesh, Hadi Azimi, Roghayeh Samadi, Narges Nodeh Farahani, Gita Eslami.)

We report a case of subconjunctival worm with a rare presentation of diurnal photophobia and temporal conjunctival injection. This case report describes a subconjunctival dirofilariasis in a 59-year-old man presented with foreign body sensation, localized tenderness, and eye redness during the day. After removal of subconjunctival 10 cm worm, the diagnosis was compatible with Dirofilaria immitis . Proof of identity was based on the morphological appearance, which were reliable diagnostic clues. Ocular examination was normal one month later except for faint temporal conjunctival scar. Subconjunctival dirofilariasis could present as diurnal photophobia and conjunctival injection., Competing Interests: Conflict of Interests The authors declare that there is no conflict of interests.

Background & Objectives: Bacterial vaginosis (BV) is the most prevalent vaginal infection in women of reproductive age group which has been found to be associated with vitamin D deficiency. The purpose of this study was to investigate the effectiveness of the administration of 2000 IU/day edible vitamin D for 15 wk to eliminate asymptomatic BV among reproductive age women with vitamin D deficiency., Methods: A total of 208 women with asymptomatic BV, who were found to be eligible after interviews and laboratory tests, were randomly assigned to a control group (n=106) or an intervention group (n=105). They used vitamin D drops daily for 105 days. Vaginal and blood samples were taken before and after the second intervention using identical methods (Nugent score for BV diagnosis, serum 25-hydroxyvitamin D for vitamin D determination)., Results: The cure rate of asymptomatic BV was 63.5 per cent in the intervention and 19.2 per cent in the control group (P <0.001). The results showed that being unmarried (P=0.02), being passive smoker (P<0.001), and being in the luteal phase of a menstrual cycle during sampling (P=0.01) were significantly associated with post-intervention BV positive results. After these elements were controlled, the odds of BV positive results in the control group was 10.8 times more than in the intervention group (P<0.001)., Interpretation & Conclusions: Among women in reproductive age group with vitamin D deficiency, the administration of 2000 IU/day edible vitamin D was effective in eliminating asymptomatic BV. This treatment could be useful in preventing the symptoms and side effects of BV.

Background and Objectives: The appearance of antibiotic resistance in Streptococcus pneumoniae has raised a global concern over the past three decades. This study was conducted to determine the antimicrobial susceptibility of S. pneumoniae isolated from patients in Children´s Medical Center (CMC) Hospital during 2001 to 2011., Materials and Methods: During the 11 years period, a total of 194 S. pneumoniae isolates were collected in CMC Hospital. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disk diffusion method and time-series analysis was used to evaluate the antimicrobial susceptibility changes over the time., Results and Conclusion: Antimicrobial susceptibility of S. pneumoniae to different antibiotics decreased from 2001 to 2011 as: penicillin from 78% to 32%, erythromycin from 75% to 35%, chloramphenicol from 94% to 55%, ampicillin from 70% to 62%, ceftriaxone from 100% to 87%, sulfametoxazole from 57% to 40%. We did not find any significant difference between the susceptibility of isolates from sterile and non-sterile sources. It would be an important key to consider antimicrobial stewardship as an essential factor to prevent the development of antimicrobial resistance.

Background: The aim of this study was to determine the prevalence of virulence-associated genes and enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) analysis of Campylobacter spp. isolated from children with diarrhea in Iran., Methods: A total of 200 stool specimens were obtained from children under 5 years during July 2012 to July 2013. Detection of C. jejuni and C. coli was performed by standard biochemical and molecular methods. The presence of virulence-associated genes and genetic diversity of isolates was examined using PCR and ERIC-PCR analyses., Results: A total of 12 (6%) Campylobacter spp. were isolated from patients including 10 (4.5%) C. jejuni and 2 (1.5%) C.coli. The flaA, cadF and ciaB genes were present in 100% of isolates, while no plasmid of virB11 gene was present in their genome. The prevalence of invasion-associated marker was 100% among C. coli and was not detected in C. jejuni isolates. The distribution of both pldA and the genes associated with cytolethal distending toxin (CDT) was 58.3% in C. jejuni isolates. Seven distinct ERIC-PCR profiles were distinguished in three clusters using ERIC-PCR analysis. Genotyping analysis showed a relative correlation with geographic location of patients and virulence gene content of isolates., Conclusion: To our knowledge, this is the first molecular survey of Campylobacter spp. in Iran concerning genotyping and virulence gene content of both C. jejuni and C. coli. ERIC-PCR revealed appropriate discriminatory power for clustering C. jejuni isolates with identical virulence gene content. However, more studies are needed to clearly understand the pathogenesis properties of specific genotypes.

Objectives: The clinical importance of Staphylococcus aureus (S. aureus) is attributed to notable virulence factors, surface proteins, toxins, and enzymes as well as the rapid development of drug resistance. The aim of this study was to compare the occurrence of virulence factors produced by S. aureus strains isolated from children in an Iranian referral children's hospital., Methods: The presence of genes encoding for the enterotoxins A (sea), B (seb), C (sec), D (sed), TSST-1 (tsst), exfoliative toxin A (eta), and exfoliative toxin B (etb) were detected by Multiplex polymerase chain reaction (PCR) using specific primers. In addition, the standardized Kirby-Bauer disc-diffusion method was performed on Mueller-Hinton agar., Results: In total, 133 S. aureus isolates were obtained from different patients. Of these S. aureus isolates, 64 (48%) were methicillin-resistant S. aureus (MRSA), and all of these tested positive for the mecA gene. Regarding the classical enterotoxin genes, sea gene (40.6%) was the most prevalent followed by seb (19.6%), tsst (12.8%), eta (11.3%), etb (9%), sed (4.5%), and sec (3%). Among methicillin-susceptible S. aureus (MSSA) isolates, seb and tsst were the more prevalent toxins in comparison with MRSA isolates (p < 0.05), while the frequency of sea, sed, eta, and etb genes were higher among MRSA isolates (p > 0.05)., Conclusion: In our study enterotoxin A was produced by 40.6% of the isolates (48% from MRSA and 33% from MSSA isolates) which was higher than in previous reports. According to our results, strict hygiene and preventative measures during food processing are highly recommended.

Background: The present study was aimed to investigate molecular diversity of Echinococcus granulosus isolates collected from human clinical samples using two mitochondrial genes cox1 and nad1 in Iran., Methods: Forty seven human hydatid cysts were collected through surgery from two hospitals in Tehran during 2010-2012. To determine the fertility of protoscoleces, the cyst fluids were subjected to morphological microscopic examinations. Protoscoleces were removed from each cyst and their total genomic DNAs were extracted. PCR was performed to amplify fragments of 450 and 400 base pair (bp) for cox1 and nad1 genes, respectively. Genotype diversity and sequence variation of the strains were studied by bioinformatics software and in comparison with those mtDNA sequences already deposited in GenBank., Results: Sixteen, (53.3%), 13 (43.3%), and 1 (3.3%) samples were related to lung, liver, and spleen, respectively. The remained 17 unfertile samples were excluded from the study. From the 29 isolates, 86.7% (n=26) and 10% (n=3) were related to G1, and G3 genotypes, respectively. The sole isolate with G6 genotype was obtained from lung sample. Analysis of concatenated sequences of cox1+nad1 indicated the presence of 11 haplotypes among our strains that were related to genotypes G1 (n=9), G3 (n=1) and G6 (n=1)., Conclusion: In consistent to other reports from Iran, genotypes G1, G3, and G6 were observed in our human isolates. The rate of G3 genotype was however higher than other studies implying that human can be considered as a new appropriate host for G3 genotype. Further studies with more sample size from different geographic areas of Iran are needed for E. granulosus mapping.

Type 1 diabetes is recognized as an autoimmune inflammatory disease and low grade inflammation is also observed in type 2 diabetic patients. Interleukin 17 (IL-17) is a new player in inflammation. Th17 cells, as the main source of IL-17, require transforming growth factor β (TGF-β) and interleukin 23 (IL-23). The aim of this study was to investigate serum IL-17, IL-23 and TGF-β levels in diabetic patients and controls. In this case-control study, serum levels of IL-17, IL-23, and TGF-β were measured in 24 type 1 diabetic patients and 30 healthy controls using the ELISA method. Simultaneously, the same methodology was used to compare serum concentration of these three cytokines in 38 type 2 diabetic patients and 40 healthy controls. There was no significant difference between serum levels of IL-17 and IL-23 cytokines between cases and controls. However, TGF-β was significantly lower in type 1 diabetic patients (P < 0.001). Serum IL-17 and IL-23 levels demonstrate no association with type 1 and type 2 diabetes, but, in line with previous studies, TGF-β levels were lower in type 1 diabetic patients.